XLOC_025297 (nr1d1)


Basic Information

Item Value
gene id XLOC_025297
gene name nr1d1
gene type coding
species zebrafish (Danio rerio)
category of species model fish

Chromosome Information

Item Value
chromosome id NC_007114.7
NCBI id CM002887.2
chromosome length 62628489
location 23488652 ~ 23496223 (+)
genome version GRCz11_2017_zebrafish_Genome

Sequence

>TCONS_00049943
AGAGCGATACAGATTGGGCGAGTGACAGGACAAGCGCACTGGCGTATGATTGGCTTTCACTGAATGAACCATATTTCACTGGCGTCTTTGCGCAGATCTTTTCTTCTTATAAAAGCAGATGCGCACGTATTTGGTGCGACTTTAGGAAATCAATTGCTTAGCAGTTATGGCTTTATCGTAAGAAACAGATCTTTATAGTACTTCTATAAAGAGTGCATCTTTGAGTGTTACATTGGAAATTCTGTCAAAACCCTGCATGACTTTACTGGGGCTCAACATGACGACCGCAGTAGACACGAACAACACAGGTGGGGTGATATCATACATTGGATCATGTGGAGGCTCTCCCAACCGTACCAGCCCTGTGTCCATGTACAGTGAGAATTCCAACAGCAGCATGCAGTCCCTTACACAACCCTGCTTCGGATCATCATTCCCACCATCCCCTAATGGATCTCATGATTCCTCACGGATGTAcaccagtagcagcagcagctcGAGTTCAGGATCAGGAGAGGACGGAAACTCATCATGCTCTGGTGGATCACCGAGAGGCCGTGATGATGGTGGAAGCGCACGCAATTCACCCAACAAATCAGTTGCCACCCTTACTAAGCTGAATGGAATGGTGTTGCTGTGCAAGGTGTGTGGCGATGTGGCTTCTGGATTTCACTATGGCGTCCATGCCTGTGAGGGATGCAAGGGTTTCTTTCGACGCAGCATCCAGCAGAACATCCAGTACAAAAAGTGCCTCAAGAATGAAACTTGTACCATTATGCGGATCAACCGGAATCGGTGCCAGCAGTGCCGTTTCAAAAAGTGTCTGTCAGTGGGCATGTCCCGAGATGCTGTTCGTTTTGGCCGCATCCCAAAACGTGAGAAGCAGCGGATGCTTGCTGAGATGCAGAACGCCATGAACAACATGGTGAACAACCAGCTGCAGAATGAATTCCAGCTGGCGAGCATCACCTCCAACACCCCCTGCCCTTCTTCTTCATCCCCATCCAACAcctcctcttcttcctcatcTCCATGTCCAGGCCTTACAGTGGGGCCACAGCCTCAGCCCCCAGCAGTGCCCGTAGCACAATCCCCATCCTCACCGGCTCCAACCTCCCCAACAGTCCAACTGGCTCAAAGTCCTCCACCTCTTACCTCTACCCCACCACCGTGCACTAGTCCAGGGGTAGACAAAACCATTGCCGCGATAACCAGAGCGCACCGTGAAACCTTCATCTATGCTCATGATAAACTAGGTTCACCCCTTCTGCCTCACAATAGCGAACTAGATAACCGAAGCAACAACCGCTGCATGGCGGGATATCATCTCAATGGCCATAACACTATCTACCACCATGACAACAACGTTGCTCATCACTGCAACAACTTCGAGGTGCAACAAGACAACAGCCTCCATTTTCAAGCCTCCCAAACACCTGAAAAACATCAGCAGCACAACAACAACAGCCAGCGACCTCCAAACAGTAACTTTTACAGCATTCACCATGGACAAGAGATGAACAGCGCATCCCAGGGTCAGAACTGTCCATGGAAAAAGCACAAGGAGATTCTGCTGGCTTGTCCAATGAACATGCATCCTTACTCAGACCCCAATAAAACACCCCAGGAAATTTGGGAAGACTTCTCTCTTAGCTTCACTCCAGCGGTACGAGAGGTGGTTGAGTTTGCCAAACACATCCCAGGGTTTAGCACGCTATCCCAGAATGACCAGGTCACTTTGCTGAAGGCTGGAACATTTGAGGTCCTCATGGTACGCTTCTCCTCTCTGTTCAACGTAAAAGAAAAGACCGTCACATTCATCTCAGGCGCCACCTATAGCCTGGAAGCCCTGAAAAGCATGGGCATGGGCGATCTGCTGGGAACCATGTTTGACTTCAGCGAGAAACTCAACTCATTAGAACTCTCAGCAGAAGAACTGGGTCTCTTTACTGCGGTCGTCCTGGTGTCTGCAGATCGTTCTGGCATTGAAAATGTAAATTCAGTCGAGATGCTTCAGGAGAGTCTAATCCGGGCTCTCCGAACCCTCGTCAGCAAGAGCGCCCCTACGGACGCCTCTCGATTCACCAAGCTGCTGCTCAAACTTCCTGACCTGCGCACTCTTAACAACATGCACTCAGAAAAGCTGCTGTCTTTCCGCATTGATGCCTGAGGTTGCAAACTGTGAAAACCCAGTGAAAGTGGGTCATCGCTGTTTGAAGATAAAAAGGGAACAGACATTAGAACCCTTTTAGGAAGATAAACTGATGCCTTTGGCAGTGATAAGCACTTGATGACACACTTGAAGAGACACTTTGGTGCATACTGGTCCGTCAGTGGCCTTTATGAGTAAAATAACCATATAAAAGGGTCTTTGAGCCACTCTTCATGTCAGTACTTGAAATGTGTGGCTAAGGCGAAGCTAATAATAAAGCAGGCAAAAACATTTGGACTGCATCTACATAGGGAACATGTGCAAAATGCCTTTTGTGAAGAGTCACAAACAGGCCAGGAGGATGTCCAAGCCACTTCCAGAGAGGGAACGACTGAAGCAAAATGTCTAAACTCTCCTCAAACTCAGTCTGGCCTGGGTTTCTACTGGACCCAGAGGCAAAGATTAAACAATCATTTCAACTATAATGCAGATGACAGACTATACGTGGTATATTCTCATCCTTGGGAATTGTAAATTGTGTAAATATGatatatacattaaaatgtataatatatatattttttttgtaaagttcaCATTCAATACAAAGTATATcgataaatatacatatatatatatatatatatatatacatatatatatatatatatatattatgagcACAGACATATAAGTAGAGTGTATGCATATAATAGAATAATACATGTATTTCAGGTGACTTTTACTTCATAAAGACATTTTATGAAACAAAAA

