Practical 01: Retrieval of FASTA Sequence: 01: Insr Gene

Practical 01:
Retrieval of FASTA sequence
01: INSR GENE:

Official Symbol: INSR provided by HGNC
Official Full Name: insulin receptor provided by HGNC
Primary source: HGNC: HGNC: 6091
Ensemble: ENSG00000171105 MIM: 147670q
Gene type: protein coding
Organism: Homo sapiens
Lineage Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini;
Hominidae; Homo
Location: 19p13.2
Exon count: 22
Summary
This gene encodes a member of the receptor tyrosine kinase family of proteins.
The encoded preproprotein is proteolytically processed to generate alpha and beta
subunits that form a heterotetrametric receptor. Binding of insulin or other ligands
to this receptor activates the insulin signaling pathway, which regulates glucose
uptake and release, as well as the synthesis and storage of carbohydrates, lipids and
protein. Mutations in this gene underlie the inherited severe insulin resistance
syndromes including type A insulin resistance syndrome, Donohue syndrome and
Rabson-Mendenhall syndrome. Alternative splicing results in multiple transcript
variants. [Provided by RefSeq, Oct 2015].
Homo sapiens chromosome 19, GRCh38.p13 Primary Assembly
TCCACCAAGAAATGTGCTTATTGGATTGGGAGGTGTTTATTTGTAGTCTGCTGTAACACGTGTGAAAGAG
CAGGAGCGTCATCAGCATATGACTTGCGCTGGTCATCCGGTAAATGGATGTGCTGTAGTCCCAGTGCTAA
TCATTTCTCTCCTTCACAGTGGGTGGAAGTTTAGGGTTAAATGTCCTTTGAATGTCACCTGGTGAGTCCT
TGACACCTTAGGCTCTTCAGAAACAATGGTTTTGTTGAGGATGGGGAACAGGGAATGCCGATTTTATATA
CATGGTACACAGAGAGGGGTGTCACTTCAGAAAATCTTCCAGCATGTTCTTCAGAATATTAATTTATATG
CGAGGTGAGGTTGGGAATGAAAAGAACAGGTCAGCACTTTTTTTTTTCCTAGAACATACAAAAGAACATG
GTGGACTTTCAGGGAGTGCAATGGAAGGTGAATATTTCCTTAAGGGTCCCCGAGAAATGGGAGTGAGGGG
AGGGGACACAATGGCTTTTTGAGCTTACTTTTACCTTCTGATACTAGTCAAGGTCCAGAACCAGCCACCA
GCCAAATTTCTATCTGGGTGCGGGCCACTGAAAATCCTTGTTAAAAACCAGATCACAAATCTGGGGCTCT
TGGTCCCATTGGAGAAGGAAGGAAGAGCCTCAAAATAAGTGTGCACCCATGCACATATTCAGGAACAGCT
TGTTTAGTCTTTACACTTTGCCTGAAAGTTGCTTCTCCTCGTCCCTTTGTGTGCCTGGGTGGCCTCGGCC
CTGTGCGTTGGCAACGCAGGATCAAATGTGCTGCAGCTTTTGCAGAAAACAACTCAGAAACACAAAACCC
CCCAACAGCTCAATTATTATTTTTTCAATGTTTTCCTACAAGAGCCAAGTAGCACCATGTACAGAAGACG
CCTTTTTTTTTGGAATATTGAAATCGTTCTGCATGTAAAATATGGGATAATGACCTGTTTATATTAAAAT
TCTGATTAAATTATCTGAGAA
02: ADIPOQ gene

Official Symbol: ADIPOQ provided by HGNC
Official Full Name: adiponectin, C1Q and collagen domain containing provided
by HGNC
Ensemble: ENSG00000181092 MIM: 605441
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
Hominidae; Homo
Location: 3q27.3
Exon count: 4
Summary
This gene is expressed in adipose tissue exclusively. It encodes a protein with
similarity to collagens X and VIII and complement factor C1q. The encoded
protein circulates in the plasma and is involved with metabolic and hormonal
processes. Mutations in this gene are associated with adiponectin deficiency.
Multiple alternatively spliced variants, encoding the same protein, have been
identified. [Provided by RefSeq, Apr 2010]

ATTCTGACTGCAGTCTGTGGTTCTGATTCCATACCAGAGGGTAAGAGCAATTCTGTGAAGTTCCAGGCTG
GGTGGGGGATGCATGCATAGCCTCTGGCTGGGATCACCCAGGCTCTCCCGTCCGTAGTAGTGTGGGAGTG
GATACAGGTGGATACTCTGGTCAGAGCAGCACTGGTGGAGGCAGATATGCACTGGGCTTCTTCCTCCGTT
CTCCCACAGCCCCAAGAGAGAAAGGGTTATTTCAGACATTCCTTCTAAGATGCATGGAACCATTCTGAAT
TTTGCCCAGTTCGCTCTGTAGCAGGATACCTATTGAGAAAAAGTTAGGGTCAGTAAGGTGGAAGGGTCTG
TCCACAGATGAAGTCCAATTCGATTAAGGGGGATAAGGGAATACATTGCCTCTTAGCTTGACCAGGTAGG
GCAAAGGAAGAAGCATATATGAAGGCAGCTTCAGAAAAGTCAAGCTGAGCACTGACTTCAGACTGGAATT
AGGAATCCAGCTCTGCCACTTTATTCTACTCAGCAAATATTTACTGAGCAAATTCTATGGGCTAGACAGT
GGATTGGGTTCACAAGATACAATGAGTGTGACATGGTTGTTGTCTATGGATTTGGGGATATATGTAGGTA
TAGGGATATCTTACAAGGTAATCAAGAGGTTCTAATGAGGCCAGCCATGGTGGCTCACACCTGTAATCCC
AGCAATTTGGGAGACCGAGGCGGGTGGATCACCTGAGGTCAGGAGTTCCAGACTAGCCTGACCAACATGG
TGAAACCCCGCCTCTACCAAAAATACAAAAATTAGTTGGGCGTGATGGCAGGTGCCTGTAATCCCAGCTT
CTCGGGAGGCTGAGGCAGGAGAATTGTCTGAACCTGGGAGGCAGAGGTTGCAGTGAGCCGAGATTGTTGC
CACTGCATTCCAGCCTGGGTGACAGAGCGAGACTTTGTGTCAAAAAAAAAAAAAAAAGAAAGAAAAGAAA
AAGAGGCTCTAATGAGATAAA
03: Leptin receptor gene
Official Symbol: LEPR provided by HGNC

Official Full Name: leptin receptor provided by HGNC





Hominidae; Homo
Location: 1p31.3
Exon count: 24
Summary:
The protein encoded by this gene belongs to the gp130 family of cytokine
receptors that are known to stimulate gene transcription via activation of cytosolic
STAT proteins. This protein is a receptor for leptin (an adipocyte-specific hormone
that regulates body weight), and is involved in the regulation of fat metabolism, as
well as in a novel hematopoietic pathway that is required for normal
lymphopoiesis. Mutations in this gene have been associated with obesity and
pituitary dysfunction. Alternatively, spliced transcript variants encoding different
isoforms have been described for this gene. It is noteworthy that this gene and
LEPROT gene (GeneID: 54741) share the same promoter and the first 2 exons,
however, encode distinct proteins (PMID: 9207021). [Provided by RefSeq, Nov
2010]


