Bioinformática: DNA e Proteínas

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Aula 2 – Bioinformática
1. DNA
2. A proteína codificada por este gene é uma glicoproteína da superfície celular envolvidas nas 
interacções célula-célula, migração e adesão celular. É um receptor de ácido hialurónico 
(HA) e também pode interagir com outros ligandos, tais como osteoportina, colagéno, e as 
metaloproteinases de matriz (MMPs). Esta proteína participa numa grande variedade de 
funções celulares, incluindo a ativação dos linfócitos, recirculação e homing, hematopoiese, 
e metástases tumorais. Os transcritos para esta sofrer splicing alternativo do gene complexo 
que resulta em muitas isoformas funcionalmente distintas, no entanto, não foi determinada a 
natureza de comprimento completo de algumas destas variantes. O splicing alternativo é a 
base para a diversidade estrutural e funcional desta proteína, e pode ser relacionado com a 
metástase tumoral.
3. 100533 bp 
4. exon 1 5001..5501
exon 2 42706..42871
exon 3 46405..46538
exon 4 52963..53031
exon 5 55966..56196
exon 6 80983..81045
exon 7 85447..85518
exon 8 87785..87863
exon 9 95260..98533
5. NM_001001391.1
6.
Formato FASTA refere-se a sequencia de nucleotídeos em formato compatível 
com programa de comparação.
>gi|48255940|ref|NM_001001391.1| Homo sapiens CD44 molecule (Indian blood 
group) (CD44), transcript variant 4, mRNA
GAGAAGAAAGCCAGTGCGTCTCTGGGCGCAGGGGCCAGTGGGGCTCGGAGGCACAGGCACCCCGCGACAC
TCCAGGTTCCCCGACCCACGTCCCTGGCAGCCCCGATTATTTACAGCCTCAGCAGAGCACGGGGCGGGGG
CAGAGGGGCCCGCCCGGGAGGGCTGCTACTTCTTAAAACCTCTGCGGGCTGCTTAGTCACAGCCCCCCTT
GCTTGGGTGTGTCCTTCGCTCGCTCCCTCCCTCCGTCTTAGGTCACTGTTTTCAACCTCGAATAAAAACT
GCAGCCAACTTCCGAGGCAGCCTCATTGCCCAGCGGACCCCAGCCTCTGCCAGGTTCGGTCCGCCATCCT
CGTCCCGTCCTCCGCCGGCCCCTGCCCCGCGCCCAGGGATCCTCCAGCTCCTTTCGCCCGCGCCCTCCGT
TCGCTCCGGACACCATGGACAAGTTTTGGTGGCACGCAGCCTGGGGACTCTGCCTCGTGCCGCTGAGCCT
GGCGCAGATCGATTTGAATATAACCTGCCGCTTTGCAGGTGTATTCCACGTGGAGAAAAATGGTCGCTAC
AGCATCTCTCGGACGGAGGCCGCTGACCTCTGCAAGGCTTTCAATAGCACCTTGCCCACAATGGCCCAGA
TGGAGAAAGCTCTGAGCATCGGATTTGAGACCTGCAGGTATGGGTTCATAGAAGGGCACGTGGTGATTCC
CCGGATCCACCCCAACTCCATCTGTGCAGCAAACAACACAGGGGTGTACATCCTCACATCCAACACCTCC
CAGTATGACACATATTGCTTCAATGCTTCAGCTCCACCTGAAGAAGATTGTACATCAGTCACAGACCTGC