Function

symbol description
nr1d1 Enables DNA-binding transcription repressor activity, RNA polymerase II-specific and sequence-specific DNA binding activity. Acts upstream of or within autophagy; circadian regulation of gene expression; and regulation of locomotor rhythm. Located in chromatin. Is expressed in nervous system. Orthologous to human NR1D1 (nuclear receptor subfamily 1 group D member 1).

GO:

id name namespace
GO:0006914 autophagy biological_process
GO:0006355 regulation of transcription, DNA-templated biological_process
GO:0030154 cell differentiation biological_process
GO:0032922 circadian regulation of gene expression biological_process
GO:0000122 negative regulation of transcription by RNA polymerase II biological_process
GO:0010468 regulation of gene expression biological_process
GO:1904059 regulation of locomotor rhythm biological_process
GO:0045944 positive regulation of transcription by RNA polymerase II biological_process
GO:0009755 hormone-mediated signaling pathway biological_process
GO:0000785 chromatin cellular_component
GO:0005634 nucleus cellular_component
GO:0043565 sequence-specific DNA binding molecular_function
GO:0001227 DNA-binding transcription repressor activity, RNA polymerase II-specific 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:

id description
ko04710 Circadian rhythm
ko03000 Transcription factors
ko03310 Nuclear receptors

ZFIN:

id description
ZDB-GENE-050105-1 Enables DNA-binding transcription repressor activity, RNA polymerase II-specific and sequence-specific DNA binding activity. Acts upstream of or within autophagy; circadian regulation of gene expression; and regulation of locomotor rhythm. Located in chromatin. Is expressed in nervous system. Orthologous to human NR1D1 (nuclear receptor subfamily 1 group D member 1).

Ensembl:

ensembl_id ENSDARG00000033160

RNA

RNA id representative length rna type GC content exon number start site end site
TCONS_00049943 True 2926 mRNA 0.46 8 23488652 23496223

Neighbor

gene id symbol gene type direction distance location
XLOC_025296 NA coding upstream 77131 23406471 ~ 23411521 (+)
XLOC_025295 ppp1r9ba coding upstream 140568 23247325 ~ 23348084 (+)
XLOC_025294 col1a1a coding upstream 249194 23221047 ~ 23239458 (+)
XLOC_025293 NA coding upstream 275323 23096442 ~ 23213329 (+)
XLOC_025292 gngt2a coding upstream 392511 23092762 ~ 23096141 (+)
XLOC_025298 NA coding downstream 21736 23517959 ~ 23524650 (+)
XLOC_025299 NA coding downstream 108255 23604478 ~ 23616801 (+)
XLOC_025300 hoxb13a coding downstream 158010 23654233 ~ 23655834 (+)
XLOC_025301 NA coding downstream 168938 23665161 ~ 23668197 (+)
XLOC_025302 hoxb10a coding downstream 173044 23669267 ~ 23671863 (+)
XLOC_025429 BX649540.1 misc downstream 6752516 30248739 ~ 30249036 (+)
XLOC_025286 BX322574.1 non-coding upstream 608205 22854673 ~ 22880447 (+)
XLOC_025285 NA non-coding upstream 640456 22846336 ~ 22848196 (+)
XLOC_025283 BX649557.1 non-coding upstream 919546 22568987 ~ 22569106 (+)
XLOC_025303 mir196b non-coding downstream 177154 23673377 ~ 23673455 (+)
XLOC_025311 dre-mir-10c non-coding downstream 224428 23720651 ~ 23720745 (+)

Expression


Co-expression Network

Homologous

species gene id symbol gene type chromosome NCBI id location
grasscarp (Ctenopharyngodon idella) CI01000034_01842093_01847705 NR1D1 coding CI01000034 null 1840937 ~ 1847705 (-)
bowfin (Amia calva) AMCG00016688 nr1d1,LOC102302421 coding CM030122.1 CM030122.1 27509645 ~ 27516973 (-)