CCGGTCTGGCTTGGGCAGGCTGCCCGGGCCGTGGCAGGAAGCCGGAAGCAGCCGCGGCCCCAGTTCGGGA
GACATGGCGGGCGTTAAAGGTACATCGCGGTCCCCGGCTCGCTTGTCGTGTGGTGGGGTTGCCACCTCCG
TTCCGGTCAAGCCTGGGGCTGCGCCTTCCGCGCGCCGTTGGGGAACGGCCTCACCACCCTTCCCGCCTCT
CCGGTTCGGGAGGCGATCGACCGCTCCCTTCGTCCCTTGGGGTGTGGGTGGAGCGGCGTTTCGGGGGAGC
CTTGGCCCTTTTTGCAAGGCCGCTGGCCTTCCTGCTCTCCAGTGGCGGCACCAGACCCCTCCCCAGCCTG
AGCCCTCGGCGAGAGCGGCGCCCTCCACCTCTCCTGAGTTTTTAAACAAGGTTTCCACTTCTTGACGCCA
CCCTAACGCCTTTCTTCTGGTTTTCTGCCCCTCCGCAGTTTCCTATTTGCCACAAAGGACCCTTTGTCTC
CAGCGTTCTTAGCATTGGGAAACTTAATCCTCTTTTTCCTAATGATTTTTCCAACTGGGCAGAGTTGACC
GCGGGCGGGTGTCAATGGAAAGCACCCAGAAAGACGGTGTTTCTCGCAGTCGTGGAGAGTAGATTACGTG
TAATTTTAATACTGCTTTCTTCGGTGTTTTCTCTGTTTATGGACAGAGAAGAAACCAGTGTGTGTGTAGT
ATGTGTTTTTTGCATGGGGCAGTTGGTAAAAACACCGCGTCCCTTATCTGTATGGCTTCAGAGCAATGCG
AGACGGAAAAGGTTTTTTGCAAGGCTTCCTGTATTTTGGTAGGAAAACATTCCATTTCTAATCTGTCGAA
TAGAGTAGCATGACTTGTTTTTATATTGGCTTTTATATCATCCTTGAAATTTGCACCCAAAGATATCCCC
AGTTAACATCTGCTATAAACATGTAGATAGTATATATACGAGTACGCCTCTGTTCACTATGAATTTATCC
GAGTATGTGAGCTGTTAGCAG
04: BRCA 1 gene
Official Symbol: BRCA1provided by HGNC
Official Full Name: BRCA1 DNA repair associated provided by HGNC
Hominidae; Homo
Location: 17q21.31
Exon count: 24
Summary
This gene encodes a 190 kD nuclear phosphoprotein that plays a role in
maintaining genomic stability, and it also acts as a tumor suppressor. The BRCA1
gene contains 22 exons spanning about 110 kb of DNA. The encoded protein
combines with other tumor suppressors, DNA damage sensors, and signal
transducers to form a large multi-subunit protein complex known as the BRCA1-
associated genome surveillance complex (BASC). This gene product associates
with RNA polymerase II, and through the C-terminal domain, also interacts with
histone deacetylase complexes. This protein thus plays a role in transcription, DNA
repair of double-stranded breaks, and recombination. Mutations in this gene are
responsible for approximately 40% of inherited breast cancers and more than 80%
of inherited breast and ovarian cancers. Alternative splicing plays a role in
modulating the subcellular localization and physiological function of this gene.
Many alternatively spliced transcript variants, some of which are disease-
associated mutations, have been described for this gene, but the full-length natures
of only some of these variants has been described. A related pseudogene, which is
also located on chromosome 17, has been identified. [Provided by RefSeq, May
2020]

TCCCTAAGTTTACTTCTCTAAAACCCTGTGTTCACAAAGGCAGAGAGTCAGACCCTTCAATGGAAGGAGA
GTGCTTGGGATCGATTATGTGACTTAAAGTCAGAATAGTCCTTGGGCAGTTCTCAAATGTTGGAGTGGAA
CATTGGGGAGGAAATTCTGAGGCAGGTATTAGAAATGAAAAGGAAACTTGAAACCTGGGCATGGTGGCTC
ACGCCTGTAATCCCAGCACTTTGGGAGGCCAAGGTGGGCAGATCACTGGAGGTCAGGAGTTCGAAACCAG
CCTGGCCAACATGGTGAAACCCCATCTCTACTAAAAATACAGAAATTAGCCGGTCATGGTGGTGGACACC
TGTAATCCCAGCTACTCAGGTGGCTAAGGCAGGAGAATCACTTCAGCCCGGGAGGTGGAGGTTGCAGTGA
GCCAAGATCATACCACGGCACTCCAGCCTGGGTGACAGTGAGACTGTGGCTCAAAAAAAAAAAAAAAAAA
AGGAAAATGAAACTAGAAGAGATTTCTAAAAGTCTGAGATATATTTGCTAGATTTCTAAAGAATGTGTTC
TAAAACAGCAGAAGATTTTCAAGAACCGGTTTCCAAAGACAGTCTTCTAATTCCTCATTAGTAATAAGTA
AAATGTTTATTGTTGTAGCTCTGGTATATAATCCATTCCTCTTAAAATATAAGACCTCTGGCATGAATAT
TTCATATCTATAAAATGACAGATCCCACCAGGAAGGAAGCTGTTGCTTTCTTTGAGGTGATTTTTTTCCT
TTGCTCCCTGTTGCTGAAACCATACAGCTTCATAAATAATTTTGCTTGCTGAAGGAAGAAAAAGTGTTTT
TCATAAACCCATTATCCAGGACTGTTTATAGCTGTTGGAAGGACTAGGTCTTCCCTAGCCCCCCCAGTGT
GCAAGGGCAGTGAAGACTTGATTGTACAAAATACGTTTTGTAAATGTTGTGCTGTTAACACTGCAAATAA
ACTTGGTAGCAAACACTTCCA
05: FSH receptor gene
Official Symbol: FSHR provided by HGNC
Official Full Name: follicle stimulating hormone receptor provided by HGNC
Hominidae; Homo
Location: 2p16.3
Exon count: 14
Summary
The protein encoded by this gene belongs to family 1 of G-protein coupled
receptors. It is the receptor for follicle stimulating hormone and functions in gonad
development. Mutations in this gene cause ovarian dysgenesis type 1, and also
ovarian hyperstimulation syndrome. Alternative splicing results in multiple
transcript variants. [Provided by RefSeq, Mar 2010]