CCAATGCCTTTGATGGACCAATTACCATAACTATTGTTAACCGTGATGGCACCCGCTATGTCCAGAAAGG
AGAATACAGAACGAATCCTGAAGACATCTACCCCAGCAACCCTACTGATGATGACGTGAGCAGCGGCTCC
TCCAGTGAAAGGAGCAGCACTTCAGGAGGTTACATCTTTTACACCTTTTCTACTGTACACCCCATCCCAG
ACGAAGACAGTCCCTGGATCACCGACAGCACAGACAGAATCCCTGCTACCAGAGACCAAGACACATTCCA
CCCCAGTGGGGGGTCCCATACCACTCATGGATCTGAATCAGATGGACACTCACATGGGAGTCAAGAAGGT
GGAGCAAACACAACCTCTGGTCCTATAAGGACACCCCAAATTCCAGAATGGCTGATCATCTTGGCATCCC
TCTTGGCCTTGGCTTTGATTCTTGCAGTTTGCATTGCAGTCAACAGTCGAAGAAGGTGTGGGCAGAAGAA
AAAGCTAGTGATCAACAGTGGCAATGGAGCTGTGGAGGACAGAAAGCCAAGTGGACTCAACGGAGAGGCC
AGCAAGTCTCAGGAAATGGTGCATTTGGTGAACAAGGAGTCGTCAGAAACTCCAGACCAGTTTATGACAG
CTGATGAGACAAGGAACCTGCAGAATGTGGACATGAAGATTGGGGTGTAACACCTACACCATTATCTTGG
AAAGAAACAACCGTTGGAAACATAACCATTACAGGGAGCTGGGACACTTAACAGATGCAATGTGCTACTG
ATTGTTTCATTGCGAATCTTTTTTAGCATAAAATTTTCTACTCTTTTTGTTTTTTGTGTTTTGTTCTTTA
AAGTCAGGTCCAATTTGTAAAAACAGCATTGCTTTCTGAAATTAGGGCCCAATTAATAATCAGCAAGAAT
TTGATCGTTCCAGTTCCCACTTGGAGGCCTTTCATCCCTCGGGTGTGCTATGGATGGCTTCTAACAAAAA
CTACACATATGTATTCCTGATCGCCAACCTTTCCCCCACCAGCTAAGGACATTTCCCAGGGTTAATAGGG
CCTGGTCCCTGGGAGGAAATTTGAATGGGTCCATTTTGCCCTTCCATAGCCTAATCCCTGGGCATTGCTT
TCCACTGAGGTTGGGGGTTGGGGTGTACTAGTTACACATCTTCAACAGACCCCCTCTAGAAATTTTTCAG
ATGCTTCTGGGAGACACCCAAAGGGTGAAGCTATTTATCTGTAGTAAACTATTTATCTGTGTTTTTGAAA
TATTAAACCCTGGATCAGTCCTTTGATCAGTATAATTTTTTAAAGTTACTTTGTCAGAGGCACAAAAGGG
TTTAAACTGATTCATAATAAATATCTGTACTTCTTCGATCTTCACCTTTTGTGCTGTGATTCTTCAGTTT
CTAAACCAGCACTGTCTGGGTCCCTACAATGTATCAGGAAGAGCTGAGAATGGTAAGGAGACTCTTCTAA
GTCTTCATCTCAGAGACCCTGAGTTCCCACTCAGACCCACTCAGCCAAATCTCATGGAAGACCAAGGAGG
GCAGCACTGTTTTTGTTTTTTGTTTTTTGTTTTTTTTTTTTGACACTGTCCAAAGGTTTTCCATCCTGTC
CTGGAATCAGAGTTGGAAGCTGAGGAGCTTCAGCCTCTTTTATGGTTTAATGGCCACCTGTTCTCTCCTG
TGAAAGGCTTTGCAAAGTCACATTAAGTTTGCATGACCTGTTATCCCTGGGGCCCTATTTCATAGAGGCT
GGCCCTATTAGTGATTTCCAAAAACAATATGGAAGTGCCTTTTGATGTCTTACAATAAGAGAAGAAGCCA
ATGGAAATGAAAGAGATTGGCAAAGGGGAAGGATGATGCCATGTAGATCCTGTTTGACATTTTTATGGCT
GTATTTGTAAACTTAAACACACCAGTGTCTGTTCTTGATGCAGTTGCTATTTAGGATGAGTTAAGTGCCT
GGGGAGTCCCTCAAAAGGTTAAAGGGATTCCCATCATTGGAATCTTATCACCAGATAGGCAAGTTTATGA
CCAAACAAGAGAGTACTGGCTTTATCCTCTAACCTCATATTTTCTCCCACTTGGCAAGTCCTTTGTGGCA
TTTATTCATCAGTCAGGGTGTCCGATTGGTCCTAGAACTTCCAAAGGCTGCTTGTCATAGAAGCCATTGC
