XB-FEAT-960953

hcar1

This is the community wiki page for the gene hcar1. Please feel free to add any information that is relevant to this gene that is not already captured elsewhere in Xenbase.

nomenclature updates

16MAY2023

This gene was previously named hcar3 on Xenbase. It is now changed to hcar1 in accordance with the most ancestral human gene of the three (HCAR1, HCAR3, HCAR2) that share synteny with this locus in Xenopus.

The following evidence informed this decision to change the name this gene from hcar3 to hcar1 on 16MAY2023:

X. tropicalis “hcar3” v9.1 (chr.1) - XB-GENEPAGE-960953 - 100491947 vps37b> hip1r< ccdc62< denr> hcar3> kntc1< rsrc2> zcchc8> clip1>

X. tropicalis “XB5886923 [provisional:hcar2]” v10.0 (chr.1) - XB-GENEPAGE-5886923 - 100492010 vps37b> hip1r< ccdc62< denr> hcar2> kntc1< rsrc2> zcchc8> clip1>

X. laevis “hcar3.L” v10.1 (chr.1L) - XB-GENEPAGE-960953 - 108716697 vps37b.L> hip1r.L< ccdc62.L< denr.L> hcar3.L> kntc1.L< rsrc2.L> zcchc8.L> clip1.L>

X. laevis “hcar3.S” v10.1 (chr.1S) - XB-GENEPAGE-960953 - 108705662 vps37b.S> hip1r.S< denr.L> hcar3.S> rsrc2.L> zcchc8.L> clip1.S>

H. sapiens “HCAR1, HCAR3, HCAR2” (chr.1) - 100491947 HIP1R< CCDC62< DENR< HCAR1> HCAR3> HCAR2> KNTC1< RSRC2> ZCCHC8> CLIP1>

The following sequences were then used in a multiple alignment, and it was found these all share high sequence identity:

XTR - v9.1 - ‘hcar3’ - XP_004910574.2

XTR - v10.0 - ‘XB5886923 [provisional:hcar2]’ - XP_012824453.1

XLA L - v10.1 - ‘hcar3.L’ - XP_041423517.1

XLA S - v10.1 - ‘hcar3.S’ - XP_018098031.1

HSA - ‘HCAR1’ - NP_115943.1

HSA - ‘HCAR3’ - NP_006009.2

HSA - ‘HCAR2’ - NP_808219.1

This and the phylogenetic tree generated from these sequences could not determine that the two X.trop genes should be distinct, nor for the X.laev genes, and could also not determine which of the three HCAR# genes is the correct human ortholog to the Xenopus ortholog. Therefore, we assess that the Xenopus ortholog is named after the most ancestral human gene, found to be HCAR1 in our phylogeny.

Actions taken:

- Move the v10.0 gene model XBXT10g000396 and NCBI ID:100492010 and associated mRNAs, proteins (associated with what is currently "XB5886923 [provisional:hcar2]") from XB-GENEPAGE-5886923 to the XB-GENEPAGE-960953 and re-name to hcar1.

- Re-name the umbrella gene and genes associated with the XB-GENEPAGE-960953 from hcar3 to hcar1.

- Retire the v9.1 gene model gene16494 (ie. XT-9_1-gene16494) and NCBI ID:100491947 and associated mRNAs, proteins (associated with what is currently "hcar3") and allow to remain on XB-GENEPAGE-960953. Promote the gene model XBXT10g000396 and NCBI ID:100492010 in its place as the latest version.

- Submit for XB-GENEPAGE-5886923 to be deprecated.

- Change other species orthologous genes listed from HCAR3 to HCAR1 in human and other species where NCBI orthology tool lists them for HCAR1.

Xenbase curator AJB