ACTGTGGGGTATCACATTCTGAGCCCTAACACTTCCAATATTATGCTATGAATTTACATCATGATTTCAG
GTAATTATTCCAACAATGCCACAAGGTGAGCATTTGTGTTATCCAGTTTCACAGATGCAGAAACTGAAGT
GGAAAAAATTGACTAGCATTATATGGCTGGCAAGTGATCAAACAGGATTTTCTCATTATTTCATTCACTC
AATAGTTATTGAGCTCATAATATATGCCAGGCATTATGTCAGACTTCATGGATACAGACAGGTACACAGT
AAACAAGGTGGCCACTGCCCAAATGGAGCTTGCATTCTGGTGGGGAAGACAGATAATAAACAACAAGAAA
GAAGCAATATAACAGATTGGGACAGTGCTATTAATATAAGTAAATGAAGGAGGGATATCATCAGGAGAAT
CTGGGAAGGAGTGGATGCTACCTGAGACAGGATGGTCAAGGATCTGCCTAGTTGCAAAGCACTAGACTTT
CCACAACCCCTTCTACCCTCCAGTGGGCCTCTGCAGTATATATGGCAACCAATTCTGGTTTCATGTATTC
TACCACTTACTCCAACTCTAGTAAATATCTGCAAAGCTTACCATTGCCTACGACTCTCAGATTATTTCCC
CAAGATGCTGCAGAATCCTTATAATGTTTCTCAGCCTCAATAGAATGAAAAGCAGGTCTGTGCTTATATC
ACTTAATGACCAAAGAGGAAGGAAATTTACAATTAAAGTGTACTTTGCCAACTGTGGATGAATTAGTTAG
GTCACTGTGATCTACAGGTTAGATGTCTGTTCAGCAGTGTCCTCTACTTGAGATTCCAAGGAGGTTGAAG
CTCACTACTCGCCACCCCTCGCACCCCCCTCCGTTCTCTTCTTTCCCTTACCTGCTTCCTCACACTGATT
CAAAATCTCCCCCATGGCCCGGGCACGGTGGCTCACACCTGTAATCCCAGCACTTTGGGAGGCCGAGCCA
GGTGGGTCACCTAAGGTCA
Practical no 2
Finding similar sequence for DNA
BLAST: Basic Local Alignment Search Tool
BLAST finds regions of similarity between biological sequences. The
program compares nucleotide or protein sequences to sequence databases and
calculates the statistical significance.
1) Similar sequence for INSR Gene

FASTA Sequence;

CATGGTACACAGAGAGGGGTGTCACTTCAGAAAATCTTCCAGCATGTTCTTCAGAATATTAATTTATATG
CGAGGTGAGGTTGGGAATGAAAAGAACAGGTCAGCACTTTTTTTTTTCCTAGAACATACAAAAGAACATG
BLAST:
This FASTA sequence with 210 nucleotide sequence is 100% match with accession number of
following three.
1) Homo sapiens insulin receptor (INSR), transcript variant 2, mRNA
Score Expect Identities Gaps Strand
388
6e-104 210/210(100%) 0/210(0%) Plus/Plus
bits(210)
Query 1 TGACACCTTAGGCTCTTCAGAAACAATGGTTTTGTTGAGGATGGGGAACAGGGAATGCCG 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 8645 TGACACCTTAGGCTCTTCAGAAACAATGGTTTTGTTGAGGATGGGGAACAGGGAATGCCG 8704
Query 61 ATTTTATATACATGGTACACAGAGAGGGGTGTCACTTCAGAAAATCTTCCAGCATGTTCT 120

||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 8705 ATTTTATATACATGGTACACAGAGAGGGGTGTCACTTCAGAAAATCTTCCAGCATGTTCT 8764
Query 121 TCAGAATATTAATTTATATGCGAGGTGAGGTTGGGAATGAAAAGAACAGGTCAGCACttt 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 8765 TCAGAATATTAATTTATATGCGAGGTGAGGTTGGGAATGAAAAGAACAGGTCAGCACTTT 8824
Query 181 tttttttCCTAGAACATACAAAAGAACATG 210

||||||||||||||||||||||||||||||
Sbjct 8825 TTTTTTTCCTAGAACATACAAAAGAACATG 8854
2) Accession number: NM_000208.4

3) Accession Number: NG_008852.2
2) Similar sequence for ADIPOQ gene:
FASTA Sequence;
GGTGGGGGATGCATGCATAGCCTCTGGCTGGGATCACCCAGGCTCTCCCGTCCGTAGTAGTGTGGGAGTG
BLAST:
following three.
1) Homo sapiens adiponectin enhancer region (LOC106660625) on
chromosome 3
Sequence ID: NG_044949.1Length: 13241Number of Matches: 1
388 bits(210) 6e-104 210/210(100%) 0/210(0%) Plus/Plus
Query 1 GGTGGGGGATGCATGCATAGCCTCTGGCTGGGATCACCCAGGCTCTCCCGTCCGTAGTAG 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 2871 GGTGGGGGATGCATGCATAGCCTCTGGCTGGGATCACCCAGGCTCTCCCGTCCGTAGTAG 2930
Query 61 TGTGGGAGTGGATACAGGTGGATACTCTGGTCAGAGCAGCACTGGTGGAGGCAGATATGC 120

||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 2931 TGTGGGAGTGGATACAGGTGGATACTCTGGTCAGAGCAGCACTGGTGGAGGCAGATATGC 2990
Query 121 ACTGGGCTTCTTCCTCCGTTCTCCCACAGCCCCAAGAGAGAAAGGGTTATTTCAGACATT 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 2991 ACTGGGCTTCTTCCTCCGTTCTCCCACAGCCCCAAGAGAGAAAGGGTTATTTCAGACATT 3050
Query 181 CCTTCTAAGATGCATGGAACCATTCTGAAT 210

||||||||||||||||||||||||||||||
Sbjct 3051 CCTTCTAAGATGCATGGAACCATTCTGAAT 3080
2) Homo sapiens adiponectin, C1Q and collagen domain containing

(ADIPOQ), RefSeqGene on chromosome 3
Accession number: NG_021140.1
3) Homo sapiens chromosome 3 clone WI2-3182J7, complete sequence
Accession Number: AC193164.1
3) LAPTIN Receptor Gene;

FASTA Sequence:
CTTGGCCCTTTTTGCAAGGCCGCTGGCCTTCCTGCTCTCCAGTGGCGGCACCAGACCCCTCCCCAGCCTG
AGCCCTCGGCGAGAGCGGCGCCCTCCACCTCTCCTGAGTTTTTAAACAAGGTTTCCACTTCTTGACGCCA
BLAST:
following three.
1) Homo sapiens Leptin receptor (LEPR) gene, partial cds
Sequence ID: MK050966.1Length: 982Number of Matches: 1
Alignment statistics for match #1
388 210/210(100%
6e-104 0/210(0%) Plus/Plus
bits(210) )
Query 1 CCGGTTCGGGAGGCGATCGACCGCTCCCTTCGTCCCTTGGGGTGTGGGTGGAGCGGCGTT 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 275 CCGGTTCGGGAGGCGATCGACCGCTCCCTTCGTCCCTTGGGGTGTGGGTGGAGCGGCGTT 334
Query 61 TCGGGGGAGCCTTGGCCCTTTTTGCAAGGCCGCTGGCCTTCCTGCTCTCCAGTGGCGGCA 120

||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 335 TCGGGGGAGCCTTGGCCCTTTTTGCAAGGCCGCTGGCCTTCCTGCTCTCCAGTGGCGGCA 394
Query 121 CCAGACCCCTCCCCAGCCTGAGCCCTCGGCGAGAGCGGCGCCCTCCACCTCTCCTGAGTT 180

||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 395 CCAGACCCCTCCCCAGCCTGAGCCCTCGGCGAGAGCGGCGCCCTCCACCTCTCCTGAGTT 454
Query 181 TTTAAACAAGGTTTCCACTTCTTGACGCCA 210

||||||||||||||||||||||||||||||
Sbjct 455 TTTAAACAAGGTTTCCACTTCTTGACGCCA 484
2) Homo sapiens Leptin receptor (LEPR), RefSeqGene (LRG_283) on

chromosome 1
Accession number: NG_015831.2
3) Homo sapiens cDNA FLJ37482 fis, clone BRAWH2013941
Accession number: AK094801.1
4) BRCA1
FASTA Sequence
CCTGGCCAACATGGTGAAACCCCATCTCTACTAAAAATACAGAAATTAGCCGGTCATGGTGGTGGACACC
BLAST:
following three.

