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  • Gene Structure and Identification: Genes and Genomes Orfs and More Consensus Sequences Gene Finding

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    imaem
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    This document discusses gene structure and identification. It describes protein coding genes and RNA genes, and how open reading frames and regulatory signals can help identify genes. It then covers prokaryotic and eukaryotic gene expression, including promoters, transcription, translation, and differences between prokaryotes and eukaryotes. Finally, it discusses finding consensus sequences and using databases to search for genes.

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    genes　structure

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    This document discusses gene structure and identification. It describes protein coding genes and RNA genes, and how open reading frames and regulatory signals can help identify genes. It then covers prokaryotic and eukaryotic gene expression, including promoters, transcription, translation, and differences between prokaryotes and eukaryotes. Finally, it discusses finding consensus sequences and using databases to search for genes.

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    Download as pptx, pdf, or txt
    25 views16 pages

    Gene Structure and Identification: Genes and Genomes Orfs and More Consensus Sequences Gene Finding

    Uploaded by

    imaem
    This document discusses gene structure and identification. It describes protein coding genes and RNA genes, and how open reading frames and regulatory signals can help identify genes. It then covers prokaryotic and eukaryotic gene expression, including promoters, transcription, translation, and differences between prokaryotes and eukaryotes. Finally, it discusses finding consensus sequences and using databases to search for genes.

    Copyright:

    Attribution Non-Commercial (BY-NC)
    Download as PPTX, PDF, TXT or read online from Scribd
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    of 16

    Gene Structure and Identification

    Genes and Genomes


    ORFs and more
    Consensus Sequences
    Gene Finding
    Genes
    • Protein Coding

    • RNA genes
    – rRNA
    – tRNA
    – snRNA, snoRNA…
    Protein Coding Genes
    • ORF
    – long (usually >100 aa)
    – “known” proteins likely
    • Regulatory signals
    – Depend on organism
    • Prokaryotes vs Eukaryotes
    • Verterbrate vs fungi, eg.
    Prokaryotic Gene Expression
    Promoter Cistron1 Cistron2 CistronN Terminator

    Transcription RNA Polymerase


    mRNA 5’ 3’
    1 2 N
    Ribosome, tRNAs,
    Translation
    Protein Factors
    N N
    N C
    C
    C
    1 2 3
    Polypeptides
    Bacterial Promoter
    -35
    T82T84G78A65C54A45…
    (16-18 bp)…
    T80A95T45A60A50T96…(A,G)
    -10 +1
    Alternate sigma factors
    CCCTTGAA….CCCGATNT
    Terminators
    • Stem/loop • C-rich
    – structural only • G-poor
    • 3’-U tail • “loose” consensus

    Rho-independent Rho-dependent
    Translation
    Ribosome Binding Site, Shine-
    Dalgarno Site

    nnGGAGGnnnnnATG…

    typical E. coli

    nnaaAGGnnnnnATG
    Eukaryotic Gene Expression

    Enhancer Promoter Transcribed Region Terminator

    Transcription RNA Polymerase II


    Primary transcript 5’ Intron1 3’
    Exon1 Exon2

    Cap
    Splice
    Translation Cleave/Polyadenylate
    7m
    G An
    N
    C Transport
    Polypeptide 7m
    G An
    Eukaryotic Gene Complexity
    • Yeast
    – introns rare
    – promoters adjacent
    – genome dense
    Exon/Intron Structure

    CCACATTgtn(30-10,000)an(5-20)agCAGAA

    ...CCACATTCAGAA...
    ...ProHisSerGlu...
    Alternative Splice

    CCACATTgtn(30-10,000)an(5-20)agcagAA

    ...CCACATTAA...
    ...ProHisSTOP
    Consensus Sequences
    • Promoter sites
    • Intron/Exon
    • Transcription Termination/PolyA

    • Translation initation
    Finding Functional Sequences

    Known Consensus Sequences


    Consensus Sequence Generation
    Functional Tests
    Consensus Inference
    • Position Weight Matrices
    • Sequence Logos
    ProfileScan
    • Hidden Markov Models
    Basal Promoter Analysis
    Myers and Maniatis, Genes VI, 831

    • ATATAA -30 TBP


    • GGCCAATC -75 CTF/NF1
    • GCCACACCC -90 SP1
    +1

    GC CAAT TATA
    DATABASE SEARCH
    • BLASTN
    – DNA:DNA comparison (ALWAYS!)
    – Not sensitive (DNA conservation low)
    • BLASTX/TBLASTX
    – 6 frame ORFS:polypeptide database
    – 6 frames vs. 6 frames of a DNA database

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