XLOC_021860 (hoxc3a)


Basic Information

Item Value
gene id XLOC_021860
gene name hoxc3a
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 36087219 ~ 36149371 (+)
genome version GRCz11_2017_zebrafish_Genome

Sequence

>TCONS_00043330
GTGCTGGCCTCACTGACGCGCTCTGCAGTCTGCCTGGCTGTTTTGGAACCAGGAACCTTTCATTATGGAGTAATAAGACGCTACGATATGATGGACTGAACACGGAAGAATTAAAGAGCTACAGCCGCGGCGAATGAATGAGAGAATCCTATGAGCGACGTTAATCAGACCATGTGCAGAACGCTCAAGCTCATGAGGAAATTGTGAACGTGAGTGAAAGGACAACCTCATCGTTGCACTGGAAAATCACTCGAAATGGCAAAACAGTCGAAGAATGCGGATGAAAACGGAATCACCGTTTGGCTGCTTACATGCAGTTTACAACTCAAACACCGAGTGCGCAAGGCTATTGGAGGAGGCCACCACGTGACTACATTGTTTACTCTTGTTGGCAAACAATTAAAGACGCGAGAGAACAGTTCTACGTGGAAACGACATGCTGAAGAAAGTTCATCAGAAAATGATAAAGGCAACGTGTGGAACTTTCAAAACCTCTCGAATGTCCAACATCCCTATTCATTCTCTGATGATGGCAACCACTCTTTGGACCCTGCGAATGCATTGGAAAGAGAAAAGGCATGTGAGCTGTCAACTTCCTGCTTATCAACCATGAAGTACCCTTGGATGAGAGAGACACATGCACCCACGCACTTCAGCTCCATTAACGCCATGGAATCAGGTGATTCTAAATACAGCAATGGTGAAGCAGTTGTACGGAATAGCAGCAGTAAACGGGCTCGTGTGGCGTTCACCTCCTCTCAGCTGCTGGAGTTAGAGAAGGAGTTTCACTTCAGCGCTTACCTGTGCCGCAACCGGAGACTTGAAATGGCTGAGCTGCTGAAGCTCACCGACCGGCAGATTAAAATCTGGTTCCAAAACCGTCGCATGAAGTATAAGAAGGACCACAAGGAAAAGTCAACGGCAAAGTCCTCTTACACCTACCTGGGAACAGAAAACCAGCCATTAATAATTAGCAGAAGCACAACAGATTCTCCAGTGCCATTGAAATTCCAGAATAACTATGAAA
>TCONS_00043334
AGAACAAGACACAAGGCAAGCAACGTGGACGTGGGACAGCTTTAAGTTTATCTCATGAGGAAATTGTGAACGTGAGTGAAAGGACAACCTCATCGTTGCACTGGAAAATCACTCGAAATGGCAAAACAGTCGAAGAATGCGGATGAAAACGGAATCACCGTTTGGCTGCTTACATGCAGTTTACAACTCAAACACCGAGTGCGCAAGGCTATTGGAGGAGGCCACCACGTGACTACATTGTTTACTCTTGTTGGCAAACAATTAAAGACGCGAGAGAACAGTTCTACGTGGAAACGACATGCTGAAGAAAGTTCATCAGAAAATGATAAAGGCAACGTGTGGAACTTTCAAAACCTCTCGAATGTCCAACATCCCTATTCATTCTCTGATGATGGCAACCACTCTTTGGACCCTGCGAATGCATTGGAAAGAGAAAAGGCATGTGAGCTGTCAACTTCCTGCTTATCAACCATGAAGTACCCTTGGATGAGAGAGACACATGCACCCACGCACTTCAGCT
>TCONS_00043335
CTTGCGAGCTCGCGGTGGTGTTGAAATGATCTTAGCACCAGACATTTTCCCCGTTTTCTGTTCGCCCACTAGTTTAGGCGGATTTTAAAACGCTTTAAAACTCCATCTTGTCTCGTCTGCTTTATCGCTAGTAATGACTGACTGTCCTCAGACGTCGCCGCCTCCCCAGTCTCATTTCTACCTATCTGGTCCCCTAGAGGGAAAACAATATTGATAGCTGGAGCTCGAGGGGTTAGAGTGTGTAAATATGGTTATTTGTCCTCGAAAGACTACATTTTTCCAGAGCACAGGAGAGTGGGATCTAGATCCTAGTGCCGTTGCCTAGTAAGATATGCTGCTATCCGCCACCGAACGTGCGTCACACAGACAACAGCGACCGCTGCTCATGAGGAAATTGTGAACGTGAGTGAAAGGACAACCTCATCGTTGCACTGGAAAATCACTCGAAATGGCAAAACAGTCGAAGAATGCGGATGAAAACGGAATCACCGTTTGGCTGCTTACATGCAGTTTACAACTCAAACACCGAGTGCGCAAGGCTATTGGAGGAGGCCACCACGTGACTACATTGTTTACTCTTGTTGGCAAACAATTAAAGACGCGAGTAAGTGTATTTTTTGGCTTTCCTACACCTCGAATGAACAATTATATATTTCGGGTGATTAGGACGATTAGAAATGAACAATAACTCGTTTCACGAATATAATTTTAACAGTGAATACTTAAACAAAATATGT