ATCTATAAAGCAACGGCTCCTGTTAAATGGTATCTCCTTTCTGAGGCTCCTACTAAAAGTCATTTGTTAC
CTAAACTTATGTGCTTAACAGGCAATGCTTCTCAGACCACAAAGCAGAAAGAAGAAGAAAAGCTCCTGAC
TAAATCAGGGCTGGGCTTAGACAGAGTTGATCTGTAGAATATCTTTAAAGGAGAGATGTCAACTTTCTGC
ACTATTCCCAGCCTCTGCTCCTCCCTGTCTACCCTCTCCCCTCCCTCTCTCCCTCCACTTCACCCCACAA
TCTTGAAAAACTTCCTTTCTCTTCTGTGAACATCATTGGCCAGATCCATTTTCAGTGGTCTGGATTTCTT
TTTATTTTCTTTTCAACTTGAAAGAAACTGGACATTAGGCCACTATGTGTTGTTACTGCCACTAGTGTTC
AAGTGCCTCTTGTTTTCCCAGAGATTTCCTGGGTCTGCCAGAGGCCCAGACAGGCTCACTCAAGCTCTTT
AACTGAAAAGCAACAAGCCACTCCAGGACAAGGTTCAAAATGGTTACAACAGCCTCTACCTGTCGCCCCA
GGGAGAAAGGGGTAGTGATACAAGTCTCATAGCCAGAGATGGTTTTCCACTCCTTCTAGATATTCCCAAA
AAGAGGCTGAGACAGGAGGTTATTTTCAATTTTATTTTGGAATTAAATACTTTTTTCCCTTTATTACTGT
TGTAGTCCCTCACTTGGATATACCTCTGTTTTCACGATAGAAATAAGGGAGGTCTAGAGCTTCTATTCCT
TGGCCATTGTCAACGGAGAGCTGGCCAAGTCTTCACAAACCCTTGCAACATTGCCTGAAGTTTATGGAAT
AAGATGTATTCTCACTCCCTTGATCTCAAGGGCGTAACTCTGGAAGCACAGCTTGACTACACGTCATTTT
TACCAATGATTTTCAGGTGACCTGGGCTAAGTCATTTAAACTGGGTCTTTATAAAAGTAAAAGGCCAACA
TTTAATTATTTTGCAAAGCAACCTAAGAGCTAAAGATGTAATTTTTCTTGCAATTGTAAATCTTTTGTGT
CTCCTGAAGACTTCCCTTAAAATTAGCTCTGAGTGAAAAATCAAAAGAGACAAAAGACATCTTCGAATCC
ATATTTCAAGCCTGGTAGAATTGGCTTTTCTAGCAGAACCTTTCCAAAAGTTTTATATTGAGATTCATAA
CAACACCAAGAATTGATTTTGTAGCCAACATTCATTCAATACTGTTATATCAGAGGAGTAGGAGAGAGGA
AACATTTGACTTATCTGGAAAAGCAAAATGTACTTAAGAATAAGAATAACATGGTCCATTCACCTTTATG
TTATAGATATGTCTTTGTGTAAATCATTTGTTTTGAGTTTTCAAAGAATAGCCCATTGTTCATTCTTGTG
CTGTACAATGACCACTGTTATTGTTACTTTGACTTTTCAGAGCACACCCTTCCTCTGGTTTTTGTATATT
TATTGATGGATCAATAATAATGAGGAAAGCATGATATGTATATTGCTGAGTTGAAAGCACTTATTGGAAA
ATATTAAAAGGCTAACATTAAAAGACTAAAGGAAACAGAAAAAAAAAAAAAAAAA
7. polyA_site 1661
 
regulatory 2102..2107 polyA_site 2135
regulatory 2186..2191 polyA_site 2214
regulatory 4553..4558
regulatory 4567..4572
 polyA_site 4589
8.NP_001001391.1
>gi|48255941|ref|NP_001001391.1| CD44 antigen isoform 4 precursor [Homo sapiens]
MDKFWWHAAWGLCLVPLSLAQIDLNITCRFAGVFHVEKNGRYSISRTEAADLCKAFNSTLPTMAQMEKAL
SIGFETCRYGFIEGHVVIPRIHPNSICAANNTGVYILTSNTSQYDTYCFNASAPPEEDCTSVTDLPNAFD
GPITITIVNRDGTRYVQKGEYRTNPEDIYPSNPTDDDVSSGSSSERSSTSGGYIFYTFSTVHPIPDEDSP
WITDSTDRIPATRDQDTFHPSGGSHTTHGSESDGHSHGSQEGGANTTSGPIRTPQIPEWLIILASLLALA
LILAVCIAVNSRRRCGQKKKLVINSGNGAVEDRKPSGLNGEASKSQEMVHLVNKESSETPDQFMTADETR
NLQNVDMKIGV
9.
