XLOC_003134 (rargb)


Basic Information

Item Value
gene id XLOC_003134
gene name rargb
gene type coding
species zebrafish (Danio rerio)
category of species model fish

Chromosome Information

Item Value
chromosome id NC_007122.7
NCBI id CM002895.2
chromosome length 45484837
location 2089461 ~ 2096469 (+)
genome version GRCz11_2017_zebrafish_Genome

Sequence

>TCONS_00006194
gtttttgtgtgtttgatttgtgCAGCGGTGGAGACGCAGAGCACCAGTTCTGAAGAGATGATCCCCAGCTCTCCttctccacctcctcctccacGGGTCTACAAACCCTGCTTCGTGTGCCAGGACAAATCTTCTGGATACCATTATGGAGTCAGCTCTTGTGAGGGCTGCAAGGGTTTTTTCCGCCGCAGTATCCAGAAGAACATGGTGTACACCTGTCACAGAGACAAAAACTGCCAGATCAACAAAGTGACGCGCAACCGCTGCCAGTACTGCAGACTGCAGAAGTGCTTCGAGGTCGGAATGTCCAAAGAAGCGGTGCGGAACGACAGGAATAAGAAGAAGAAGGATGTAAAAGAGGAGGTGGTTCTGCCTGAAAGCTACGAGCTGAGCGGCGAACTGGAGGAACTGGTTAATAAAGTCAGCAAAGCACACAGAGAAACCTTCCCTTCGCTCTGTCAGCTGGGGAAATACACAACTAACTCTAGTGCAGACCACAGGGTTCAGCTGGATCTGGGACTGTGGGATAAATTCAGTGAGCTCTCCACAAAGTGCATTATAAAGATAGTGGAGTTCGCCAAACGTCTGCCAGGATTTACATCGCTCACTATCGCAGACCAGATCACCTTACTCAAATCTGCCTGCCTCGATATACTGATGTTGCGGATCTGCACTCGCTACACTCCTGAGCAGGACACCATGACGTTTTCAGACGGACTGACCCTCAATAGGACACAGATGCACAACGCCGGCTTCGGGCCGCTCACAGACCTGGTGTTTGCGTTCGCCGGGCAGCTCCTGCCTCTGGAGATGGATGACACAGAGACGGGGCTCCTCAGCGCCATCTGCCTCATCTGTGGAGACCGTATGGACCTGGAGGAGCCTCACCGTGTGGATCAGCTGCAGGAGCCGCTGCTGGAGGCGCTGAAGATCTACGCTCGCCGCCGCCGTCCCAACAAACCTCACATGTTCCCCCGAATGCTGATGAAAGTCACCGACCTGCGGGGCATCAGCACTAAAGgagCGGAGCGTGCCATCACCCTGAAGATGGAGATCCCGGGCCCAATGCCTCCTCTGATCAGAGAGATGCTGGAGAATCCGGAGATTTTTGAGGACAGCAGCGACTCTAATGACTCCGGTGCTGCCGCCGTCGTCCCGGCGCCGAACATCAAACGT

Function

symbol description
rargb Predicted to enable RNA polymerase II cis-regulatory region sequence-specific DNA binding activity and nuclear receptor activity. Acts upstream of or within determination of left/right symmetry; intrahepatic bile duct development; and negative regulation of BMP signaling pathway. Predicted to be located in nucleus. Is expressed in several structures, including blastoderm; head; neural crest; pectoral fin; and tail bud. Orthologous to human RARG (retinoic acid receptor gamma).

