基因组数据分析中涉及基因结构的问题

探序基因肿瘤研究院  整理

基因的结构：

以F5基因为例子，查看gtf文件对于这个基因的描述：

NC_000001.10    BestRefSeq    transcript    169481189    169555719    .    -    .    gene_id "F5"; transcript_id "NM_000130.5"; db_xref "GeneID:2153"; exception "annotated by transcript or proteomic data"; gbkey "mRNA"; gene "F5"; inference "similar to RNA sequence, mRNA (same species):RefSeq:NM_000130.5"; note "The RefSeq transcript has 1 substitution compared to this genomic sequence"; product "coagulation factor V"; tag "RefSeq Select"; transcript_biotype "mRNA";

NC_000001.10    BestRefSeq    exon    169555467    169555719    .    -    .    gene_id "F5"; transcript_id "NM_000130.5"; db_xref "GeneID:2153"; exception "annotated by transcript or proteomic data"; gene "F5"; inference "similar to RNA sequence, mRNA (same species):RefSeq:NM_000130.5"; note "The RefSeq transcript has 1 substitution compared to this genomic sequence"; product "coagulation factor V"; tag "RefSeq Select"; transcript_biotype "mRNA"; exon_number "1";

NC_000001.10    BestRefSeq    CDS    169555467    169555624    .    -    0    gene_id "F5"; transcript_id "NM_000130.5"; db_xref "CCDS:CCDS1281.1"; db_xref "GeneID:2153"; exception "annotated by transcript or proteomic data"; gbkey "CDS"; gene "F5"; inference "similar to AA sequence (same species):RefSeq:NP_000121.2"; note "The RefSeq protein has 1 substitution compared to this genomic sequence"; product "coagulation factor V preproprotein"; protein_id "NP_000121.2"; tag "RefSeq Select"; exon_number "1";

NC_000001.10    BestRefSeq    start_codon    169555622    169555624    .    -    0    gene_id "F5"; transcript_id "NM_000130.5"; db_xref "CCDS:CCDS1281.1"; db_xref "GeneID:2153"; exception "annotated by transcript or proteomic data"; gbkey "CDS"; gene "F5"; inference "similar to AA sequence (same species):RefSeq:NP_000121.2"; note "The RefSeq protein has 1 substitution compared to this genomic sequence"; product "coagulation factor V preproprotein"; protein_id "NP_000121.2"; tag "RefSeq Select"; exon_number "1";