1) Homo sapiens BRCA1 DNA repair associated (BRCA1), transcript
variant 1, mRNA
Sequence ID: NM_007294.4Length: 7088Number of Matches: 1

388 210/210(100%
6e-104 0/210(0%) Plus/Plus
bits(210) )
Query 1 CATTGGGGAGGAAATTCTGAGGCAGGTATTAGAAATGAAAAGGAAACTTGAAACCTGGGC 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 6228 CATTGGGGAGGAAATTCTGAGGCAGGTATTAGAAATGAAAAGGAAACTTGAAACCTGGGC 6287
Query 61 ATGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCAAGGTGGGCAGATCACTGGA 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 6288 ATGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCAAGGTGGGCAGATCACTGGA 6347
Query 121 GGTCAGGAGTTCGAAACCAGCCTGGCCAACATGGTGAAACCCCATCTCTACTAAAAATAC 180

||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 6348 GGTCAGGAGTTCGAAACCAGCCTGGCCAACATGGTGAAACCCCATCTCTACTAAAAATAC 6407
Query 181 AGAAATTAGCCGGTCATGGTGGTGGACACC 210

||||||||||||||||||||||||||||||
Sbjct 6408 AGAAATTAGCCGGTCATGGTGGTGGACACC 6437
2) Homo sapiens BRCA1 DNA repair associated (BRCA1), transcript variant
6, non-coding RNA
Accession number: NR_027676.2
3) Homo sapiens BRCA1 DNA repair associated (BRCA1), transcript variant
2, mRNA
Accession Number: NM_007300.4
5) FSH Receptor Gene:

FASTA Sequence
BLAST:
following three.

1) Homo sapiens follicle stimulating hormone receptor (FSHR),
transcript variant X4, mRNA
Sequence ID: XM_011532735.2Length: 11453Number of Matches: 1

388
6e-104 210/210(100%) 0/210(0%) Plus/Plus
bits(210)
Query 1 GTAATTATTCCAACAATGCCACAAGGTGAGCATTTGTGTTATCCAGTTTCACAGATGCAG 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 10523 GTAATTATTCCAACAATGCCACAAGGTGAGCATTTGTGTTATCCAGTTTCACAGATGCAG 10582
Query 61 AAACTGAAGTGGAAAAAATTGACTAGCATTATATGGCTGGCAAGTGATCAAACAGGATTT 120

||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 10583 AAACTGAAGTGGAAAAAATTGACTAGCATTATATGGCTGGCAAGTGATCAAACAGGATTT 10642
Query 121 TCTCATTATTTCATTCACTCAATAGTTATTGAGCTCATAATATATGCCAGGCATTATGTC 180

||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 10643 TCTCATTATTTCATTCACTCAATAGTTATTGAGCTCATAATATATGCCAGGCATTATGTC 10702
Query 181 AGACTTCATGGATACAGACAGGTACACAGT 210

||||||||||||||||||||||||||||||
Sbjct 10703 AGACTTCATGGATACAGACAGGTACACAGT 10732
2) Homo sapiens follicle stimulating hormone receptor (FSHR), transcript

variant X3, mRNA
Accession Number; XM_011532736.2
3) Homo sapiens follicle stimulating hormone receptor (FSHR), transcript
variant X2, mRNA
Accession Number: XM_011532734.2
Practical no: 03
Use ExPSXy to translate DNA sequence into protein sequence and

tell what translation frame is:
1) INSR gene
FASTA Sequence:
TCCACCAAGAAATGTGCTTATTGGATTGGGAGGTGTTTATTTGTAGTCTGCTGTAACACGTGTGAAAGAG
CAGGAGCGTCATCAGCATATGACTTGCGCTGGTCATCCGGTAAATGGATGTGCTGTAGTCCCAGTGCTAA
TCATTTCTCTCCTTCACAGTGGGTGGAAGTTTAGGGTTAAATGTCCTTTGAATGTCACCTGGTGAGTCCT
Protein Sequence:
5'3' Frame 1
STKKCAYWIGRCLFVVCCNTCERAGASSAYDLRWSSGKWMCCSPSANHFSPSQWVEV-G-
MSFECHLVSP-HLRLFRNNGFVEDGEQGMPILY
5'3' Frame 2
PPRNVLIGLGGVYL-
SAVTRVKEQERHQHMTCAGHPVNGCAVVPVLIISLLHSGWKFRVKCPLNVTW-
VLDTLGSSETMVLLRMGNRECRFYI
5'3' Frame 3
HQEMCLLDWEVFICSLL-HV-KSRSVISI-LALVIR-MDVL-SQC-SFLSFTVGGSLGLNVL-
MSPGESLTP-ALQKQWFC-GWGTGNADFI
3'5' Frame 1
YIKSAFPVPHPQQNHCF-RA-GVKDSPGDIQRTFNPKLPPTVKERND-
HWDYSTSIYRMTSASHMLMTLLLFHTCYSRLQINTSQSNKHISWW
3'5' Frame 2
I-NRHSLFPILNKTIVSEEPKVSRTHQVTFKGHLTLNFHPL-RREMISTGTTAHPFTG-
PAQVIC--RSCSFTRVTADYK-TPPNPISTFLGG
3'5' Frame 3
YKIGIPCSPSSTKPLFLKSLRCQGLTR-HSKDI-P-TSTHCEGEK-
LALGLQHIHLPDDQRKSYADDAPALSHVLQQTTNKHLPIQ-AHFLV
Translation frame:
MTCAGHPVNGCAVVPVLIISLLHSGWKFRVKCPLNVTW-
Reason:
This is translated frame because it has the maximum length and also
start with start codon methionine and ends with stop codon.
02: ADIPOQ gene

