XB-FEAT-484571: Difference between revisions

From XenWiki
Jump to navigation Jump to search
 
(3 intermediate revisions by the same user not shown)
Line 2: Line 2:
This is the community wiki page for the gene ''carm1'' 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 ''carm1'' please feel free to add any information that is relevant to this gene that is not already captured elsewhere in Xenbase.


=geneome annoation notes=
=genome annotation notes=


31JAN2023
31JAN2023
Line 15: Line 15:


=synteny of ''Xenopus carm1 v carm1l''=
=synteny of ''Xenopus carm1 v carm1l''=
‘’Xenopus carm1’’
''Xenopus carm1''


Xtr '''''carm1''''' chr3: ''dnm2> … tmed1< … LOC10173343>… '''carm1'''>  ….ylpf2< … timm29> Loc100495666> smarca4>''  
Xtr '''''carm1''''' chr3: ''dnm2> … tmed1< … LOC10173343>… '''carm1'''>  ….ylpf2< … timm29> Loc100495666> smarca4>''  


  Compared with Xenopus ‘’carm1-like’’
  Compared with ''Xenopus carm1-like''


Xtr.'''''carm1l''''' chr1:  ''crygbl.1> … crygbl.2> … LOC100496840<(likely another crygb) … '''carm1l'''> …pum> … kcnv2< … vldlr<''  
Xtr.'''''carm1l''''' chr1:  ''crygbl.1> … crygbl.2> … LOC100496840<(likely another crygb) … '''carm1l'''> …pum> … kcnv2< … vldlr<''  
Line 25: Line 25:
Xla.S  scaffold58on v9.2:  ''vldir.S> … kcnv2.S> … pum3 …'''carm1l''' … Xetrov(unch) <….. upstream string of crygb’s''
Xla.S  scaffold58on v9.2:  ''vldir.S> … kcnv2.S> … pum3 …'''carm1l''' … Xetrov(unch) <….. upstream string of crygb’s''


  Looked in In v10 Xlaevis to see if we can get v10 model on XB-GENEPAGE-484571- no!
  Looked in v10 Xlaevis assembly to see if we could find a v10 model for XB-GENEPAGE-484571- but no!


Xla V10 chr1.L (no model):
Xla V10 chr1.L (no model):
Line 31: Line 31:
''pum3.L>  …LOC121401372(lncRNA)< … kcnv2.L< … vldir.L< … smarca2.L< … LOC#5489(pseudo) … LOC121394124(dmrt2.2)< … dmrt2.L>  …  dmrt3.L< …  dmrt 1.L …''
''pum3.L>  …LOC121401372(lncRNA)< … kcnv2.L< … vldir.L< … smarca2.L< … LOC#5489(pseudo) … LOC121394124(dmrt2.2)< … dmrt2.L>  …  dmrt3.L< …  dmrt 1.L …''


Xla.chr1S: no v 10 model:
Xla.chr1S: (no v 10 model):


''pum3.S>  …. LOC108704909(lncRNA)< … kcnv2.S< … vldir.S< … LOC432089(snf2l2) <… LOC108704897(UNCH ncRNA) … dmrt2.S<  dmrt3.S< …  dmrt 1.S<''  …
''pum3.S>  …. LOC108704909(lncRNA)< … kcnv2.S< … vldir.S< … LOC432089(snf2l2) <… LOC108704897(UNCH ncRNA) … dmrt2.S<  dmrt3.S< …  dmrt 1.S<''  …

Latest revision as of 09:24, 31 January 2023

carm1

This is the community wiki page for the gene carm1 please feel free to add any information that is relevant to this gene that is not already captured elsewhere in Xenbase.

genome annotation notes

31JAN2023

XB had 2 gene pages called ‘’carm1’’

XB-GENEPAGE-6072890 ( not much data) Xtr (Chr1) and Xla.L(chr3)

Change name to ‘’carm1l, coactivator associated arginine methyltransferase 1-like’’

XB-GENEPAGE-484571 ( with literature and images)  Xtr, Xla.S model on Chr3 = true carm1

Request MOVE of Xla.carm.L models from XB-GENEPAGE-6072890 to XB-GENEPAGE-484571

synteny of Xenopus carm1 v carm1l

Xenopus carm1

Xtr carm1 chr3: dnm2> … tmed1< … LOC10173343>… carm1> ….ylpf2< … timm29> Loc100495666> smarca4>

Compared with Xenopus carm1-like

Xtr.carm1l chr1: crygbl.1> … crygbl.2> … LOC100496840<(likely another crygb) … carm1l> …pum> … kcnv2< … vldlr<

Xla.S scaffold58on v9.2: vldir.S> … kcnv2.S> … pum3 …carm1l … Xetrov(unch) <….. upstream string of crygb’s

Looked in v10 Xlaevis assembly to see if we could find a v10 model for  XB-GENEPAGE-484571- but no!

Xla V10 chr1.L (no model):

pum3.L> …LOC121401372(lncRNA)< … kcnv2.L< … vldir.L< … smarca2.L< … LOC#5489(pseudo) … LOC121394124(dmrt2.2)< … dmrt2.L> … dmrt3.L< … dmrt 1.L …

Xla.chr1S: (no v 10 model):

pum3.S> …. LOC108704909(lncRNA)< … kcnv2.S< … vldir.S< … LOC432089(snf2l2) <… LOC108704897(UNCH ncRNA) … dmrt2.S< dmrt3.S< … dmrt 1.S<