XLOC_004562 (raraa)


Basic Information

Item Value
gene id XLOC_004562
gene name raraa
gene type coding
species zebrafish (Danio rerio)
category of species model fish

Chromosome Information

Item Value
chromosome id NC_007123.7
NCBI id CM002896.2
chromosome length 49182954
location 10952794 ~ 11157237 (+)
genome version GRCz11_2017_zebrafish_Genome

Sequence

>TCONS_00009068
AGAAAGAAATGCAACTTCAAAAGACTTTTTCATCGCAAGACAACCACAATAagGAATATTAAAGGAAAAACCAAATGGAGGACATCATGTCAGAACGCAAATCCCCGCCGTTGGATTCACTAAACACAATCAAATCTTTTCGGAAGTTAACCTGTGTGAAATGGAAATAAAACCCAACAGAAAACCCATGAACAGCAAAGAAGAGCAACTCCTCCATTCATCGGTCTAGACTCCCCCATTGTTTCTCTATCTACCGGCATCACATTAAATAAGCATCACCTAGTCTTTTCTCTGGGCGGCCTTATGGATGAATAACCCTTGCATATCACCCACGTCGAGTGTCGTTTTGGATTCTTCTGTTTGACGGTGGGCGAACTGTAGAGGTGGCCATGTCTGGTAAGGGCAACCCCAGCCCACACCTCAATGGCTTCCCAATGGCCCACTTTTCCTATTTCTTCCCGCACATGCTGGGGGGGCTTTCTCCACCTTCACTTCCCACTCTGCCCCTCAGTGGATACAGCACACCTTCGCCAGCCACTATTGAGACCCAGAGTACGAGTTCAGAAGAGATCGTCCCGAGCCCACCCTCTCCACCCCCTCCTCCTCGCATCTACAAGCCCTGCTTTGTGTGTCAGGAC
>TCONS_00009069
GAAGTTAACCTGTGTGAAATGGAAATAAAACCCAACAGAAAACCCATGAACAGCAAAGAAGAGCAACTCCTCCATTCATCGGTCTAGACTCCCCCATTGTTTCTCTATCTACCGGCATCACATTAAATAAGCATCACCTAGTCTTTTCTCTGGGCGGCCTTATGGATGAATAACCCTTGCATATCACCCACGTCGAGTGTCGTTTTGGATTCTTCTGTTTGACGGTGGGCGAACTGTAGAGGTGGCCATGTCTGGTAAGGGCAACCCCAGCCCACACCTCAATGGCTTCCCAATGGCCCACTTTTCCTATTTCTTCCCGCACATGCTGGGGGGGCTTTCTCCACCTTCACTTCCCACTCTGCCCCTCAGTGGATACAGCACACCTTCGCCAGCCACTATTGAGACCCAGAGTACGAGTTCAGAAGAGATCGTCCCGAGCCCACCCTCTCCACCCCCTCCTCCTCGCATCTACAAGCCCTGCTTTGTGTGTCAGGACAAATCTTCAGGGTACCACTATGGCGTCAGTGCCTGTGAGGGCTGCAAGGGTTTCTTCAGGCGAAGCATTCAGAAGAATATGGTGTACACGTGCCACCGAGAGAAGAACTGCATCATCAACAAAGTCACCCGCAACCGCTGTCAATACTGCCGGCTGCAGAAGTGCCTGGAAGTGGGGATGTCCAAAGAATCGGTGAGGAATGACAGaaataagaagaagaaagaagagaaaaagCCCGAATGCACAGAGAACTACACGCTGAGCCCAGACACAGAGCAGATGATCGACAGAGTTAGAAAAGCCCACCAAGAGACCTTCCCCTCGCTCTGTCAGCTCGGCAAATACACCACGAGTAATAGCTCGGAGCGGCGTGTGGCCCTGGATGTGGATTTATGGGATAAGTTTAGCGAACTCTCCACAAAGTGTATCATAAAGACAGTGGAGTTTGCTAAGCAGCTGCCAGGGTTCACCACCCTTACCATCGCAGACCAGATCACCCTGCTGAAGGCCGCCTGCCTCGACATACTGaTTCTGAGGATCTGCACCCGCTACACGCCCGAGCAGGACACCATGACGTTCTCTGATGGTTTAACACTCAACCGAACACAGATGCACAACGCAGGCTTCGGTCCGCTAACAGACCTGGTGTTCGCTTTCGCTAATCAGCTACTACCGCTAGAGATGGATGACGCTGAGACGGGACTGCTCAGTGCTATATGTCTGCTGTGTGGagATCGGCAGGACCTGGAACAGGCTGATAAGGTGGATGTACTGCAGGAACCCCTTCTGGAAGCACTGAAGATCTACGTGAGGAACAGAAGGCCACACAAACCACACATGTTCCCTAAGATGCTGATGAAGATTACTGATCTGAGGAGCATCAGTGCAAAGGGAGCGGAGCGTGTGATCACCCTGAAGATGGAGATTCCGGGCTCCATGCCTCCTCTAATCCAGGAGATGTTGGAGAACTCTGAGGGTTTGGAGAGCTCCTCAGGCGCACAGGGCTCACGGGCCTCCGCCACTACTCCGGGCAGTTGTAGCCCCTCCCTCTCTCCCAACTCCGCCCAGAGCAGCCCGCCCACACAGTCACCGTGA
