The same location shares different GeneBank Accession in IGV and UCSC?

Question

[Andrew Liu]

I'm now using IGV to visualize genome of C. elegans. But I found that the same locations shares different GeneBank Accession like his-51 and his-19 gene. And I checked the gtf and bed files downloaded from UCSC, and found that his-51(NM_072895) and his-19(NM_072892) have an completely same location. I'm wondering why?

Answer 1

[harold.smith.tarheel]

The difference is RNA vs DNA. The histone genes are repetitive. There are four identical copies (plus several nearly identical ones) of this gene in the genome (DNA). The accession numbers you list are RefSeq RNAs for those four copies. So each (identical) RNA maps to multiple loci - and, conversely, each locus indicates multiple mapped RNAs.

[Andrew Liu]

Thank you very much! It's helpful!

[WouterDeCoster]

If an answer was helpful you should upvote it, if the answer resolved your question you should mark it as accepted.

Answer 2

[MohammadAlkadi]

Maybe you are using different assembly releases. make sure they are the same (for example ce11, ce10 ..etc)

[Andrew Liu]

Umm, thanks first, and I just downloaded gtf and bed file from UCSC of ce11 version, and his-51, his-19, even his-21 and his-53 have the same location. I didn't make any alignment steps. I'm questioning the gtf(or bed) file itself.