Hi everyone.
What I'm trying to find out is the meaning of the 4th column of the file I
obtain when I select in Table Browser: genome assembly hg19, RefSeq Genes ->
Exons. Am i doing this right?What I want is to obtain the coordinates of the
exons in the human genes and compare them to another set of coordinates and see
how many overlap. The thing is I don't really understand what I see on the 4th
coloumn: For example I have this set of exons:chr1 8384389 8384786
NM_001080397_exon_0_0_chr1_8384390_f 0 +
chr1 8385357 8385450 NM_001080397_exon_1_0_chr1_8385358_f 0 +
chr1 8385877 8386102 NM_001080397_exon_2_0_chr1_8385878_f 0 +
chr1 8390268 8390996 NM_001080397_exon_3_0_chr1_8390269_f 0 +
chr1 8395496 8395650 NM_001080397_exon_4_0_chr1_8395497_f 0 +
chr1 8397875 8398052 NM_001080397_exon_5_0_chr1_8397876_f 0 +
chr1 8399552 8399758 NM_001080397_exon_6_0_chr1_8399553_f 0 +
chr1 8403806 8404227 NM_001080397_exon_7_0_chr1_8403807_f 0 +
Am i given the coordinates for each exons on a certain gene? And if so why is
it that when I look at the coordinates of the gene that corresponds to the id
NM_001080397 it starts later than the exon??:chr1 hg19_refGene CDS
8384390 8384786 0.000000 + 0 gene_id "NM_001080397";
transcript_id "NM_001080397";
chr1 hg19_refGene exon 8384390 8384786 0.000000 + .
gene_id "NM_001080397"; transcript_id "NM_001080397";
chr1 hg19_refGene CDS 8385358 8385450 0.000000 + 2
gene_id "NM_001080397"; transcript_id "NM_001080397";
chr1 hg19_refGene exon 8385358 8385450 0.000000 + .
gene_id "NM_001080397"; transcript_id "NM_001080397";
chr1 hg19_refGene CDS 8385878 8386102 0.000000 + 2
gene_id "NM_001080397"; transcript_id "NM_001080397";
chr1 hg19_refGene exon 8385878 8386102 0.000000 + .
gene_id "NM_001080397"; transcript_id "NM_001080397";
chr1 hg19_refGene CDS 8390269 8390996 0.000000 + 2
gene_id "NM_001080397"; transcript_id "NM_001080397";
chr1 hg19_refGene exon 8390269 8390996 0.000000 + .
gene_id "NM_001080397"; transcript_id "NM_001080397";
chr1 hg19_refGene CDS 8395497 8395650 0.000000 + 0
gene_id "NM_001080397"; transcript_id "NM_001080397";
chr1 hg19_refGene exon 8395497 8395650 0.000000 + .
gene_id "NM_001080397"; transcript_id "NM_001080397";
chr1 hg19_refGene CDS 8397876 8398052 0.000000 + 2
gene_id "NM_001080397"; transcript_id "NM_001080397";
chr1 hg19_refGene exon 8397876 8398052 0.000000 + .
gene_id "NM_001080397"; transcript_id "NM_001080397";
chr1 hg19_refGene CDS 8399553 8399758 0.000000 + 2
gene_id "NM_001080397"; transcript_id "NM_001080397";
chr1 hg19_refGene exon 8399553 8399758 0.000000 + .
gene_id "NM_001080397"; transcript_id "NM_001080397";
chr1 hg19_refGene CDS 8403807 8404070 0.000000 + 0
gene_id "NM_001080397"; transcript_id "NM_001080397";Thank you,Best,Adriana
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