FASTA Sequence:
TTTGCCCAGTTCGCTCTGTAGCAGGATACCTATTGAGAAAAAGTTAGGGTCAGTAAGGTGGAAGGGTCTG
TCCACAGATGAAGTCCAATTCGATTAAGGGGGATAAGGGAATACATTGCCTCTTAGCTTGACCAGGTAGG
Protein Sequence;
5'3' Frame 1
DTGGYSGQSSTGGGRYALGFFLRSPTAPREKGLFQTFLLRCMEPF-
ILPSSLCSRIPIEKKLGSVRWKGLSTDEVQFD-GG-GNTLPLSLTR-
5'3' Frame 2
IQVDTLVRAALVEADMHWASSSVLPQPQERKGYFRHSF-DAWNHSEFCPVRSVAGYLLRKS-GQ-
GGRVCPQMKSNSIKGDKGIHCLLA-PGR
5'3' Frame 3
YRWILWSEQHWWRQICTGLLPPFSHSPKRERVISDIPSKMHGTILNFAQFAL-QDTY-
EKVRVSKVEGSVHR-SPIRLRGIREYIAS-LDQV
3'5' Frame 1
PTWSS-EAMYSLIPLNRIGLHLWTDPSTLLTLTFSQ-
VSCYRANWAKFRMVPCILEGMSEITLSLLGLWENGGRSPVHICLHQCCSDQSIHLY
3'5' Frame 2
LPGQAKRQCIPLSPLIELDFICGQTLPPY-P-LFLNRYPATERTGQNSEWFHAS-KECLK-
PFLSWGCGRTEEEAQCISASTSAALTRVSTCI
3'5' Frame 3
YLVKLRGNVFPYPP-SNWTSSVDRPFHLTDPNFFSIGILLQSELGKIQNGSMHLRRNV-
NNPFSLGAVGERRKKPSAYLPPPVLL-PEYPPV
Translated Frame:
MYSLIPLNRIGLHLWTDPSTLLTLTFSQ-
Reason:
This is translated frame because it start with start codon methionine
and ends with stop codon.
3) Leptin receptor gene

FASTA Sequence:
CCGGTCTGGCTTGGGCAGGCTGCCCGGGCCGTGGCAGGAAGCCGGAAGCAGCCGCGGCCCCAGTTCGGGA
GACATGGCGGGCGTTAAAGGTACATCGCGGTCCCCGGCTCGCTTGTCGTGTGGTGGGGTTGCCACCTCCG
TTCCGGTCAAGCCTGGGGCTGCGCCTTCCGCGCGCCGTTGGGGAACGGCCTCACCACCCTTCCCGCCTCT
Protein Sequence:
5'3' Frame 1
PVWLGQAARAVAGSRKQPRPQFGRHGGR-
RYIAVPGSLVVWWGCHLRSGQAWGCAFRAPLGNGLTTLPASPVREAIDRSLRPLGCGWSGVSGE
5'3' Frame 2
RSGLGRLPGPWQEAGSSRGPSSGDMAGVKGTSRSPARLSCGGVATSVPVKPGAAPSARRWGTASPPFPPL
RFGRRSTAPFVPWGVGGAAFRGS
5'3' Frame 3
GLAWAGCPGRGRKPEAAAAPVRETWRALKVHRGPRLACRVVGLPPPFRSSLGLRLPRAVGERPHHPSRLS
GSGGDRPLPSSLGVWVERRFGG
3'5' Frame 1
APPKRRSTHTPRDEGSGRSPPEPERREGW-
GRSPTARGRRSPRLDRNGGGNPTTRQASRGPRCTFNARHVSRTGAAAASGFLPRPGQPAQARP
3'5' Frame 2
LPRNAAPPTPQGTKGAVDRLPNRRGGKGGEAVPQRRAEGAAPGLTGTEVATPPHDKRAGDRDVPLTPAMS
PELGPRLLPASCHGPGSLPKPDR
3'5' Frame 3
SPETPLHPHPKGRRERSIASRTGEAGRVVRPFPNGARKAQPQA-PERRWQPHHTTSEPGTAMYL-
RPPCLPNWGRGCFRLPATARAACPSQT
Translation frame:
MYL-
Reason:
This is translated frame because it start with start codon methionine
4) BRCA 1 gene
FASTA Sequence:
TCCCTAAGTTTACTTCTCTAAAACCCTGTGTTCACAAAGGCAGAGAGTCAGACCCTTCAATGGAAGGAGA
GTGCTTGGGATCGATTATGTGACTTAAAGTCAGAATAGTCCTTGGGCAGTTCTCAAATGTTGGAGTGGAA
Protein Sequence:
5'3' Frame 1
SLSLLL-NPVFTKAESQTLQWKESAWDRLCDLKSE-
SLGSSQMLEWNIGEEILRQVLEMKRKLETWAWWLTPVIPALWEAKVGRSLEVRSSKP
5'3' Frame 2
P-VYFSKTLCSQRQRVRPFNGRRVLGIDYVT-SQNSPWAVLKCWSGTLGRKF-GRY-K-
KGNLKPGHGGSRL-SQHFGRPRWADHWRSGVRNQ
5'3' Frame 3
PKFTSLKPCVHKGRESDPSMEGECLGSIM-LKVRIVLGQFSNVGVEHWGGNSEAGIRNEKET-
NLGMVAHACNPSTLGGQGGQITGGQEFET
3'5' Frame 1
LVSNS-PPVICPPWPPKVLGLQA-
ATMPRFQVSFSFLIPASEFPPQCSTPTFENCPRTILTLSHIIDPKHSPSIEGSDSLPL-
TQGFREVNLG
3'5' Frame 2
WFRTPDLQ-SAHLGLPKCWDYRREPPCPGFKFPFHF-YLPQNFLPNVPLQHLRTAQGLF-L-VT-
SIPSTLLPLKGLTLCLCEHRVLEK-T-G
3'5' Frame 3
GFELLTSSDLPTLASQSAGITGVSHHAQVSSFLFISNTCLRISSPMFHSNI-
ELPKDYSDFKSHNRSQALSFH-RV-LSAFVNTGF-RSKLR
Translation frame:
MPRFQVSFSFLIPASEFPPQCSTPTFENCPRTILTLSHIIDPKHSPSIEGSDSLPL-
Reason:
This is translated frame because it has the maximum length and also
start with start codon methionine and ends with stop codon.

5) FSH receptor gene
FASTA Sequence:
ACTGTGGGGTATCACATTCTGAGCCCTAACACTTCCAATATTATGCTATGAATTTACATCATGATTTCAG
Protein Sequence:
5'3' Frame 1
TVGYHILSPNTSNIML-IYIMISGNYSNNATR-AFVLSSFTDAETEVEKID-HYMAGK-
SNRIFSLFHSLNSY-AHNICQALCQTSWIQTGTQ
5'3' Frame 2
LWGITF-ALTLPILCYEFTS-
FQVIIPTMPQGEHLCYPVSQMQKLKWKKLTSIIWLASDQTGFSHYFIHSIVIELIIYARHYVRLH
GYRQVHS
5'3' Frame 3
CGVSHSEP-HFQYYAMNLHHDFR-LFQQCHKVSICVIQFHRCRN-SGKN-
LALYGWQVIKQDFLIISFTQ-LLSS-YMPGIMSDFMDTDRYT
3'5' Frame 1
TVYLSVSMKSDIMPGIYYELNNY-VNEIMRKSCLITCQPYNASQFFPLQFLHL-
NWITQMLTLWHCWNNYLKS-CKFIA-YWKC-GSECDTPQ
3'5' Frame 2
LCTCLYP-SLT-CLAYIMSSITIE-MK--ENPV-SLASHIMLVNFFHFSFCICETG-
HKCSPCGIVGIIT-NHDVNS-HNIGSVRAQNVIPHS
3'5' Frame 3
CVPVCIHEV-HNAWHIL-AQ-LLSE-NNEKILFDHLPAI-C-
SIFSTSVSASVKLDNTNAHLVALLE-LPEIMM-IHSIILEVLGLRM-YPT