>TCONS_00043338
tatatatatatatatatatatatatttacatatatatttacattacgTTTATGTGgcgttcatagtgtatttaaaatgCTGACGAATATTTATAAAACCCACATTTCTTAAAATTATGGATGCGACAATTACACACACATTAGTTTattctaaaaaattaaatacagttaGCTAGTCAATTTATACTACTGATCCAAAAGTGCTTTCATTTCAGAATCGTCTCACTCACCTATATCGAAGGTTCAATGTAAATTTCCATGCTTCTTTCAATTTCTACACTCGCAATCTTGACCGAAAGGGCCACATTGCGAGTTACTGTGGTTAGTATGTTGCTTTTTACACAAAGCCCTCTTTTTTAGCCCTCTTGCTACGTATTTTGAAGTTTAGAGGGTTATTTATGCCAATTGCCCAAAGCAGGACCAGTGAGTGGTGCAGGAAGAGCACGTGGGGTCATTAAAGTGGGTTTTATGGCCTGCAAGACCTGACAAACCCTCAATATATTTACATCATATATAATGTTAACTGTCCGTAATCGCAGCTGTTGGCTACTCTTATCTCTGAGAGAACGGCTTAGAGCCTGTTAGTGCGGGTTACTCGCGTCAGGGTCTGTAGAAGTTCGACTCTCCCAAATGGATCCCAGGCGGCTGCCCTCATGAGGAAATTGTGAACGTGAGTGAAAGGACAACCTCATCGTTGCACTGGAAAATCACTCGAAATGGCAAAACAGTCGAAGAATGCGGATGAAAACGGAATCACCGTTTGGCTGCTTACATGCAGTTTACAACTCAAACACCGAGTGCGCAAGGCTATTGGAGGAGGCCACCACGTGACTACATTGTTTACTCTTGTTGGCAAACAATTAAAGACGCGAGTAAGTGTATTTTTTGGCTTTCCTACACCTCGAATGAACAATTATATATTTCGGGTGATTAGGACGATTAGAAATGAACAATAACTCGTTTCACGAATATAATTTTAACAGTGAATACTTAAACAAAATATGTTGCAATAAATCTTATGTTTGTTATATGGGGCAACATTTCTCCCCCTGTGCTCTGCAGGAGAACAGTTCTACGTGGAAACGACATGCTGAAGAAAGTTCATCAGAAAATGATAAAGGCAACGTGTGGAACTTTCAAAACCTCTCGAATGTCCAACATCCCTATTCATTCTCTGATGATGGCAACCACTCTTTGGACCCTGCGAATGCATTGGAAAGAGAAAAGGCATGTGAGCTGTCAACTTCCTGCTTATCAACCATGAAGTACCCTTGGATGAGAGAGACACATGCACCCACGCACTTCAGCTCCATTAACGCCATGGAATCAGGTGATTCTAAATACAGCAATGGTGAAGCAGTTGTACGGAATAGCAGCAGTAAACGGGCTCGTGTGGCGTTCACCTCCTCTCAGCTGCTGGAGTTAGAGAAGGAGTTTCACTTCAGCGCTTACCTGTGCCGCAACCGGAGACTTGAAATGGCTGAGCTGCTGAAGCTCACCGACCGGCAGATTAAAATCTGGTTCCAAAACCGTCGCATGAAGTATAAGAAGGACCACAAGGAAAAGTCAACGGCAAAGTCCTCTTACACCTACCTGGGAACAGAAAACCAGCCATTAATAATTAGCAGAAGCACAACAGATTCTCCAGTGCCATTGAAATTCCAGAATAACTATGAAACACCATCAATGAACTGGTGA
>TCONS_00043341
GATCCTTTTACTTGTGTTGCAATTTCCTTAACATTaaagaaacacatttttacaAAGCACGATGATAGAGATAGACAATGTAGCCAATATGCTATTATTACTAAAGTATTTTATTCGCAATAAAACATCGCTAAAATGTACATCACTATTTACGTAAGATTAAAACCGGTTAAAATACGCAACTGAAGAACATTGGCAAGCGTAAGGAACTGTTGTTAGATCAGCAAAGTGTGAAATGAATAGTTATTTAACCATAAAGCTAAACAAGTCGATCATTTTTAAATACCTACCACAAGAGGACTGAAAAGTCAGTCAAAgatttaaacattgttttataaaacattatcacGGAAATTAAGTCAGTATTCTTCAATCCATTGAAGCAAAAACTAAGACGACGCGATCCCAGACATGTCTTTTCTCTGTCCAAaatgggtctctctctctctccctcccacCTCACGCTCTCTGAACTCGTGTCAGCACGATGACAGGGTAATGTATGCGCCCTGCTCATGGTTTTTCGTCTGTCCACAGGAAAATCACTCGAAATGGCAAAACAGTCGAAGAATGCGGATGAAAACGGAATCACCGTTTGGCTGCTTACATGCAGTTTACAACTCAAACACCGAGTGCGCAAGGCTATTGGAGGAGGCCACCACGTGACTACATTGTTTACTCTTGTTGGCAAACAATTAAAGACGCGAGTAAGTGTATTTTTTGGCTTTCCTACACCTCGAATGAACAATTATATATTTCGGGTGATTAGGACGATTAGAAATGAACAATAACTCGTTTCACGAATATAATTTTAACAGTGAATACTTAAACAAAATATGTTGCAATAAATCTTATGTTTGTTATATGGGGCAACATTTCTCCCCCTGTGCTCTGCAGGAGAACAGTTCTACGTGGAAACGACATGCTGAAGAAAGTTCATCAGAAAATGATAAAGGCAACGTGTGGAACTTTCAAAACCTCTCGAATGTCCAACATCCCTATTCATTCTCTGATGATGGCAACCACTCTTTGGACCCTGCGAATGCATTGGAAAGAGAAAAGGCATGTGAGCTGTCAACTTCCTGCTTATCAACCATGAAGTACCCTTGGATGAGAGAGACACATGCACCCACGCACTTCAGCTCCATTAACGCCATGGAATCAGGTGATTCTAAATACAGCAATGGTGAAGCAGTTGTACGGAATAGCAGCAGTAAACGGGCTCGTGTGGCGTTCACCTCCTCTCAGCTGCTGGAGTTAGAGAAGGAGTTTCACTTCAGCGCTTACCTGTGCCGCAACCGGAGACTTGAAATGGCTGAGCTGCTGAAGCTCACCGACCGGCAGATTAAAATCTGGTTCCAAAACCGTCGCATGAAGTATAAGAAGGACCACAAGGAAAAGTCAACGGCAAAGTCCTCTTACACCTACCTGGGAACAGAAAACCAGCCATTAATAATTAGCAGAAGCACAACAGATTCTCCAGTGCCATTGAAATTCCAGAATAACTATGAAACACCATCAATGAACTGGTGAAATTACAGAAAAACTGAAAACTGGTGACTTTTGCTTTTAGAACTTATATAATGATAGTAATCTGCATCAACCATAAagactgaaaatgaatgaatgaatgaatgaatgaatgtgtgaatgaatgaaatttctaCAAAACATGTACATGATCTGTCACTGTTCAGCTATTTCTCCATTTGTAACTCTCTCTGACatgatttatatttaaaaacattgatgaTTAATTGCCTCTGGATGATGATTTATGTGCAAAGTTAACTTGGAAGAGTTCAATAGGCAAGCTCGCTCTGAACCAGATTACATGATATCAGCTAGTACATTTCAGAGTTAGTCTCTATTGTGCATAAACTGCTGTAGTAATATCTTTGCAAAGCACCAAGATTTATTGCAACCCTACTTGTGCAAGTTTATCTCTTGGGCAcagaaaatacaattttaaaagggCATTCAAGACTTTGAATGGTCATTAACATCCTCTCAACTTTTTAAGTGcacaacatattttttattactctCAAAATGATATGCTACTTTTCCCAAGGCATGAGCTAAAATGTACAACTTGCAGCGTTGTTCATTATGATGGTCACAATTGTTCCATGTTAAAGCCTATTGACCTGCTCTACTATTAACAATGAATTTGAATGACTTTTTTTCTGCTTTACACTGAAAGTAGGTGCGTTTAAGTCTGAATTTACAGCATATCTACtgacaaaatgaatgaaagagcAAAGCAGGATTTTCACAATGCTATATCAATGCATTTATAGTGTAATTACTTTACCCATTCATGTACACAAAAGTGTCAACATGGCAGCTGCAATGTAAAATATGTGCATATTTGTAATTTATACCATTTCAATTATAACCTGTCCATATTTgacaaaaaaacatgcattttgaaaataataagtggttgttttttaaactgatttattcCCTCTGGATAGTCAATAAATAATCATTGTAATTCATGTAACTGAcaataatgttgttttgtttagttaAAACAGGTAATGGTGAGtctaaatttagcttaaaggtgctTCTGTGAATCTTACTTGATACTTTTTGAATTAGGCAATACTGTACTTTGCATTCTTAAAACATAACCTTACATATATGCCTTCCTCCGCCTCCGCCTACCAACCTCGGAACATTAATCATTTAGAcaaggctctctctctctctctctctctctctctcagcttcACAAGTGCTCAACCCGCTGGGCCAAATGACAGGCTGTGCGCTTCTCTTCCAACACACTTCTCTCCAATACGGGAGCTGAAATACATCTAGA

