different IQCF1 region between UCSC and Ensembl

[mingchen]

Dear UCSC,

While I'm search some informations about an gene called IQCF1, I found that in Ensembl(hg19), the gene region is from chr3:51,928,892-51,937,351. But in UCSC Genes(RefSeq,UniProt,CCDS,Rfam,tRNAs&Comparative Genomics)Track, there is an mRNA of IQCF1 is from chr3:51,840,728-51,937,386 (BC034228-Homo sapiens IQ motif containing F1, mRNA (cDNA clone IMAGE:5266078), complete cds). Why the gene region is so different between UCSC and Ensembl? Can I treat the different part as UTR regions?

Looking forward to your reply~

Sincerely,

Chen Ming

[Luvina Guruvadoo]

Hi Chen,

There are actually two UCSC gene models for IQCF5:

uc003dbq.4 chr3:51,840,728-51,937,386 (which matches Ensembl)
uc011bdx.2 chr3:51,907,737-51,909,600

Note, the transcript you are referred to in your email corresponds to IQCF5. You can read more about how UCSC genes are built on the track description page: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=knownGene

If you have further questions please feel free to contact the mailing list again at gen...@soe.ucsc.edu.

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Luvina Guruvadoo
UCSC Genome Bioinformatics Group

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