>TCONS_00009070
CACACTCTCAGCAGCTCCGTGAGCCTGAACACACGAGTTCCGCGCGGATTaacaacacaagcacacacaagcTGATTAAACCCGCGTCTGTGCGCTGTTTCCAACCGGGAGGACACGAGACATTTAAAAGGAACCTGTTTAAATATCGCTGCACCATATCACGGAGGTATAAACGAGACTAAATAACCGGAGCTCCGCTAATATAATACTGGACCAAACTCCTCGTTCAACACTGGACATTTGATGGATTTATTGTTTATtctgtattgtttatttttataactgTTTTGCTAATGTGAGATTTCGAGAATACAAAACACAATAAGCTATTGTCTAAAATATCTACTTTCTAGACATTACACTTTTGAAACAAGGACATTGTTGATCTTTTatgacaatataatttttttattattattgaatttttttgcaaaaagtaTTTCAGAGGACATTGATCGCACCTATCCCCGATCATGCACTCGCGCTTCAGCTGTAGTTTTACTCGCTTCTGTAGTTCCTGATCTCCGCTGGGAATAACAGGGATGTCTGGGATGGATCCATCGCTCTGTTAAATCTCTATGTGAATTCTACAGTCGTGGATCAGCCGTTGTCTTGAGGAATTGTGTCCGATCTGATCATGTATGAGAGTGTGGATGTGAACCCTTTCCTCATGATGGATTACTATAATCAGAGCAGAGGATGTCTGATCCCGGACAAGATGCCCCATCCCTTCAGCTCATCCATCAGACATCAGCACTGGAGCGGATCCAACCACTCTATTGAGACCCAGAGTACGAGTTCAGAAGAGATCGTCCCGAGCCCACCCTCTCCACCCCCTCCTCCTCGCATCTACAAGCCCTGCTTTGTGTGTCAGGACAAATCTTCAGGGTACCACTATGGCGTCAGTGCCTGTGAGGGCTGCAAGGGTTTCTTCAGGCGAAGCATTCAGAAGAATATGGTGTACACGTGCCACCGAGAGAAGAACTGCATCATCAACAAAGTCACCCGCAACCGCTGTCAATACTGCCGGCTGCAGAAGTGCCTGGAAGTGGGGATGTCCAAAGAATCGGTGAGGAATGACAGaaataagaagaagaaagaagagaaaaagCCCGAATGCACAGAGAACTACACGCTGAGCCCAGACACAGAGCAGATGATCGACAGAGTTAGAAAAGCCCACCAAGAGACCTTCCCCTCGCTCTGTCAGCTCGGCAAATACACCACGAGTAATAGCTCGGAGCGGCGTGTGGCCCTGGATGTGGATTTATGGGATAAGTTTAGCGAACTCTCCACAAAGTGTATCATAAAGACAGTGGAGTTTGCTAAGCAGCTGCCAGGGTTCACCACCCTTACCATCGCAGACCAGATCACCCTGCTGAAGGCCGCCTGCCTCGACATACTGaTTCTGAGGATCTGCACCCGCTACACGCCCGAGCAGGACACCATGACGTTCTCTGATGGTTTAACACTCAACCGAACACAGATGCACAACGCAGGCTTCGGTCCGCTAACAGACCTGGTGTTCGCTTTCGCTAATCAGCTACTACCGCTAGAGATGGATGACGCTGAGACGGGACTGCTCAGTGCTATATGTCTGCTGTGTGGagATCGGCAGGACCTGGAACAGGCTGATAAGGTGGATGTACTGCAGGAACCCCTTCTGGAAGCACTGAAGATCTACGTGAGGAACAGAAGGCCACACAAACCACACATGTTCCCTAAGATGCTGATGAAGATTACTGATCTGAGGAGCATCAGTGCAAAGGGAGCGGAGCGTGTGATCACCCTGAAGATGGAGATTCCGGGCTCCATGCCTCCTCTAATCCAGGAGATGTTGGAGAACTCTGAGGGTTTGGAGAGCTCCTCAGGCGCACAGGGCTCACGGGCCTCCGCCACTACTCCGGGCAGTTGTAGCCCCTCCCTCTCTCCCAACTCCGCCCAGAGCAGCCCGCCCACACAGTCACCGTGACAACCATCATCTAAACCATCATTAGCCACTTACGGACTACTGTGTGCTCTCCCGACACACTCGAAAAACACACTCTCAGTGCCGATACTCTGCCTGTGGGAGAATCAAAGCTGTGTTAccggaatttttattttttttcctcagatcAGACTGTGATTGTATTCCTCCTTAATTCCCAAGGGGGGACAAGGgtgaagaaagaaaagaaaaaagaaaaaaaaaacttaagaatgaatgaatggacaaattTGTAGAAGGACTTTTCTTCTGCTTCGATTCTTCTGGCCTGCAATGACCAGAGACTGATTTCCTACAAactaaaaacacataaatatatatagagaaaACCTGGAATGATTGTGATTGCGAATAGAATGAAACATGGACTTGATGTAAAAATGCATTTCCTCACTTTTTCTCTTAATGCCTGTGAAAGGACAAAGAGTGAATTGTTTTCTTTCAGACTGATTATGATGTTtttcatggagaaaaaaaaacattgaaaagatTATTAATTTTC

