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ZSO 1 bioinformatica
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ZSO 1 - Uitgewerkte oefeningen van ZSO 1 van bioinformatica, biomedische wetenschappen UHasselt
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ZSO 1: BIO-INFORMATICAOPDRACHTEN 1
OEFENING 1:
GA NAAR DE NCBI HOME PAGE (HTTP://WWW.NCBI.NLM.NIH.GOV/), SELECTEER “NUCLEOTIDE”
EN GEEF DE VOLGENDE ACCESSION CODE IN “U54469”. BEKIJK DE INHOUD VAN DEZE FILE.
Inhoud: Drosophila melanogaster eukaryotic initiation factor 4E (eIF4E) gene, complete cds,
alternatively spliced
WAAROM STAAT ER IN DE ANNOTATED INFORMATIE 2 X MRNA EN 2 X CDS VOOR EENZELFDE
GEN?
door alternatieve splicing kunnen we verschillende mRNA’s verkrijgen => 2 verschillende
producten:
Eukaryotic initiation factor 4E-II
Eukaryotic initiation factor 4E-I
WELKE VERSCHILLENDE FILEFORMATEN KAN JE BEKOMEN VOOR DEZE SEQUENTIES?
- GenBank
- FASTA
- Graphics
1
Bij de varianten nemen zij vaak 1 of 5.
, OEFENING 2:
ZOEK HET HUMANE ICAM-1 PROTEÏNE OP. WAT IS DE ACCESSION CODE?
ICAM-1 (homo sapiens) = GenBank: CAA41977
https://www.ncbi.nlm.nih.gov/protein/CAA41977.1
ZOEK VERVOLGENS HET BIJHORENDE MRNA OP. UIT HOEVEEL BASEPAREN BESTAAT DIT MRNA?
GEEF HET CDS IN FASTA FORMAAT. HOEVEEL EXONEN ZIJN ER?
*om dit te doen hebben we het nucleotide nodig => onder nucleotide moeten we dan ICAM-1
aangeven*
Baseparen = 2967
Aantal exonen = zeven
CDS in fasta formaat:
>NM_000201.3:41-1639 Homo sapiens intercellular adhesion molecule 1
(ICAM1), mRNA
ATGGCTCCCAGCAGCCCCCGGCCCGCGCTGCCCGCACTCCTGGTCCTGCTCGGGGCTCTGTTCCCAGGAC
CTGGCAATGCCCAGACATCTGTGTCCCCCTCAAAAGTCATCCTGCCCCGGGGAGGCTCCGTGCTGGTGAC
ATGCAGCACCTCCTGTGACCAGCCCAAGTTGTTGGGCATAGAGACCCCGTTGCCTAAAAAGGAGTTGCTC
CTGCCTGGGAACAACCGGAAGGTGTATGAACTGAGCAATGTGCAAGAAGATAGCCAACCAATGTGCTATT
CAAACTGCCCTGATGGGCAGTCAACAGCTAAAACCTTCCTCACCGTGTACTGGACTCCAGAACGGGTGGA
ACTGGCACCCCTCCCCTCTTGGCAGCCAGTGGGCAAGAACCTTACCCTACGCTGCCAGGTGGAGGGTGGG
GCACCCCGGGCCAACCTCACCGTGGTGCTGCTCCGTGGGGAGAAGGAGCTGAAACGGGAGCCAGCTGTGG
GGGAGCCCGCTGAGGTCACGACCACGGTGCTGGTGAGGAGAGATCACCATGGAGCCAATTTCTCGTGCCG
CACTGAACTGGACCTGCGGCCCCAAGGGCTGGAGCTGTTTGAGAACACCTCGGCCCCCTACCAGCTCCAG
ACCTTTGTCCTGCCAGCGACTCCCCCACAACTTGTCAGCCCCCGGGTCCTAGAGGTGGACACGCAGGGGA
CCGTGGTCTGTTCCCTGGACGGGCTGTTCCCAGTCTCGGAGGCCCAGGTCCACCTGGCACTGGGGGACCA
GAGGTTGAACCCCACAGTCACCTATGGCAACGACTCCTTCTCGGCCAAGGCCTCAGTCAGTGTGACCGCA
GAGGACGAGGGCACCCAGCGGCTGACGTGTGCAGTAATACTGGGGAACCAGAGCCAGGAGACACTGCAGA
CAGTGACCATCTACAGCTTTCCGGCGCCCAACGTGATTCTGACGAAGCCAGAGGTCTCAGAAGGGACCGA
GGTGACAGTGAAGTGTGAGGCCCACCCTAGAGCCAAGGTGACGCTGAATGGGGTTCCAGCCCAGCCACTG
GGCCCGAGGGCCCAGCTCCTGCTGAAGGCCACCCCAGAGGACAACGGGCGCAGCTTCTCCTGCTCTGCAA
CCCTGGAGGTGGCCGGCCAGCTTATACACAAGAACCAGACCCGGGAGCTTCGTGTCCTGTATGGCCCCCG
ACTGGACGAGAGGGATTGTCCGGGAAACTGGACGTGGCCAGAAAATTCCCAGCAGACTCCAATGTGCCAG
GCTTGGGGGAACCCATTGCCCGAGCTCAAGTGTCTAAAGGATGGCACTTTCCCACTGCCCATCGGGGAAT
CAGTGACTGTCACTCGAGATCTTGAGGGCACCTACCTCTGTCGGGCCAGGAGCACTCAAGGGGAGGTCAC
CCGCAAGGTGACCGTGAATGTGCTCTCCCCCCGGTATGAGATTGTCATCATCACTGTGGTAGCAGCCGCA
GTCATAATGGGCACTGCAGGCCTCAGCACGTACCTCTATAACCGCCAGCGGAAGATCAAGAAATACAGAC
TACAACAGGCCCAAAAAGGGACCCCCATGAAACCGAACACACAAGCCACGCCTCCCTGA
OEFENING 3:
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