Christina: /* cetn2 */

2023-04-24T19:09:34Z

cetn2

← Older revision		Revision as of 19:09, 24 April 2023
Line 1:		Line 1:
	=cetn2=		=''cetn2''=
	This is the community wiki page for the gene ''cetn2'' please feel free to add any information that is relevant to this gene that is not already captured elsewhere in Xenbase.		This is the community wiki page for the gene ''cetn2'' please feel free to add any information that is relevant to this gene that is not already captured elsewhere in Xenbase.

Christina: /* nomenclature changes */

2023-01-25T19:13:42Z

nomenclature changes

← Older revision		Revision as of 19:13, 25 January 2023
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	XB-GENEPAGE-967616 (Xtr GeneID: 549903) was renamed, changes from "CETN1" to "CETN2" - see details below.		XB-GENEPAGE-967616 (Xtr GeneID: 549903) was renamed, changes from "CETN1" to "CETN2" - see details below.

	Details of the CETN1, CETN2, and CETN4 ~~analaysis~~ and orthology.		Details of the CETN1, CETN2, and CETN4 analysis and orthology below:

	The CETN1 gene of human (GeneID: 1068, HGNC: 1866) and all placental mammals likely arose as a retrotransposition event because only placentals have this single-coding-exon gene between COLEC12 and CLUL1. The gene is absent in other animals despite the gene synteny being very stable.		The CETN1 gene of human (GeneID: 1068, HGNC: 1866) and all placental mammals likely arose as a retrotransposition event because only placentals have this single-coding-exon gene between COLEC12 and CLUL1. The gene is absent in other animals despite the gene synteny being very stable.

Christina: /* cetn2 */

2023-01-25T19:13:14Z

cetn2

← Older revision		Revision as of 19:13, 25 January 2023
Line 1:		Line 1:
	=~~cetn1~~=		=cetn2=
	This is the community wiki page for the gene ''~~cetn1~~'' please feel free to add any information that is relevant to this gene that is not already captured elsewhere in Xenbase		This is the community wiki page for the gene ''cetn2'' please feel free to add any information that is relevant to this gene that is not already captured elsewhere in Xenbase.

			=nomenclature changes=
			24JAN2023

			Nomenclature changed following analayis by David Webb as NCBI RefSeq.

			Basic issue: CETN1 is only in placental mammals and CETN4 is a pseudogene in humans.

			XB-GENEPAGE-967616 (Xtr GeneID: 549903) was renamed, changes from "CETN1" to "CETN2" - see details below.

			Details of the CETN1, CETN2, and CETN4 analaysis and orthology.

			The CETN1 gene of human (GeneID: 1068, HGNC: 1866) and all placental mammals likely arose as a retrotransposition event because only placentals have this single-coding-exon gene between COLEC12 and CLUL1. The gene is absent in other animals despite the gene synteny being very stable.

			Thus, chicken and Xenopus should not have genes named "CETN1". The "CETN1" genes of chicken (GeneID: 422303, CGNC:51692) and X. tropicalis (GeneID: 549903, XB-GENE-967617) are actually the orthologs of human CETN2 (GeneID:1069, HGNC: 1867) based on highly conserved synteny of CETN2 always being adjacent to ZNF185 and NSDHL throughout gnathostomes.

			Furthermore, chicken and other archosaurs have tandemly duplicated "CETN1" (ie CETN2) and thus chicken "CETN1L" (GeneID:422304, CGNC: 66428) should actually be named CETN2L. I've confirmed with a NJ tree of nt alignments that "CETN1L" (GeneID:422304) is a duplication of the chicken CETN2 gene.

			In addition, chicken GeneID: 422668 is misnamed "CETN2" (CGNC:66439) but is actually the ortholog of CETN4 (eg, mouse GeneID:207175) based on highly conserved synteny of this gene between BBS12 and ADAD1 throughout gnathostomes. In human and higher-(non-prosimian) primates CETN4 is a pseudogene (human CETN4P GeneID: 729338, HGNC:35450).

			A NJ tree of RefSeq nt accessions (not shown) supports these conclusions.

			Gg

			ZNF185< NSDHL< "CETN1"> CETN1L> GATD3AL2< LOC>

			emu

			ZNF185< NSDHL< cetn2> cetnL> gatd3al2< LOC> acod1> GLOD5<

			gharial

			ZNF185< NSDHL< cetn2> cetnL> gatd3al2< LOC>

			Chelonia mydas

			ZNF185< NSDHL< cetn2> aire< LOC< SCLY> KLHL30>

			Chrysemys picta, Trachemys scripta

			ZNF185< NSDHL< cetn2> AIRE< LOC< SCLY> ESPNL> KLHL30>

			lizards

			ZNF185< NSDHL< cetn2> DACH2< CHM> POF1B>

			Hs

			ZNF185< NSDHL< CETN2> MAGEA6> CSAG3< MAGEA2> MAGEA12< CSAG1>

			Bufo

			ZNF185< NSDHL< CETN2> OR> OR> P2RY10< LPAR4<

			Xtr

			ZNF185< NSDHL< "CETN1"> P2RY10< LPAR4<

			Coelacanth

			ZNF185< NSDHL< CETN2>//

			Protopterus lungfish

			OGT<…LOC< NSDHL< CETN2> PRPS1> HDAC8>

			Osteichthyes

			ZNF185< NSDHL< CETN2> GCNA< OGT<

			Thorny skate

			slain-like< NSDHL< cetn2> ENOX2< LOC>


			Gg

			SPATA5< NUDT6> FGF2< BBS12< "CETN2"> IL21> IL2> adad1< KIAA1109<

			emu, Calypte anna

			SPATA5< NUDT6> FGF2< BBS12< cetn4> IL21> ADAD1< kiaa1109<

			Crocidilians, turtles, lizards

			SPATA5< NUDT6> FGF2< BBS12< cetn4> ADAD1< KIAA1109<

			Human, apes, NWmonkeys, OWmonkeys

			SPATA5< NUDT6> FGF2< BBS12< CETN4p> IL21> IL2> ADAD1< KIAA1109<

			Non-anthropoid-primate placental mammals, tree shrew, lemurs,

			SPATA5< NUDT6> FGF2< BBS12< CETN4> IL21> IL2> ADAD1< KIAA1109<

			Ampibia

			SPATA5< NUDT6> FGF2< BBS12< CETN4> IL21> IL2> ADAD1< KIAA1109<

			Coelacanth

			BBS12< CETN4>

			Protopterus lungfish

			SPATA5< NUDT6> FGF2< BBS12< CETN4> FAT4> LOC<

			Osteichthyes, chondrichthyes

			SPATA5< NUDT6> FGF2< BBS12< CETN4> ADAD1< KIAA1109<


			Placental mammals

			USP14> THOC1< COLEC12< CETN1> CLUL1> TYMS> ENOSF1< YES1<

			Non-placental sarcopterygians

			USP14> THOC1< COLEC12< /// CLUL1> TYMS> ENOSF1< YES1<

			Non-sarcopterygian gnathostomes

			COLEC12< /// CLUL1> TYMS> ENOSF1< YES1<

imported>Xenbase gene generator at 12:00, 10 February 2010

2010-02-10T12:00:00Z

New page

=cetn1=
This is the community wiki page for the gene ''cetn1'' please feel free to add any information that is relevant to this gene that is not already captured elsewhere in Xenbase

XB-FEAT-967616 - Revision history

Christina: /* cetn2 */

Christina: /* nomenclature changes */

Christina: /* cetn2 */

imported>Xenbase gene generator at 12:00, 10 February 2010