Function

symbol description
raraa Enables nuclear receptor activity. Involved in hindbrain morphogenesis and response to retinoic acid. Acts upstream of or within liver development. Predicted to be located in nucleus. Is expressed in several structures, including endoderm; gonad; mesoderm; nervous system; and neural keel. Human ortholog(s) of this gene implicated in acute promyelocytic leukemia; lung carcinoma (multiple); and syndromic microphthalmia 12. Orthologous to several human genes including RARA (retinoic acid receptor alpha).

GO:

id name namespace
GO:0006355 regulation of transcription, DNA-templated biological_process
GO:0021575 hindbrain morphogenesis biological_process
GO:0030154 cell differentiation biological_process
GO:0000122 negative regulation of transcription by RNA polymerase II biological_process
GO:0001889 liver 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:0032526 response to retinoic acid biological_process
GO:0009755 hormone-mediated signaling pathway 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-980526-284 Enables nuclear receptor activity. Involved in hindbrain morphogenesis and response to retinoic acid. Acts upstream of or within liver development. Predicted to be located in nucleus. Is expressed in several structures, including endoderm; gonad; mesoderm; nervous system; and neural keel. Human ortholog(s) of this gene implicated in acute promyelocytic leukemia; lung carcinoma (multiple); and syndromic microphthalmia 12. Orthologous to several human genes including RARA (retinoic acid receptor alpha).

Ensembl:

ensembl_id ENSDARG00000056783

RNA

RNA id representative length rna type GC content exon number start site end site
TCONS_00009068 False 638 mRNA 0.48 3 10952794 11124991
TCONS_00009069 False 1591 mRNA 0.53 8 11007286 11156717
TCONS_00009070 True 2492 mRNA 0.46 8 11080776 11157237

Neighbor

gene id symbol gene type direction distance location
XLOC_004561 top2a coding upstream 212558 10706772 ~ 10740236 (+)
XLOC_004560 csf3a coding upstream 315622 10631266 ~ 10637172 (+)
XLOC_004559 lrrc3ca coding upstream 343013 10599604 ~ 10609781 (+)
XLOC_004558 crym coding upstream 490291 10448226 ~ 10462503 (+)
XLOC_004557 snu13b coding upstream 505616 10443785 ~ 10447178 (+)
XLOC_004563 vps35l coding downstream 10633 11167870 ~ 11198776 (+)
XLOC_004564 si:rp71-19m20.1 coding downstream 195393 11352630 ~ 11371291 (+)
XLOC_004565 CR450852.1 coding downstream 486314 11643551 ~ 11643671 (+)
XLOC_004566 waplb coding downstream 492909 11650146 ~ 11763658 (+)
XLOC_004567 grid1b coding downstream 955147 12112384 ~ 12833736 (+)
XLOC_004556 CU459020.1 non-coding upstream 741746 10210932 ~ 10211048 (+)
XLOC_004550 NA non-coding upstream 1002305 9941133 ~ 9950489 (+)
XLOC_004546 NA non-coding upstream 1140308 9797037 ~ 9812486 (+)
XLOC_004542 NA non-coding upstream 1503063 9443721 ~ 9449731 (+)
XLOC_004536 NA non-coding upstream 1981762 8968317 ~ 8971032 (+)
XLOC_004568 NA non-coding downstream 1258019 12415256 ~ 12415835 (+)
XLOC_004569 BX548041.1 non-coding downstream 1456098 12613335 ~ 12613451 (+)
XLOC_004579 BX649204.1 non-coding downstream 2300000 13457237 ~ 13457356 (+)
XLOC_004581 CR354395.1 non-coding downstream 2500785 13658022 ~ 13658144 (+)

Expression


Co-expression Network

Homologous

species gene id symbol gene type chromosome NCBI id location
grasscarp (Ctenopharyngodon idella) CI01000161_02698024_02718143 RARA, RARAA, RARAB coding CI01000161 null 2697528 ~ 2718405 (-)