gene 1..4605
 /gene="CD44"
 /gene_synonym="CDW44; CSPG8; ECMR-III; HCELL; HUTCH-I; IN;
 LHR; MC56; MDU2; MDU3; MIC4; Pgp1"
 /note="CD44 molecule (Indian blood group)"
 /db_xref="GeneID:960"
 /db_xref="HGNC:HGNC:1681"
 /db_xref="HPRD:00115"
 /db_xref="MIM:107269"
 mRNA join(5001..5501,42706..42871,46405..46538,52963..53031,
 55966..56196,80983..81045,85447..85518,87785..87863,
 95260..98533)
 /gene="CD44"
 /gene_synonym="CDW44; CSPG8; ECMR-III; HCELL; HUTCH-I; IN;
 LHR; MC56; MDU2; MDU3; MIC4; Pgp1"
 /product="CD44 molecule (Indian blood group), transcript
 variant 4"
 /transcript_id="NM_001001391.1"
 /db_xref="GI:48255940"
 /db_xref="GeneID:960"
 /db_xref="HGNC:HGNC:1681"
 /db_xref="MIM:107269"
 exon 1..501
 /gene="CD44"/gene_synonym="CDW44; CSPG8; ECMR-III; HCELL; HUTCH-I; IN;
 LHR; MC56; MDU2; MDU3; MIC4; Pgp1"
 /inference="alignment:Splign:1.39.8"
 exon 502..667
 /gene="CD44"
 /gene_synonym="CDW44; CSPG8; ECMR-III; HCELL; HUTCH-I; IN;
 LHR; MC56; MDU2; MDU3; MIC4; Pgp1"
 /inference="alignment:Splign:1.39.8"
 exon 668..801
 /gene="CD44"
 /gene_synonym="CDW44; CSPG8; ECMR-III; HCELL; HUTCH-I; IN;
 LHR; MC56; MDU2; MDU3; MIC4; Pgp1"
 /inference="alignment:Splign:1.39.8"
 exon 802..870
 /gene="CD44"
 /gene_synonym="CDW44; CSPG8; ECMR-III; HCELL; HUTCH-I; IN;
 LHR; MC56; MDU2; MDU3; MIC4; Pgp1"
 /inference="alignment:Splign:1.39.8"
 exon 871..1101
 /gene="CD44"
 /gene_synonym="CDW44; CSPG8; ECMR-III; HCELL; HUTCH-I; IN;
 LHR; MC56; MDU2; MDU3; MIC4; Pgp1"
 /inference="alignment:Splign:1.39.8"
 exon 1102..1164
 /gene="CD44"
 /gene_synonym="CDW44; CSPG8; ECMR-III; HCELL; HUTCH-I; IN;
 LHR; MC56; MDU2; MDU3; MIC4; Pgp1"
 /inference="alignment:Splign:1.39.8"
 exon 1165..1236
 /gene="CD44"
 /gene_synonym="CDW44; CSPG8; ECMR-III; HCELL; HUTCH-I; IN;
 LHR; MC56; MDU2; MDU3; MIC4; Pgp1"
 /inference="alignment:Splign:1.39.8"
 exon 1237..1315
 /gene="CD44"
 /gene_synonym="CDW44; CSPG8; ECMR-III; HCELL; HUTCH-I; IN;
 LHR; MC56; MDU2; MDU3; MIC4; Pgp1"
 /inference="alignment:Splign:1.39.8"
 exon 1316..4589
 /gene="CD44"
 /gene_synonym="CDW44; CSPG8; ECMR-III; HCELL; HUTCH-I; IN;
 LHR; MC56; MDU2; MDU3; MIC4; Pgp1"
 /inference="alignment:Splign:1.39.8"
 
 CDS 435..1520
 /gene="CD44"
 /gene_synonym="CDW44; CSPG8; ECMR-III; HCELL; HUTCH-I; IN;
 LHR; MC56; MDU2; MDU3; MIC4; Pgp1"
