XB-FEAT-485843

hoxd11

This is the community wiki page for the gene hoxd11 please feel free to add any information that is relevant to this gene that is not already captured elsewhere in Xenbase.

annotation in earlier genome assemblies and synteny for Xenopus hoxd11 genes

25MARCH2024

Note that the annotation and naming for hoxd9' through hoxd13 in X .tropicals and X. laevis has improved over time, with each new genome annotation, however misnaming has occurred (see synteny below). Xenbase gene pages for these hoxd# genes have been recently updated by our curators ( see nomenclature changes below)

synteny patterns/annotations

X. tropicalis v8.0 chr9: hoxd3< hoxd9< hoxd10< Xetrov14037309m.g< hoxd11< Xetrov14037311m.g< hoxd13< Xetrov14037313m.g>

X. tropicalis v9.1 chr9: hoxd3< hocd8< Xetrov90024221m.g> hoxd9< hoxd10< (2 models gene12917 and gene26541)< hoxd11< hoxd13< evx2>

X. tropicalis v10.0 chr9: hoxd3< hoxd4< mir10b> hocd8< LOC116407696(unch)> LOC116407707(unch)< hoxd9< 'LOC116406456(the real hoxd10, model:XBXT10g001416)<' hoxd10 (GeneID:100038085 actually= hoxd11, model:XBXT10g019897)< hoxd13< evx2>

2) X. laevis X. laevis v10 chr9_10L: mtx2.L< hoxd1.L< hoxd3.L< hoxd4.L< hocd8.L< hoxd9.L< hoxd10.L< hoxd11.L< LOC121397930<(unchar. spans 9-11)<. hoxd13.L< evx2.L>

X. laevis v9.1 (UCBerkeley release) chr9_10S: mtx2.S< hoxd1.S< hoxd3.S< hoxd4.S< hocd8.S< hoxd9.S< hoxd10.S< hoxd11.S< hoxd13.S< evx2.SL>

X. laevis v10 (NCBI RELEASE) chr9_10S: mtx2.S< hoxd1.S< hoxd3.S< hoxd4.S< hocd8.S< hoxd9.S< hoxd10.S< LOC108703010(NEW hoxd11.S model:XBXL10_1g43530)< hoxd13.S< LOC108703011(PSUEDOGENE XBXL10_1g43532)>

Nomenclature changes

25MAR2024 1) X. tropicalis: added/replaced v10 GeneIDs and v10 gene models to hoxd10 and hoxd11.

2) added v10 model for hoxd11.S, LOC108703010 as synonym