Translation frame:
MRKSCLITCQPYNASQFFPLQFLHL-
Reason:
This is translated frame because it starts with start codon methionine
Prac 4:
Physical and chemical properties of protein using
ProtParam.
1) Keratin:
VTLARTDLEMQIEGLKEELAYLRKNHEEEMLALRGQTGGDVNVEMDAAPGVDLSRILNEMRDQYEQMAEK
NRRDAETWFLSKTEELNKEVASNSELVQSSRSEVTELRRVLQGLEIELQSQLSTKASLENSLEETKGRYC
MQLSQIQGLIGSVEEQLAQLRCEMEQQSQEYQILLDVKTRLEHEIATYRRLLXGEDAHLSSQQASGQSYS
SREVFTSSSSSSSRQTRPILKEQSSSSFSQGQSS
Properties:
Number of amino acids: 244

Molecular weight: 27659.84

Theoretical pI: 4.81

Amino acid composition:
Ala (A) 13 5.3%
Arg (R) 18 7.4%
Asn (N) 7 2.9%
Asp (D) 8 3.3%
Cys (C) 2 0.8%
Gln (Q) 24 9.8%
Glu (E) 33 13.5%
Gly (G) 12 4.9%
His (H) 3 1.2%
Ile (I) 8 3.3%
Leu (L) 30 12.3%
Lys (K) 9 3.7%
Met (M) 7 2.9%
Phe (F) 3 1.2%
Pro (P) 2 0.8%
Ser (S) 34 13.9%
Thr (T) 12 4.9%
Trp (W) 1 0.4%
Tyr (Y) 6 2.5%
Val (V) 11 4.5%
Pyl (O) 0 0.0%
Sec (U) 0 0.0%

(B) 0 0.0%
(Z) 0 0.0%
(X) 1 0.4%

Total number of negatively charged residues (Asp + Glu): 41
Total number of positively charged residues (Arg + Lys): 27

Atom composition:

As there is at least one ambiguous position (B,Z or X) in the sequence
considered, the atomic composition cannot be computed.

Extinction coefficients:

Extinction coefficients are in units of M-1
cm , at 280 nm measured in water.
-1

Ext. coefficient 14565
Abs 0.1% (=1 g/l) 0.527, assuming all pairs of Cys residues form cystines

Abs 0.1% (=1 g/l) 0.522, assuming all Cys residues are reduced

Estimated half-life:

The N-terminal of the sequence considered is V (Val).

The estimated half-life is: 100 hours (mammalian reticulocytes, in vitro).
>20 hours (yeast, in vivo).
>10 hours (Escherichia coli, in vivo).

Instability index:

The instability index (II) is computed to be 76.14
This classifies the protein as unstable.

Aliphatic index: 79.14

Grand average of hydropathicity (GRAVY): -0.753
2) Gloverin:
Number of amino acids: 175

Molecular weight: 19064.25

Theoretical pI: 9.14

Amino acid composition:
Ala (A) 14 8.0%
Arg (R) 9 5.1%
Asn (N) 8 4.6%
Asp (D) 14 8.0%
Cys (C) 1 0.6%
Gln (Q) 12 6.9%
Glu (E) 4 2.3%
Gly (G) 24 13.7%
His (H) 2 1.1%
Ile (I) 7 4.0%
Leu (L) 6 3.4%
Lys (K) 13 7.4%
Met (M) 4 2.3%
Phe (F) 11 6.3%
Pro (P) 6 3.4%
Ser (S) 12 6.9%
Thr (T) 7 4.0%
Trp (W) 2 1.1%
Tyr (Y) 7 4.0%
Val (V) 12 6.9%
Pyl (O) 0 0.0%
Sec (U) 0 0.0%

(B) 0 0.0%
(Z) 0 0.0%
(X) 0 0.0%

Total number of negatively charged residues (Asp + Glu): 18
Total number of positively charged residues (Arg + Lys): 22

Atomic composition:

Carbon C 841
Hydrogen H 1289
Nitrogen N 241
Oxygen O 258
Sulfur S 5

Formula: C H N O S
841 1289 241 258 5
Total number of atoms: 2634

Extinction coefficients:

Extinction coefficients are in units of M-1
cm , at 280 nm measured in water.
-1

Abs 0.1% (=1 g/l) 1.124, assuming all pairs of Cys residues form cystines

Abs 0.1% (=1 g/l) 1.124, assuming all Cys residues are reduced

Estimated half-life:

The N-terminal of the sequence considered is M (Met).

The estimated half-life is: 30 hours (mammalian reticulocytes, in vitro).
>20 hours (yeast, in vivo).
>10 hours (Escherichia coli, in vivo).

Instability index:

The instability index (II) is computed to be 21.47
This classifies the protein as stable.

Aliphatic index: 56.86

Grand average of hydropathicity (GRAVY): -0.597
…………………………………………………………………………………………………………………………………………………….
Prac 5
Primer designing
Leptin:
GAGCCCCGTAGGAATCGCAGCGCCAGCGGTTGCAAGGTAAGGCCCCGGCGCGCTCCTTCCTCCTTCTCTG
CTGGTCTTTCTTGGCAGGCCACAGGGCCCCACACAACTCTGGATCCCGGGGAAACTGAGTCAGGAGGGAT
GCAGGGCGGATGGCTTAGTTCTGGACTATGATAGCTTTGTACCGAGTTCTAGCCAGATAGAAGGTTACCG
GGAGCTGGGGAGCGTTGGATTTGCTGCTGGGCTGTGCCGGTGCCCAGAAGGCAGGACCTTGCAGAACCAG
LEFT PRIMER TCCTTCCTCCTTCTCTGCTG 54 20 59.67 55.00 2.00 2.00
RIGHT PRIMER CAGCTCCCGGTAACCTTCTA 217 20 59.33 55.00 5.00 2.00
Complementary Strand TAGAAGGTTACCGGGAGCTG
SEQUENCE SIZE: 280
INCLUDED REGION SIZE: 280
PRODUCT SIZE: 164
Primer BLAST
Sequence (5'->3') Template strand Length Start Stop Tm GC% Self complementarity Self 3' complementarity
Forward primer GATCCCGGGGAAACTGAGTC Plus 20 112 131 59.82 60.00 7.00 3.00
Reverse primer CAGCAGCAAATCCAACGCTC Minus 20 239 220 60.46 55.00 3.00 0.00
Product length 128
FSH:
AAACAAGGTGGCCACTGCCCAAATGGAGCTTGCATTCTGGTGGGGAAGACAGATAATAAACAACAAGAAA
PRIMER 3
LEFT PRIMER TGGCAAGTGATCAAACAGGA 98 20 60.24 45.00 6.00 0.00
RIGHT PRIMER ATCTGTCTTCCCCACCAGAA 264 20 59.51 50.00 4.00 0.00
Complementary Strand TTCTGGTGGGGAAGACAGAT
SEQUENCE SIZE: 280
INCLUDED REGION SIZE: 280
PRODUCT SIZE: 167
PRIMER BLAST
Sequence (5'->3') Template strand Length Start Stop Tm GC% Self complementarity Self 3' complementarity
Forward primer AACAATGCCACAAGGTGAGC Plus 20 12 31 59.32 50.00 3.00 3.00
Reverse primer TGTCTTCCCCACCAGAATGC Minus 20 261 242 59.96 55.00 3.00 2.00
Product length 250
……………………………………………………………………………………………………………………………………………………….
Prac 6
Multiple sequence alignment of protein using ClustalW
Clustal omega and T.Coffee.
Coronin protein
In human
>EAW74626.1MSFRKVVRQSKFRHVFGQPVKNDQCYEDIRVSRVTWDSTFCAVNPKFLAVIVEASGGGAFLVLPLSKTGR
IDKAYPTVCGHTGPVLDIDWCPHNDEVIASGSEDCTVMVWQIPENGLTSPLTEPVVVLEGHTKRVGIIAW
In rabbit
>AAD23736.1MSFRKVVRQSKFRHVFGQPVKNDQCYEDIRVSRVTWDSTFCAVNPKFLAVIVEASGGGAFLVLPLSKTGR
IDKAYPTVCGHTGPVLDIEWCPHNDGVIASGSEDCTVMVWQIPEDGLTSPLTEPVVVLEGHTKRVGIVTW
In mouse
>EDL33019.1MSFRKVVRQSKFRHVFGQPVKNDQCYEDIRVSRVTWDSTFCAVNPKFLAVIVEASGGGAFMVLPLNKTGR
IDKAYPTVCGHTGPVLDIDWCPHNDEVIASGSEDCTVMVWQIPENGLTSPLTEPVVVLEGHTKRVGIITW