 /note="isoform 4 precursor is encoded by transcript
 variant 4; hematopoietic cell E- and L-selectin ligand;
 chondroitin sulfate proteoglycan 8; cell surface
 glycoprotein CD44; GP90 lymphocyte homing/adhesion
 receptor; heparan sulfate proteoglycan; hyaluronate
 receptor; Hermes antigen; CD44 antigen; homing function
 and Indian blood group system; epican; soluble CD44;
 phagocytic glycoprotein 1; extracellular matrix receptor
 III"
 /codon_start=1
 /product="CD44 antigen isoform 4 precursor"
 /protein_id="NP_001001391.1"
 /db_xref="GI:48255941"
 /db_xref="CCDS:CCDS31457.1"
 /db_xref="GeneID:960"
 /db_xref="HGNC:HGNC:1681"
 /db_xref="HPRD:00115"
 /db_xref="MIM:107269"
 /translation="MDKFWWHAAWGLCLVPLSLAQIDLNITCRFAGVFHVEKNGRYSI
 SRTEAADLCKAFNSTLPTMAQMEKALSIGFETCRYGFIEGHVVIPRIHPNSICAANNT
 GVYILTSNTSQYDTYCFNASAPPEEDCTSVTDLPNAFDGPITITIVNRDGTRYVQKGE
 YRTNPEDIYPSNPTDDDVSSGSSSERSSTSGGYIFYTFSTVHPIPDEDSPWITDSTDR
 IPATRDQDTFHPSGGSHTTHGSESDGHSHGSQEGGANTTSGPIRTPQIPEWLIILASL
 LALALILAVCIAVNSRRRCGQKKKLVINSGNGAVEDRKPSGLNGEASKSQEMVHLVNK
 ESSETPDQFMTADETRNLQNVDMKIGV"
 regulatory 2102..2107
 /regulatory_class="polyA_signal_sequence"
 /gene="CD44"
 /gene_synonym="CDW44; CSPG8; ECMR-III; HCELL; HUTCH-I; IN;
 LHR; MC56; MDU2; MDU3; MIC4; Pgp1"
 regulatory 2186..2191
 /regulatory_class="polyA_signal_sequence"
 /gene="CD44"
 /gene_synonym="CDW44; CSPG8; ECMR-III; HCELL; HUTCH-I; IN;
 LHR; MC56; MDU2; MDU3; MIC4; Pgp1"
 regulatory 4553..4558
 /regulatory_class="polyA_signal_sequence"
 /gene="CD44"
 /gene_synonym="CDW44; CSPG8; ECMR-III; HCELL; HUTCH-I; IN;
 LHR; MC56; MDU2; MDU3; MIC4; Pgp1"
 regulatory 4567..4572
 /regulatory_class="polyA_signal_sequence"
 /gene="CD44"
 /gene_synonym="CDW44; CSPG8; ECMR-III; HCELL; HUTCH-I; IN;
 LHR; MC56; MDU2; MDU3; MIC4; Pgp1"
polyA_site 1661
 /gene="CD44"
 /gene_synonym="CDW44; CSPG8; ECMR-III; HCELL; HUTCH-I; IN;
 LHR; MC56; MDU2; MDU3; MIC4; Pgp1"
 polyA_site 2135
 /gene="CD44"
 /gene_synonym="CDW44; CSPG8; ECMR-III; HCELL; HUTCH-I; IN;
 LHR; MC56; MDU2; MDU3; MIC4; Pgp1"
 polyA_site 2214
 /gene="CD44"
 /gene_synonym="CDW44; CSPG8; ECMR-III; HCELL; HUTCH-I; IN;
 LHR; MC56; MDU2; MDU3; MIC4; Pgp1"
 polyA_site 4589
 /gene="CD44"
 /gene_synonym="CDW44; CSPG8; ECMR-III; HCELL; HUTCH-I; IN;
 LHR; MC56; MDU2; MDU3; MIC4; Pgp1"
FIM