GO:

id name namespace
GO:0006355 regulation of transcription, DNA-templated biological_process
GO:0030154 cell differentiation biological_process
GO:0003140 determination of left/right asymmetry in lateral mesoderm biological_process
GO:0000122 negative regulation of transcription by RNA polymerase II biological_process
GO:0071907 determination of digestive tract left/right asymmetry biological_process
GO:0071910 determination of liver left/right asymmetry biological_process
GO:0030514 negative regulation of BMP signaling pathway biological_process
GO:0035622 intrahepatic bile duct development biological_process
GO:0045944 positive regulation of transcription by RNA polymerase II biological_process
GO:0048384 retinoic acid receptor signaling pathway biological_process
GO:0009755 hormone-mediated signaling pathway biological_process
GO:0035469 determination of pancreatic left/right asymmetry biological_process
GO:0061371 determination of heart left/right asymmetry biological_process
GO:0005634 nucleus cellular_component
GO:0043565 sequence-specific DNA binding molecular_function
GO:0046872 metal ion binding molecular_function
GO:0003677 DNA binding molecular_function
GO:0004879 nuclear receptor activity molecular_function
GO:0003700 DNA-binding transcription factor activity molecular_function
GO:0000978 RNA polymerase II cis-regulatory region sequence-specific DNA binding molecular_function
GO:0003707 steroid hormone receptor activity molecular_function
GO:0008270 zinc ion binding molecular_function

KEGG: NA

ZFIN:

id description
ZDB-GENE-070314-1 Predicted to enable RNA polymerase II cis-regulatory region sequence-specific DNA binding activity and nuclear receptor activity. Acts upstream of or within determination of left/right symmetry; intrahepatic bile duct development; and negative regulation of BMP signaling pathway. Predicted to be located in nucleus. Is expressed in several structures, including blastoderm; head; neural crest; pectoral fin; and tail bud. Orthologous to human RARG (retinoic acid receptor gamma).

Ensembl:

ensembl_id ENSDARG00000054003

RNA

RNA id representative length rna type GC content exon number start site end site
TCONS_00006194 True 1176 mRNA 0.54 7 2089461 2096469

Neighbor

gene id symbol gene type direction distance location
XLOC_003132 NA coding upstream 92051 1935684 ~ 1997410 (+)
XLOC_003133 NA coding upstream 136867 1951631 ~ 1952594 (+)
XLOC_003131 rbms2a coding upstream 168944 1867613 ~ 1920517 (+)
XLOC_003130 lrp1aa coding upstream 225173 1628538 ~ 1864288 (+)
XLOC_003129 si:dkey-40c23.2 coding upstream 471374 1584747 ~ 1618087 (+)
XLOC_003135 hoxc13b coding downstream 59961 2156430 ~ 2162821 (+)
XLOC_003136 hoxc12b coding downstream 75866 2172335 ~ 2175033 (+)
XLOC_003137 hoxc11b coding downstream 83603 2180072 ~ 2185174 (+)
XLOC_003138 mir196c coding downstream 94152 2190621 ~ 2190730 (+)
XLOC_003139 NA coding downstream 102061 2198530 ~ 2205798 (+)
XLOC_003250 BX324177.11 misc downstream 9249334 11345803 ~ 11346099 (+)
XLOC_003255 BX324177.14 misc downstream 9276417 11372886 ~ 11373182 (+)
XLOC_003257 BX324177.13 misc downstream 9289893 11386362 ~ 11386658 (+)
XLOC_003260 BX324177.2 misc downstream 9321564 11418033 ~ 11418323 (+)
XLOC_003262 BX324177.15 misc downstream 9332924 11429393 ~ 11429689 (+)
XLOC_003126 AL935272.1 non-coding upstream 543230 1546117 ~ 1546231 (+)
XLOC_003118 FQ311892.1 non-coding upstream 1358538 730807 ~ 730923 (+)
XLOC_003112 NA non-coding upstream 1545267 543348 ~ 544194 (+)
XLOC_003140 NA non-coding downstream 211740 2308209 ~ 2320355 (+)
XLOC_003149 FQ790208.1 non-coding downstream 518601 2615070 ~ 2616023 (+)
XLOC_003156 CT583672.1 non-coding downstream 731084 2827553 ~ 2828675 (+)

Expression


Co-expression Network

Homologous

species gene id symbol gene type chromosome NCBI id location
grasscarp (Ctenopharyngodon idella) CI01000057_01058821_01071240 RARGB, RARGA, RARG coding CI01000057 null 1057536 ~ 1071388 (+)