ClustalW;
Sequence 1: EAW74626.1 70 aa
Sequence 2: EDL33019.1 70 aa
Sequence 3: AAD23736.1 70 aa
Start of Pairwise alignments
Aligning...
Sequences (1:2) Aligned. Score: 98.5714
There are 2 groups

Start of Multiple Alignment
Aligning...
Group 1: Sequences: 2 Score: 1183
Group 2: Sequences: 3 Score: 1155

Alignment Score 1326
EAW74626.1MSFRKVVRQSKFRHVFGQPV IDKAYPTVCGHTGPVLDIDWCPHNDEVIASGSEDCTVMVWQIPENGLTSP
EDL33019.1MSFRKVVRQSKFRHVFGQPV IDKAYPTVCGHTGPVLDIDWCPHNDEVIASGSEDCTVMVWQIPENGLTSP
AAD23736.1MSFRKVVRQSKFRHVFGQPV IDKAYPTVCGHTGPVLDIEWCPHNDGVIASGSEDCTVMVWQIPEDGLTSP
******************:****** ******************:*****
EAW74626.1MSFRKVVRQSKFRHVFGQPV LTEPVVVLEGHTKRVGIIAW
EDL33019.1MSFRKVVRQSKFRHVFGQPV LTEPVVVLEGHTKRVGIITW
AAD23736.1MSFRKVVRQSKFRHVFGQPV LTEPVVVLEGHTKRVGIVTW
*****************::*
Clustal omega
AAD23736.1MSFRKVVRQSKFRHVFGQPVKNDQCYEDIRVSRVTWDSTFCAVNPKFLAVIVEASGGGAFLVLPLSKTGR
IDKAYPTVCGHTGPVLDIEWCPHNDGVIASGSEDCTVMVWQIPEDGLTSPLTEPVVVLEG 60

EAW74626.1MSFRKVVRQSKFRHVFGQPVKNDQCYEDIRVSRVTWDSTFCAVNPKFLAVIVEASGGGAFLVLPLSKTGR
IDKAYPTVCGHTGPVLDIDWCPHNDEVIASGSEDCTVMVWQIPENGLTSPLTEPVVVLEG 60

EDL33019.1MSFRKVVRQSKFRHVFGQPVKNDQCYEDIRVSRVTWDSTFCAVNPKFLAVIVEASGGGAFMVLPLNKTGR
IDKAYPTVCGHTGPVLDIDWCPHNDEVIASGSEDCTVMVWQIPENGLTSPLTEPVVVLEG 60
***********
*******:****** ******************:***************

HTKRVGIVTW 70

HTKRVGIIAW 70

HTKRVGIITW 70
*******::*
T.Coffee:
IDKAYPTVCGHTGPVLDIEWCPHNDGVIASGSEDCTVMVWQIPEDGLTSP

IDKAYPTVCGHTGPVLDIDWCPHNDEVIASGSEDCTVMVWQIPENGLTSP

IDKAYPTVCGHTGPVLDIDWCPHNDEVIASGSEDCTVMVWQIPENGLTSP
****
**************:****** ******************:*****

LTEPVVVLEGHTKRVGIVTW

LTEPVVVLEGHTKRVGIIAW

LTEPVVVLEGHTKRVGIITW
****
*************::*
…………………………………………………………………………………………………………………………………………………………
Prac 07
SNP:
ANK3
rs10994336
Alleles:
C>T [Show Flanks]
Chromosome:
10:60420054 (GRCh38)
10:62179812 (GRCh37)
Canonical SPDI:
NC_000010.11:60420053:C:T
Gene:
ANK3 (Varview)
Functional Consequence:
intron_variant,genic_upstream_transcript_variant
Validated:
by frequency,by alfa,by cluster
MAF:
T=0.063421/8173 (ALFA)
T=0.046296/10 (Qatari)
T=0.05/2 (GENOME_DK)
T=0.054207/201 (TWINSUK)
T=0.056305/217 (ALSPAC)
T=0.0722/9066 (TOPMED)
T=0.076585/87 (Daghestan)
T=0.077154/77 (GoNL)
T=0.085559/2684 (GnomAD)
T=0.11/66 (NorthernSweden)
T=0.113497/37 (HapMap)
T=0.123203/617 (1000Genomes)
T=0.130841/28 (Vietnamese)
T=0.132143/592 (Estonian)
T=0.132516/10429 (PAGE_STUDY)
T=0.282594/828 (KOREAN)
T=0.286572/525 (Korea1K)
C=0.345/69 (SGDP_PRJ)
C=0.363636/8 (Siberian)
...more
HGVS:
NC_000010.11:g.60420054C>T, NC_000010.10:g.62179812C>T, NG_029917.1:g.318473G>A
rs10994415
Variant type:
SNV
Alleles:
T>C,G [Show Flanks]
Chromosome:
10:60562276 (GRCh38)
10:62322034 (GRCh37)
Canonical SPDI:
NC_000010.11:60562275:T:C,NC_000010.11:60562275:T:G
Gene:
ANK3 (Varview)
intron_variant,genic_upstream_transcript_variant
Validated:
by frequency,by alfa,by cluster
MAF:
C=0.235513/1837 (ALFA)
C=0.064815/14 (Qatari)
C=0.074434/276 (TWINSUK)
C=0.075/3 (GENOME_DK)
C=0.079398/306 (ALSPAC)
C=0.091648/11508 (TOPMED)
C=0.093186/93 (GoNL)
C=0.095284/2990 (GnomAD)
C=0.096667/58 (NorthernSweden)
C=0.126786/568 (Estonian)
C=0.14996/751 (1000Genomes)
C=0.172727/57 (HapMap)
C=0.275701/59 (Vietnamese)
T=0.394231/82 (SGDP_PRJ)
C=0.396246/1161 (KOREAN)
C=0.400109/733 (Korea1K)
T=0.5/10 (Siberian)
...more
HGVS:
NC_000010.11:g.60562276T>C, NC_000010.11:g.60562276T>G, NC_000010.10:g.62322034T>C, NC_00
0010.10:g.62322034T>G, NG_029917.1:g.176251A>G, NG_029917.1:g.176251A>C
.

