found transcript NM_015247 missed one coding exon

[Cao, Kajia]

Hi UCSC Genome browser,

We found that Exon 7 (coding exon) of transcript NM_015247 that we downloaded from UCSC hg19 refseq table is missed.  Its a very small coding region chr16: 50809077-50809085 (hg19, grch37, sequence is CTTATCAG).  We believe the coding regions of this transcript are all messed up even the total number of coding exons is correct.  Here is what we found on NCBI: http://www.ncbi.nlm.nih.gov/nuccore/109637772, the exon 7 (1329..1337).

This is what we found on the UCSC website using "tool --> table browser --> coding exons" and you can see there is no such region.

http://genome.ucsc.edu/cgi-bin/hgTables?hgsid=494633681_7CbtY2wcDkPU4V6UsQYdIf0qr0S7&hgta_printCustomTrackHeaders=on&boolshad.hgta_printCustomTrackHeaders=0&hgta_ctName=tb_refGene&hgta_ctDesc=table+browser+query+on+refGene&hgta_ctVis=pack&hgta_ctUrl=&fbUpBases=200&fbExonBases=0&fbIntronBases=0&fbQual=cds&fbDownBases=200&hgta_doGetBed=get+BED 

track name="tb_refGene" description="table browser query on refGene" visibility=3 url= 

chr16	50783609	50784113	NM_015247_cds_3_0_chr16_50783610_f	0	+
chr16	50785514	50785817	NM_015247_cds_4_0_chr16_50785515_f	0	+
chr16	50788229	50788335	NM_015247_cds_5_0_chr16_50788230_f	0	+
chr16	50788371	50788376	NM_015247_cds_6_0_chr16_50788372_f	0	+
chr16	50810085	50810188	NM_015247_cds_7_0_chr16_50810086_f	0	+
chr16	50811735	50811852	NM_015247_cds_8_0_chr16_50811736_f	0	+
chr16	50813575	50813955	NM_015247_cds_9_0_chr16_50813576_f	0	+
chr16	50815156	50815322	NM_015247_cds_10_0_chr16_50815157_f	0	+
chr16	50816235	50816377	NM_015247_cds_11_0_chr16_50816236_f	0	+
chr16	50818239	50818362	NM_015247_cds_12_0_chr16_50818240_f	0	+
chr16	50820765	50820857	NM_015247_cds_13_0_chr16_50820766_f	0	+
chr16	50821696	50821763	NM_015247_cds_14_0_chr16_50821697_f	0	+
chr16	50825468	50825601	NM_015247_cds_15_0_chr16_50825469_f	0	+
chr16	50826507	50826616	NM_015247_cds_16_0_chr16_50826508_f	0	+
chr16	50827456	50827575	NM_015247_cds_17_0_chr16_50827457_f	0	+
chr16	50828122	50828339	NM_015247_cds_18_0_chr16_50828123_f	0	+
chr16	50830234	50830419	NM_015247_cds_19_0_chr16_50830235_f	0	+

Could you please take a look into it?

Thanks,

Kajia Cao

[Cao, Kajia]

However, we take a closer look, we believe all coding exons are good, except cds_6:

chr16	50788371	50788376	NM_015247_cds_6_0_chr16_50788372_f	0	+

This is a coding exon that has been discarded (no longer a coding exon) but UCSC refseq table still keeps it.

We believe this coding exon position should be chr16: 50809077-50809085 (the one that we pointed out in the last email).

Thanks,

Kajia Cao

[Jayaraman, Pushkala]

Hello Matthew, 

A colleague of mine found a couple discrepancies in your labeling of exon positions for a particular transcript NM_015247 in the Refseq genes list.

we found that NCBI Refseq calls the exon position for that coding exon in a totally different region (which is the correct call) but, when we download the data from UCSC, we get a wrong region (there is no exon in that region even when we see it in the genome browser or in IGV for that transcript)

However, I did read another email in this forum about a related issue replied by you (and hence the email to you!). Not sure if the two are connected. Could you please clarify?:

Discrepancies in exon counts between UCSC RefGene table and NCBI RefSeq entries

https://groups.google.com/a/soe.ucsc.edu/forum/#!topic/genome/kJh3YJCiCDs

Our email to you with the issue is attached inline below (same as subject in this email, you will find it!):

Jayaraman, Pushkala

jayar...@email.chop.edu

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[Christopher Lee]

Hi Jayaraman and Kajia,

Thank you for your question about a missing RefSeq exon. The discrepancies between
NCBI and UCSC are thoroughly explained in the following link you referenced:
https://groups.google.com/a/soe.ucsc.edu/forum/#!topic/genome/kJh3YJCiCDs

In short, the differences between NCBI and UCSC is due in part to the process
by which we generate the RefSeq Genes track (aligning RefSeq mRNAs with Blat), and
partly due to assembly issues. You can read more about how we generate the RefSeq
genes track here:
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=refGene

Thank you again for your inquiry and using the UCSC Genome Browser. If you have any
further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address
are archived on a publicly-accessible forum. If your question includes sensitive data, you
may send it instead to genom...@soe.ucsc.edu.