Function

symbol description
hoxc3a 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.

GO:

id name namespace
GO:0006355 regulation of transcription, DNA-templated biological_process
GO:0007275 multicellular organism development biological_process
GO:0009952 anterior/posterior pattern specification biological_process
GO:0045944 positive regulation of transcription by RNA polymerase II biological_process
GO:0048704 embryonic skeletal system morphogenesis biological_process
GO:0005634 nucleus cellular_component
GO:0043565 sequence-specific DNA binding molecular_function
GO:0003677 DNA binding 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

KEGG: NA

ZFIN:

id description
ZDB-GENE-980526-532 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.

Ensembl:

ensembl_id ENSDARG00000070339

RNA

RNA id representative length rna type GC content exon number start site end site
TCONS_00043330 False 1027 mRNA 0.46 5 36087219 36148048
TCONS_00043334 False 520 mRNA 0.45 4 36106790 36145630
TCONS_00043335 False 737 lncRNA 0.44 3 36109453 36145326
TCONS_00043338 False 1697 mRNA 0.41 4 36122058 36148068
TCONS_00043341 True 2836 mRNA 0.38 2 36144487 36149371

Neighbor

gene id symbol gene type direction distance location
XLOC_021856 hoxc10a coding upstream 324 35969228 ~ 36086895 (+)
XLOC_021859 hoxc11a coding upstream 9087 36074798 ~ 36078132 (+)
XLOC_021858 hoxc12a coding upstream 22037 36063599 ~ 36065182 (+)
XLOC_021857 hoxc13a coding upstream 31333 36052944 ~ 36055886 (+)
XLOC_021855 rarga coding upstream 123484 35847200 ~ 35963735 (+)
XLOC_021868 BX005254.2 coding downstream 1059 36150430 ~ 36154411 (+)
XLOC_021869 hoxc1a coding downstream 28733 36178104 ~ 36190988 (+)
XLOC_021870 hnrnpa1b coding downstream 157168 36306539 ~ 36310418 (+)
XLOC_021871 NA coding downstream 167978 36317349 ~ 36317913 (+)
XLOC_021872 NA coding downstream 169807 36319178 ~ 36319588 (+)
XLOC_021854 BX465853.1 non-coding upstream 288940 35790808 ~ 35798279 (+)
XLOC_021852 NA non-coding upstream 357157 35729255 ~ 35730062 (+)
XLOC_021851 NA non-coding upstream 359697 35723438 ~ 35727522 (+)
XLOC_021848 NA non-coding upstream 384498 35694272 ~ 35702721 (+)
XLOC_021845 NA non-coding upstream 526707 35557190 ~ 35560512 (+)
XLOC_021874 NA non-coding downstream 215534 36364905 ~ 36365917 (+)
XLOC_021875 NA non-coding downstream 268748 36418119 ~ 36420278 (+)

Expression


Co-expression Network