inconsistency between genome browser and table browser

[Yin, Lihui]

Dear UCSC genome browser team,

 

Recently I used the table browser for the RHCE gene (NM_020485). However the exon position isn’t consistent with what I got from the genome browser. Would you please help check for me anything I didn’t do correctly?

 

In the genome browser, the exon 1 ends at chr1:25747130, which is consistent with the result calculated from NCBI (Go to:

LOCUS  NG_009208  74944 bp  DNA  linear  PRI 22-MAY-2015, /transcript_id="NM_020485.4")

 

 

 

In the table browser, the assembly is Feb. 2009 (hg19)

 

The transcript number is NM_020485

 

 

In the BED file, the exon length and start position were showed below:

track name="tb_refGene" description="table browser query on refGene" visibility=3 url=
chr1	25688739	25747363	NM_020485	0	-	25689017	25747277	0	10	305,74,80,134,138,167,148,151,187,234,	0,8218,13100,23462,26727,28500,29745,40347,46434,58390,

 

Using this table, it was calculated that the chromosome coordinate for exon 1 is 25747363-25747059 (- strand), different from the genome browser finding.

 

Could you think of anything that causes this or I might go wrong?

 

Appreciate your help!

 

Lihui

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