BIO COMPUTING LAB(BT301 & 302)

Introduction to Bioinformatics (Ch 1) & Access to Information

(Ch 2)

Assignment No.1

Description:
For the following assignment, you will use the NCBI and EMBL-EBI websites. This
assignment is meant to get you familiar with different databases and how to access
information on biological sequences available at these websites. Follow the
questions below, but do not be afraid to explore the NCBI and EBI databases on your
!own

Problem Statement:
To begin, go to the NCBI homepage and perform a search against all NCBI :1
."databases for Homo sapiens IRF1. Click “search

Report the number of search results displayed for the following databases: (2pts)
.__________PMC: ______________8263

._________________Protein Structure: ______1

.___________Clinical Variations: ________22

Online Mendelian Inheritance in Man: 0

Then, from the NCBI and EMBL-EBI databases results about Homo sapiens IRF1 :2
:gene, report the following information
Gene Name: _______ interferon regulatory factor 1
)pts 1( ._____________________________________

Gene's Main Function: Summary: The protein encoded by this gene is a

transcriptional
regulator and tumor suppressor, serving as an activator of genes
involved in both innate and acquired immune responses. The encoded
protein activates the transcription of genes involved in the body's
response to viruses and bacteria, playing a role in cell
proliferation, apoptosis, the immune response, and DNA damage
response. This protein represses the transcription of several other
genes. As a tumor suppressor, it both suppresses tumor cell growth
and stimulates an immune response against tumor cells. Defects in
this gene have been associated with gastric cancer, myelogenous
leukemia, and lung cancer.
)pts 1( .________________________________________ _________

IRF1 gene implicated in different pathways; one of them is ___ tumor suppression ___. (0.5
pts)

IRF1 gene mainly expressed in _____ bone marrow ________________. (0.5 pts)

Location: ______________ 5q31.1 ______________. (0.5 pts)

No. of Nucleotides: ____ 16165 bp _____________. (1 pts)

No. of Introns: ________9_________. (0.5 pts)

The IRF1 protein is subcellular located in ___ Localized to the Nucleoplasm &Cytosol _. (1 pts)

Insert the Genbank sequence format for the ninth exon of IRF1 gene in the following box by using
the print screen button.(1 pts)

Insert the FASTA sequence format of IRF 1 isoform 3. (1 pts)

>NM_001354925.1 Homo sapiens interferon regulatory factor 1 (IRF1), transcript

variant 3, mRNA
AGAGCTCGCCACTCCTTAGTCGAGGCAAGACGTGCGCCCGAGCCCCGCCGAACCGAGGCCACCCGGAGCC
GTGCCCAGTCCACGCCGGCCGTGCCCGGCGGCCTTAAGAACCCGGCAACCTCTGCCTTCTTCCCTCTTCC
ACTCGGAGTCGCGCTCCGCGCGCCCTCACTGCAGCCCCTGCGTCGCCGGGACCCTCGCGCGCGACCGCCG
AATCGCTCCTGCAGCAGAGCCAACATGCCCATCACTCGGATGCGCATGAGACCCTGGCTAGAGATGCAGA
TTAATTCCAACCAAATCCCGGGGCTCATCTGGATTAATAAAGAGGAGATGATCTTCCAGATCCCATGGAA
GCATGCTGCCAAGCATGGCTGGGACATCAACAAGGATGCCTGTTTGTTCCGGAGCTGGGCCATTCACACA
GGCCGATACAAAGCAGGGGAAAAGGAGCCAGATCCCAAGACGTGGAAGGCCAACTTTCGCTGTGCCATGA
ACTCCCTGCCAGATATCGAGGAGGTGAAAGACCAGAGCAGGAACAAGGGCAGCTCAGCTGTGCGAGTGTA
CCGGATGCTTCCACCTCTCACCAAGAACCAGAGAAAAGAAAGAAAGTCGAAGTCCAGCCGAGATGCTAAG
AGCAAGGCCAAGAGGAAGTCATGTGGGGATTCCAGCCCTGATACCTTCTCTGATGGACTCAGCAGCTCCA
CTCTGCCTGATGACCACAGCAGCTACACAGTTCCAGGCTACATGCAGGACTTGGAGGTGGAGCAGGCCCT
GACTCCAGCACTGTCGCCATGTGCTGTCAGCAGCACTCTCCCCGACTGGCACATCCCAGTGGAAGTTGTG
CCGGACAGCACCAGTGATCTGTACAACTTCCAGGTGTCACCCATGCCCTCCACCTCTGAAGGGGATATTG

GOOD LUCK