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    Bioinformatic-Practice BI11-246

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    Nguyễn Tuấn Thành

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    Bioinformatic-Practice BI11-246

    Uploaded by

    Nguyễn Tuấn Thành
    16 views3 pages

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    Bioinformatic-practice BI11-246 (1)

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    16 views3 pages

    Bioinformatic-Practice BI11-246

    Uploaded by

    Nguyễn Tuấn Thành

    Copyright:

    © All Rights Reserved
    Download as DOCX, PDF, TXT or read online from Scribd
    Download as docx, pdf, or txt
    of 3

    Name: Nguyen Tuan Thanh

    Class: C ( Tutor C1)

    Student-ID: BI11-246

    Introduction to Ensembl

    https://www.youtube.com/watch?time_continue=1442&v=lA2xq3YkWko

    Exercise 1 – Panda

    (a) Go to the species homepage for Panda. What is the name of the genome assembly
    for Panda?

    AgamP4

    (b) Click on More information and statistics. How long is the Panda genome (in bp)?

    2,444,060,653

    How many coding genes have been annotated?

    20,857

    Exercise 2 – Zebrafish

    What previous assemblies are available for zebrafish?

    Now: GRCz10

    Previous: Zv9 and Zv8

    Exercise 3 – Mosquitoes
    (a) Go to Ensembl Metazoa. How many species of the genus Anopheles are
    represented in Ensembl Metazoa?
    There are 22 species of genus anopheles

    (b) The current Anopheles gambiae genome assembly last revised in 2006

    Exercise 4 – Bacteria

    Go to Ensembl Bacteria and find the species Belliella baltica.

    It has 3,680 coding genes and 53 non-coding.

    Exercise 5 – Exploring the human MYH9 gene

    (a) Find the human MYH9 (myosin, heavy chain 9, non-muscle) gene, and go to the
    Gene

     On which chromosome and which strand of the genome is this gene located?
    Chromosome 22: 36,281,280-36,387,967 - Region in detail - Homo_sapiens - Ensembl genome
    browser 103

     How many transcripts (splice variants) are there and how many are protein coding?
    11 transcript and 3 protein coding
     What is the longest transcript, and how long is the protein it encodes?
    MYH9-201 is the longest transcript and has 1960aa protein

    (b) Click on Phenotype at the left side of the page. Are there any diseases associated
    with this gene, according to O-MIM (Online Mendelian Inheritance in Man)?

    Yes, there’re a lots diseases associated with this gene


    (c) In the transcript table, click on the transcript ID for MYH9-201, and go to the
    Transcript tab.

     How many exons does it have?


    41 exons
     Are any of the exons completely or partially untranslated?
    The first exon being untranslated

    Exercise 6 – Finding a gene associated with a phenotype

    Phenylketonuria is a genetic disorder caused by an inability to metabolise phenylalanine


    in any body tissue. This results in an accumulation of phenylalanine causing seizures
    and mental retardation.

    (a) Search for phenylketonuria from the Ensembl homepage and narrow down your
    search to only genes. What gene is associated with this disorder?

    1 gene PAH

    (b) How many protein coding transcripts does this gene have? View all of these in
    the transcript comparison view.

    6 protein coding transcripts

    (c) What is the MIM gene identifier for this gene?

    612349

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