ALDOB

rs1057517091

Variant type:
DEL
Alleles:
T>- [Show Flanks]
Chromosome:
9:101426633 (GRCh38)
9:104188915 (GRCh37)
Canonical SPDI:
NC_000009.12:101426632:T:
Gene:
ALDOB (Varview)
coding_sequence_variant,frameshift_variant
Clinical significance:
likely-pathogenic
HGVS:
NC_000009.12:g.101426633del, NC_000009.11:g.104188915del, NG_012387.1:g.14148del, NM_000035.4
:c.546del, NM_000035.3:c.546del, NP_000026.2:p.Leu183fs
rs1057516534
Variant type:
DELINS
Alleles:
C>- [Show Flanks]
Chromosome:
9:101430775 (GRCh38)
9:104193057 (GRCh37)
Canonical SPDI:
NC_000009.12:101430774:CC:C
Gene:
ALDOB (Varview)
coding_sequence_variant,splice_donor_variant
Clinical significance:
likely-pathogenic
HGVS:
NC_000009.12:g.101430776del, NC_000009.11:g.104193058del, NG_012387.1:g.10006del
………………………………………………………………………………………………………………………………………………………………….
Prac 08
Prediction of secondary structure of protein:
Jpred4
Insulin

MALWMRLLPLLALLALWGPDPAAAFVNQHLCGSHLVEALYLVCGERGFFYTPKTRREAEDLQVGQVELGG
GPGAGSLQPLALEGSLQKRGIVEQCCTSICSLYQLENYCN
Name: Hormone
Title: Monoclinic human insulin in complex with p-coumaric acid

Structur Insulin. Chain: a, b, c, d, e, f, g, h, i, j, k, l. Engineered: yes
e:
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: ins. Expressed in: saccharomyces cerevisiae.
Expression_system_taxid: 4932
Resoluti
on:
1.36Å R- 0.16 R- 0.
factor: 0 free: 18
8
Authors: D.-P.Triandafillidis,N.Parthenios,M.Spiliopoulou,A.Valmas,C.Kosinas, F.Gozzo,M.Reinle-
Schmitt,D.Beckers,T.Degen,M.Pop,A.Fitch, J.Wollenhaupt,M.S.Weiss,F.Karavassili,I.Margiolaki
Key ref: D.P.Triandafillidis et al. (2020). Insulin polymorphism induced by two polyphenols: new crystal forms and advances
in macromolecular powder diffraction. Acta Crystallogr D Struct Biol, 76, 1065-
1079. PubMed id: 33135678 DOI: 10.1107/S205979832001195X
Date:
04-Nov-19 Release 11-Nov-

date: 20

Myosin:
CILITGESGAGKTEASKLVMSYVAAVCGKGAEVNQVKEQLLQSNPVLEAFGNAKTVRNDNSSRFGKYMDI
EFDFKGDPLGGVISNYLLEK
Name: Structural protein
Title: High-resolution cryo-em structures of actin-bound myosin states reveal the mechanism of myosin force sensing
Structu Actin, alpha skeletal muscle. Chain: a, b, c, d, e. Synonym: alpha-actin-1. Unconventional myosin-ib. Chain: p.
re: Synonym: myosin i alpha,mmia,myosin heavy chain myr 1. Calmodulin. Chain: r
Source Oryctolagus cuniculus. Rabbit. Organism_taxid: 9986. Rattus norvegicus. Rat. Organism_taxid: 10116. Unidentified.
: Organism_taxid: 32644
Author A.Mentes,A.Huehn,X.Liu,A.Zwolak,R.Dominguez,H.Shuman,E.M.Ostap, C.V.Sindelar
s:
Key ref A.Mentes et al. (2018). High-resolution cryo-EM structures of actin-bound myosin states reveal the mechanism of
: myosin force sensing. Proc Natl Acad Sci U S A, 115, 1292-1297. PubMed id: 29358376
Date:
04-Jan-18 Release 31-Jan-

date: 18

Practical 01: Retrieval of FASTA Sequence: 01: Insr Gene

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Practical 01: Retrieval of FASTA Sequence: 01: Insr Gene

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Practical 01:

Retrieval of FASTA sequence

01: INSR GENE:

02: ADIPOQ gene

1) Similar sequence for INSR Gene

1) Homo sapiens insulin receptor (INSR), transcript variant 2, mRNA

Score Expect Identities Gaps Strand

Query 61 ATTTTATATACATGGTACACAGAGAGGGGTGTCACTTCAGAAAATCTTCCAGCATGTTCT 120

Query 181 tttttttCCTAGAACATACAAAAGAACATG 210

2) Accession number: NM_000208.4

Score Expect Identities Gaps Strand

388 bits(210) 6e-104 210/210(100%) 0/210(0%) Plus/Plus

Query 61 TGTGGGAGTGGATACAGGTGGATACTCTGGTCAGAGCAGCACTGGTGGAGGCAGATATGC 120

Query 181 CCTTCTAAGATGCATGGAACCATTCTGAAT 210

2) Homo sapiens adiponectin, C1Q and collagen domain containing

3) LAPTIN Receptor Gene;

Alignment statistics for match #1

Score Expect Identities Gaps Strand

Query 61 TCGGGGGAGCCTTGGCCCTTTTTGCAAGGCCGCTGGCCTTCCTGCTCTCCAGTGGCGGCA 120

Query 121 CCAGACCCCTCCCCAGCCTGAGCCCTCGGCGAGAGCGGCGCCCTCCACCTCTCCTGAGTT 180

Query 181 TTTAAACAAGGTTTCCACTTCTTGACGCCA 210

2) Homo sapiens Leptin receptor (LEPR), RefSeqGene (LRG_283) on

Score Expect Identities Gaps Strand

Query 121 GGTCAGGAGTTCGAAACCAGCCTGGCCAACATGGTGAAACCCCATCTCTACTAAAAATAC 180

Query 181 AGAAATTAGCCGGTCATGGTGGTGGACACC 210

5) FSH Receptor Gene:

Score Expect Identities Gaps Strand

Query 61 AAACTGAAGTGGAAAAAATTGACTAGCATTATATGGCTGGCAAGTGATCAAACAGGATTT 120

Query 121 TCTCATTATTTCATTCACTCAATAGTTATTGAGCTCATAATATATGCCAGGCATTATGTC 180

Query 181 AGACTTCATGGATACAGACAGGTACACAGT 210

2) Homo sapiens follicle stimulating hormone receptor (FSHR), transcript

Use ExPSXy to translate DNA sequence into protein sequence and

02: ADIPOQ gene

3) Leptin receptor gene

Total number of atoms: 2634

Product length 128

Product length 250

Sequences (1:2) Aligned. Score: 98.5714

Sequences (1:3) Aligned. Score: 92.8571

Sequences (2:3) Aligned. Score: 94.2857

There are 2 groups

Group 2: Sequences: 3 Score: 1155

Title: Monoclinic human insulin in complex with p-coumaric acid

04-Nov-19 Release 11-Nov-

04-Jan-18 Release 31-Jan-

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