XB-FEAT-485690: Difference between revisions

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=nomenclature history=
=nomenclature history=
23FEB2023
This gene is the true ortholog of the human SMAD4,  being flanked by ELAC1> '''SMAD4'''> MEX3C< in nearly all vertebrates, and was previously referred to as ''smad4.1'' following the description of a 2nd "smad4" gene. However, after review by Ref Seq curator David Webb, the name of this gene has reverted to SMAD4, removing the 'gene 1' suffix, as the 2nd ''Xenopus'' ''smad4'' gene (''smad4.2'') has been renamed ''smad10''.
=orthology=
The true SMAD4 orthologs are:
Gg GeneID: 121108220 (CGNC:88096)
Xtr GeneID: 100038088 (XB-GENE-485691)
Dr a GeneID: 559111 (ZDB-GENE-990603-8)
Dr b GeneID: 794669 (ZDB-GENE-141211-39)
Hs GeneID: 4089 (HGNC:6770)
= synteny of SMAD4 across vertebrate groups=
SMAD4
Human GeneID: 4089 NP_001393970.1
SKA1> MAPK4> MRO< ME2> ELAC1> '''SMAD4'''> MEX3C<...DCC>
Xtropicalis GeneID: 100038088 XB-GENE-485691 XP_002934485.1 [Xla GeneIDs: 780764 & 108707339]
MAPK4< SKA1< ME2> ELAC1> '''SMAD4>''' LIPG> LOC< ACAA2<
Chicken GeneID: 121108220 XP_040511206.1 CGNC:88096


As this is 1 of 2 genes described in ''Xenopus'',  and is the true ortholog of the human SMAD4, a general rule of adding '''.1''' to the gene symbol ( reflecting ''gene 1'' in the gene name) has been relaxed and ''smad4.1'' is listed as a synonym. This will maintain standard way to reference this gene in publications. This 'relaxing' of the nomenclature rules/ guideline will be run by the XGNC and the HGNC for approval.
myo5*< SKA1> me2> '''SMAD>''' MBD2< LOC> cupin1< tcf4<


23FEB2023
C.mydas GeneID: 102945563 XP_007063905.1
After review by Ref Seq curator David Webb, the name of this gene has reverted to SMAD4, removing the 'gene 1' suffix, as the 2nd ''smad4'' gene (''smad4.2'') has been renamed ''smad10''.
 
SKA1> MAPK4> ME2> ELAC1> '''SMAD4>''' MEX3C<...DCC>
 
lungfish GeneID: 122810552 XP_043938072.1
 
eef2> PIAS2> ME2> ELAC1> '''SMAD4>''' MEX3C< ...DCC>
 
reedfish XP_028658409.1 GeneID: 114652266
 
tspan36> ska1> mapk4> me2> elac1> '''SMAD4>''' mex3c< ...dcc>
 
zebrafish GeneID: 559111 ZDB-GENE-990603-8 NP_001116172
 
ARVCFA> LOC> NPFFR1L3> LOC> BMP10L> '''SMAD4A>''' RFX3< GLIS3< UNC5C>
 
zebrafish GeneID: 794669 (gb:cr929477) ZDB-GENE-141211-39 XP_009299441.1
 
OSTF1< AREG> ME2> ELAC1> '''SMAD4B>''' MEX3C< STPG2>
 
flounder MN868430 QOJ43526.1 = XP_019937644.1 GeneID: 109626289 
 
NUP155> avpr1a< zdhhc8> arvcf> bmp10L> '''SMAD4a'''> RFX3< glis3< unc5c>
 
flounder MN868431 QOJ43527.1=XP_019962761.1 GeneID: 109642417
 
// tle1> '''SMAD4B>''' mex3c< //
 
skate GeneID: 116980870 XP_032889379.1
 
MYO5B< CFAP53< SKA1> MAPK4> ME2> ELAC1> '''SMAD4>''' MEX3C< DCC>

Latest revision as of 07:28, 23 May 2023

smad4

This is the community wiki page for the gene smad4 please feel free to add any information that is relevant to this gene that is not already captured elsewhere in Xenbase

nomenclature history

23FEB2023 This gene is the true ortholog of the human SMAD4, being flanked by ELAC1> SMAD4> MEX3C< in nearly all vertebrates, and was previously referred to as smad4.1 following the description of a 2nd "smad4" gene. However, after review by Ref Seq curator David Webb, the name of this gene has reverted to SMAD4, removing the 'gene 1' suffix, as the 2nd Xenopus smad4 gene (smad4.2) has been renamed smad10.


orthology

The true SMAD4 orthologs are:

Gg GeneID: 121108220 (CGNC:88096)

Xtr GeneID: 100038088 (XB-GENE-485691)

Dr a GeneID: 559111 (ZDB-GENE-990603-8)

Dr b GeneID: 794669 (ZDB-GENE-141211-39)

Hs GeneID: 4089 (HGNC:6770)

synteny of SMAD4 across vertebrate groups

SMAD4 Human GeneID: 4089 NP_001393970.1

SKA1> MAPK4> MRO< ME2> ELAC1> SMAD4> MEX3C<...DCC>

Xtropicalis GeneID: 100038088 XB-GENE-485691 XP_002934485.1 [Xla GeneIDs: 780764 & 108707339]

MAPK4< SKA1< ME2> ELAC1> SMAD4> LIPG> LOC< ACAA2<

Chicken GeneID: 121108220 XP_040511206.1 CGNC:88096

myo5*< SKA1> me2> SMAD> MBD2< LOC> cupin1< tcf4<

C.mydas GeneID: 102945563 XP_007063905.1

SKA1> MAPK4> ME2> ELAC1> SMAD4> MEX3C<...DCC>

lungfish GeneID: 122810552 XP_043938072.1

eef2> PIAS2> ME2> ELAC1> SMAD4> MEX3C< ...DCC>

reedfish XP_028658409.1 GeneID: 114652266

tspan36> ska1> mapk4> me2> elac1> SMAD4> mex3c< ...dcc>

zebrafish GeneID: 559111 ZDB-GENE-990603-8 NP_001116172

ARVCFA> LOC> NPFFR1L3> LOC> BMP10L> SMAD4A> RFX3< GLIS3< UNC5C>

zebrafish GeneID: 794669 (gb:cr929477) ZDB-GENE-141211-39 XP_009299441.1

OSTF1< AREG> ME2> ELAC1> SMAD4B> MEX3C< STPG2>

flounder MN868430 QOJ43526.1 = XP_019937644.1 GeneID: 109626289

NUP155> avpr1a< zdhhc8> arvcf> bmp10L> SMAD4a> RFX3< glis3< unc5c>

flounder MN868431 QOJ43527.1=XP_019962761.1 GeneID: 109642417

// tle1> SMAD4B> mex3c< //

skate GeneID: 116980870 XP_032889379.1

MYO5B< CFAP53< SKA1> MAPK4> ME2> ELAC1> SMAD4> MEX3C< DCC>

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