Ucsc And Ncbi Cytoband Location For Human Gene Scn5A Are Different. Why?

Question

[Jarretinha]

I'm still trying to plot some gene features using cytobands as the reference scale. Nevertheless, UCSC and NCBI cytobands don't agree for certain genes. E. g.: human SCN5A is located at 3p22.2 on UCSC Genome Browser. HGNC says it's located at 3p21. NCBI's Entrez Gene agrees with HGNC. Genome coordinates are quite similar (Entrez: 38548062, 38649673; UCSC GB: 38589553, 38674850). Am I losing something? Looking with the wrong sense? Wrong version?

[Pierre Lindenbaum]

SCN5A ? FIRST ! http://www.ncbi.nlm.nih.gov/pubmed/23872634 :-)

[Jarretinha]

Ha! I've just got even more confused! Even using this information (Where do I find genomic coordinates for human cytogenetic bands according to Entrez Gene/HGCN?), I reach same conclusions. NCBI MapView and UCSC Genome Tables use the same data. Both don't agree with HGNC. Your paper say that 3p21 is inside this range:

hs3 p22.2 36500000 39400000 gneg

I've obtained these values using Neilfws hint on MapView data.

Answer 1

[Jarretinha]

Well. . . After searching in obscure places, I've got my answer!!!

I've looked into ARCHIVE folders at NCBI for cyto_gene.md files. They aren't well documented. So, I've collected a bunch of them and greped for SCN5A and voilá!

cyto_gene.md.BUILD.33.1:9606    3    3p21    SCN5A    6331    locus    3    2239    2245
cyto_gene.md.BUILD.34.1:9606    3    2189    2193    na    SCN5A    LocusID:6331    GENE    3p21    BandsAsInt    -1
cyto_gene.md.BUILD.34.2:9606    3    2189    2194    na    SCN5A    GeneID:6331    GENE    3p21    BandsAsInt    -1
cyto_gene.md.BUILD.34.3:9606    3    2189    2194    na    SCN5A    GeneID:6331    GENE    3p21    BandsAsInt    -1
cyto_gene.md.BUILD.35.1:9606    3    2188    3676    na    SCN5A    GeneID:6331    GENE    3p21    BandsAsInt    -1
cyto_gene.md.BUILD.36.1:9606    3    1971    2013    na    SCN5A    GeneID:6331    GENE    3p22.2a    BandsAsInt
cyto_gene.md.BUILD.36.2:9606    3    1971    2013    na    SCN5A    GeneID:6331    GENE    3p22.2a    BandsAsInt
cyto_gene.md.BUILD.36.3:9606    3    1971    2013    na    SCN5A    GeneID:6331    GENE    3p22.2a    BandsAsInt
cyto_gene.md.BUILD.37.1:9606    3    1971    2013    na    SCN5A    GeneID:6331    GENE    3p22.2a    BandsAsInt
cyto_gene.md.BUILD.37.2:9606    3    1971    2013    na    SCN5A    GeneID:6331    GENE    3p22.2a    BandsAsInt
cyto_gene.md.BUILD.37.3:9606    3    1971    2013    na    SCN5A    GeneID:6331    GENE    3p22.2a    BandsAsInt

BUILD.37.3 provides a header for this file:

#taxId    chromosome    iscn_start    iscn_end    orientation    featureName    featureId    featureType    printLocation    units

So, SCN5A cytoband location changed between BUILD35.1 and BUILD36.1! Nevertheless, Entrez Gene still shows the old cytoband location. Also HGNC! UCSC is probably correct. Now, I can compare the ideogram files pointed by Neilfws!!!