XLOC_021867 (hoxc4a)


Basic Information

Item Value
gene id XLOC_021867
gene name hoxc4a
gene type coding
species zebrafish (Danio rerio)
category of species model fish

Chromosome Information

Item Value
chromosome id NC_007134.7
NCBI id CM002907.2
chromosome length 46223584
location 36130883 ~ 36132563 (+)
genome version GRCz11_2017_zebrafish_Genome

Sequence

>TCONS_00043340
AAAATTGAAGGTATATTTGCGAAAGCTGTGGTTCCTTATCCGGGAACTACATCGCCCCATGCCATTGGGCCATCGAATCACGTGGTAAAAGTAACTTTACAGGGTTGCTCGCTAGTAGGAGGGCTTTATGGAGCAGAAAAACGACAAAGCTAGAAAAATTATTTTCCACTCCAGAAATTAATGATCATGAGCTCGTATTTGATGGACTCTAACTACATCGATCCGAAATTTCCTCCTTGCGAGGAATATTCGCAAAATAGCTACATTCCCGAACATAGCCCAGAATATTACAGCCGTGCAAGGGACAGTGGCTACCAGCATCACCACCAGGAGTTATACCCTCCGCGGGCAAGCTACCAGGAGCGTCAGTATAACTGTGCAAGCATCCCTGAGCCTGATACTCAAAGAGGACATGGACTGCCTCACGCGGGGCACCTGCTTGGAAAAGGGCAATCAGCCTCATGTGAGCCCCCACCGTTACCCCTGTCTCCTGCCACCCCTTCGGCTGCATCTTCCGCCTGCAATCAAGCCACCCCGGAGCATCCCAACAGCTCAGCCTCTGCCAAACAACCCGTAGTGTACCCATGGATGAAGAAAATTCACGTCAGCACCGTCAACTCTAGTTACAATGGAGCGGAACCCAAGCGGTCTAGAACTGCTTACACTCGCCAGCAAGTCTTAGAATTGGAGAAGGAATTCCACTATAATCGCTACTTAACACGGCGAAGACGTATCGAGATTGCTCATTCCTTGGTCCTCTCGGAGAGGCAAATCAAAATTTGGTTTCAGAACCGAAGGATGAAGTGGAAAAAAGACCATAGGCTGCCAAACACCAAAGTCAGATCCTCGTCCTCCACGGGCATTTCCTCCGGGTCCAACACAAGCTCAGCGGCTGGCGTTGTGGCGGCAGCTTCCACCACTAACACCATGTCAGCCTCCGAGGACCTCTCCGGAACCGAGCGTGGCGAGGATATTACAAGGTTATAAGAGAACTATTTCGAGGAGAGAAAGCAAGATCAAATGActgattatttataaaatataatatattttgttttcgtAGGTATCTTGTGCGTAAAGGGGGTTCCTTTAAGTCCACAGTTATATAAAATGCATGTTATATAGCATGGATTATTGCGAATACCTATGGATTATTTTTTA

Function

symbol description
hoxc4a Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in anterior/posterior pattern specification; embryonic skeletal system morphogenesis; and regulation of transcription by RNA polymerase II. Predicted to act upstream of or within regulation of transcription, DNA-templated. Predicted to be active in nucleus. Is expressed in several structures, including margin; nervous system; presumptive paraxial mesoderm; swim bladder bud; and tail bud. Orthologous to human HOXC4 (homeobox C4).

GO:

id name namespace
GO:0006355 regulation of transcription, DNA-templated biological_process
GO:0001501 skeletal system development biological_process
GO:0007275 multicellular organism development biological_process
GO:0009952 anterior/posterior pattern specification biological_process
GO:0048704 embryonic skeletal system morphogenesis biological_process
GO:0005634 nucleus cellular_component
GO:0043565 sequence-specific DNA binding molecular_function
GO:0001228 DNA-binding transcription activator activity, RNA polymerase II-specific molecular_function
GO:0003677 DNA binding molecular_function
GO:0003700 DNA-binding transcription factor activity molecular_function
GO:0000977 RNA polymerase II transcription regulatory region sequence-specific DNA binding molecular_function
GO:0033613 activating transcription factor binding molecular_function

KEGG: NA

ZFIN:

id description
ZDB-GENE-990415-112 Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in anterior/posterior pattern specification; embryonic skeletal system morphogenesis; and regulation of transcription by RNA polymerase II. Predicted to act upstream of or within regulation of transcription, DNA-templated. Predicted to be active in nucleus. Is expressed in several structures, including margin; nervous system; presumptive paraxial mesoderm; swim bladder bud; and tail bud. Orthologous to human HOXC4 (homeobox C4).

Ensembl:

ensembl_id ENSDARG00000070338

RNA

RNA id representative length rna type GC content exon number start site end site
TCONS_00043340 True 1161 mRNA 0.47 2 36130883 36132563

Neighbor

gene id symbol gene type direction distance location
XLOC_021866 dre-mir-10b-2 coding upstream 791 36130001 ~ 36130092 (+)
XLOC_021865 hoxc5a coding upstream 10372 36118738 ~ 36120511 (+)
XLOC_021864 hoxc6a coding upstream 13976 36115541 ~ 36116907 (+)
XLOC_021863 hoxc8a coding upstream 27248 36101185 ~ 36103635 (+)
XLOC_021862 hoxc9a coding upstream 33395 36095260 ~ 36097488 (+)
XLOC_021868 BX005254.2 coding downstream 17867 36150430 ~ 36154411 (+)
XLOC_021869 hoxc1a coding downstream 45541 36178104 ~ 36190988 (+)
XLOC_021870 hnrnpa1b coding downstream 173976 36306539 ~ 36310418 (+)
XLOC_021871 NA coding downstream 184786 36317349 ~ 36317913 (+)
XLOC_021872 NA coding downstream 186615 36319178 ~ 36319588 (+)
XLOC_021861 mir196a-1 non-coding upstream 42687 36088091 ~ 36088196 (+)
XLOC_021854 BX465853.1 non-coding upstream 332604 35790808 ~ 35798279 (+)
XLOC_021852 NA non-coding upstream 400821 35729255 ~ 35730062 (+)
XLOC_021851 NA non-coding upstream 403361 35723438 ~ 35727522 (+)
XLOC_021874 NA non-coding downstream 232342 36364905 ~ 36365917 (+)
XLOC_021875 NA non-coding downstream 285556 36418119 ~ 36420278 (+)

Expression


Co-expression Network

Homologous

species gene id symbol gene type chromosome NCBI id location
grasscarp (Ctenopharyngodon idella) CI01000001_02274875_02276207 HOXC4, HOXC4A coding CI01000001 null 2274292 ~ 2276769 (-)
bowfin (Amia calva) AMCG00008811 hoxc4 coding CM030126.1 CM030126.1 12504256 ~ 12505029 (+)