XLOC_006858 (nkx2.3)


Basic Information

Item Value
gene id XLOC_006858
gene name nkx2.3
gene type coding
species zebrafish (Danio rerio)
category of species model fish

Chromosome Information

Item Value
chromosome id NC_007124.7
NCBI id CM002897.2
chromosome length 52186027
location 40409215 ~ 40411917 (-)
genome version GRCz11_2017_zebrafish_Genome

Sequence

>TCONS_00013189
CGCCGATGAGTGGCGGTCCTCACCTCTCTTCATGCAAATCAAGCAGCCATGACAAAATGGGAGATTAATCGACACATTTAGCGCCTGATGATGCTTCCGAGCCCGGTCACATCAACGCCGTTTTCTGTGAAGGATATACTGAAACTGGAGCAGCAAACTCGCCAGCTTCAATCTCTGCACCCCGCGTCGCACCACGCGCAACTGCATCCGGAACTGCAGGATAGATTTCAGGCACCATCGTCGTGTTTTCTCGGAGGTGGAGACAGTCCCGGCTTCTCAGACAACGAGGAGAAGATGTCTTTTCTGAACTCTCTCTCCATGCAGGACAGTTTAGTGGAGAGCAGCCTTTCCCCGCCGATGTTCGTCCACCCGGCCCTGGGACACGTCGACACTAAACTTGAAGATGAACTTGAGGACCACGAAACGAAGAGCTGCGGTGCCATCCTCAGAACCCCGGAGTGTGAGGCTGAGGTGCACTCGGACACGGAGCGCGCGCAGCGGCAGAGGACGCGGCGGAAGCCGCGGGTTCTCTTCAGCCAGGCGCAGGTCTTCGAGCTCGAGCGGCGCTTCAAGCAGCAGCGATATTTATCGGCTCCTGAGAGAGAACATTTGGCGAGTACCCTAAAACTGACATCGACGCAGGTTAAAATTTGGTTCCAGAACCGCAGATACAAATGCAAGCGGCAGCGTCAAGACAAAACACTGGAAATGGCAGGACACCATCACCCACCACCGCCCAGGAGAGTAGCGGTGCCCGTCTTGGTGCGGGATGGAAAACCGTGTTTAACGGGATCACAGAGTTACAACACCACGTACGCGGTTAACCCAGGCCCGTACACATATAACGGGTATTCTTCTTATAACAACGCCGCTTACACAAACCCTTACAGCTGTACATACCCCAGTCTTCCTCCTCTACCTGCGAACACGTCCACTAATGCGCTGATGAGCATGAGTTTGAACAACCTCGGAACTTATTCCCAGCCGCAGACATCGCAAGGAACACCCGTGTCCGCGTGCCAAGGGACTCTGCAGGGTATCCGGGCATGGTAGTGCCAGTGCAACCCAGCCGCCTGTAAAAAAATGACAACTTAACAATATTAGCACACAGTTAGCCATGTTTTTAGGATCATGTATAGTCTATACCTTTTCAGTATAAACTTGAGAGTGAATTTCTTCTAGCAACAGTATACCATGATGGCTGAACGTGAATATTCATGGAAATTTGGACCAGCTATATATGGGCAACATATTCACCGAACATTTGACGGTCTAACTTTAGATGGTATCCATACTACTCATGAGACATTTGCTTCCTCATTCATTGCACTTATCGATGAGCAGTTATTATCTGAAATGTTACGAATATTGACAATGGTGTGTGTGACTTTGTGCAAACCtacattgcaaaaataaaaaaaaacgctaaacttta
>TCONS_00013190
ACCGTTTCACGCCGATGAGTGGCGGTCCTCACCTCTCTTCATGCAAATCAAGCAGCCATGACAAAATGGGAGATTAATCGACACATTTAGGTATGTTTACTTGAAATTGTTGCTTATCTAAACAATTGTTCAACAAGGCTTAGTGCTCGAAGCTGCCATTTGAAGCAGGGATAACATTGTAGATGTAATCCAACAGCGCCTGATGATGCTTCCGAGCCCGGTCACATCAACGCCGTTTTCTGTGAAGGATATACTGAAACTGGAGCAGCAAACTCGCCAGCTTCAATCTCTGCACCCCGCGTCGCACCACGCGCAACTGCATCCGGAACTGCAGGATAGATTTCAGGCACCATCGTCGTGTTTTCTCGGAGGTGGAGACAGTCCCGGCTTCTCAGACAACGAGGAGAAGATGTCTTTTCTGAACTCTCTCTCCATGCAGGACAGTTTAGTGGAGAGCAGCCTTTCCCCGCCGATGTTCGTCCACCCGGCCCTGGGACACGTCGACACTAAACTTGAAGATGAACTTGAGGACCACGAAACGAAGAGCTGCGGTGCCATCCTCAGAACCCCGGAGTGTGAGGCTGAGGTGCACTCGGACACGGAGCGCGCGCAGCGGCAGAGGACGCGGCGGAAGCCGCGGGTTCTCTTCAGCCAGGCGCAGGTCTTCGAGCTCGAGCGGCGCTTCAAGCAGCAGCGATATTTATCGGCTCCTGAGAGAGAACATTTGGCGAGTACCCTAAAACTGACATCGACGCAGGTTAAAATTTGGTTCCAGAACCGCAGATACAAATGCAAGCGGCAGCGTCAAGACAAA

Function

symbol description
nkx2.3 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 cell differentiation 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 cranial ganglion; endoderm; heart; pharyngeal arch; and pharynx. Orthologous to human NKX2-3 (NK2 homeobox 3).

GO:

id name namespace
GO:0006355 regulation of transcription, DNA-templated biological_process
GO:0006357 regulation of transcription by RNA polymerase II biological_process
GO:0030154 cell differentiation biological_process
GO:0005634 nucleus cellular_component
GO:0043565 sequence-specific DNA binding molecular_function
GO:0003677 DNA binding molecular_function
GO:0000978 RNA polymerase II cis-regulatory region sequence-specific DNA binding molecular_function
GO:0000981 DNA-binding transcription factor activity, RNA polymerase II-specific molecular_function

KEGG: NA

ZFIN:

id description
ZDB-GENE-990415-178 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 cell differentiation 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 cranial ganglion; endoderm; heart; pharyngeal arch; and pharynx. Orthologous to human NKX2-3 (NK2 homeobox 3).

Ensembl:

ensembl_id ENSDARG00000039095

RNA

RNA id representative length rna type GC content exon number start site end site
TCONS_00013189 False 1435 mRNA 0.50 3 40409215 40411908
TCONS_00013190 True 814 mRNA 0.53 2 40409951 40411917

Neighbor

gene id symbol gene type direction distance location
XLOC_006857 nkx3.3 coding downstream 7345 40397517 ~ 40401870 (-)
XLOC_006856 pyroxd2 coding downstream 92848 40284872 ~ 40316367 (-)
XLOC_006855 zgc:123010 coding downstream 126445 40247379 ~ 40282770 (-)
XLOC_006854 loxl4 coding downstream 170402 40182487 ~ 40238813 (-)
XLOC_006853 crtac1b coding downstream 267585 40064481 ~ 40141630 (-)
XLOC_006859 NA coding upstream 6399 40418316 ~ 40419308 (-)
XLOC_006860 CNNM1 coding upstream 50449 40462366 ~ 40499296 (-)
XLOC_006861 st3gal7 coding upstream 304402 40716319 ~ 40726865 (-)
XLOC_006862 morn4 coding upstream 334364 40746281 ~ 40754499 (-)
XLOC_006863 NA coding upstream 549818 40961735 ~ 40977410 (-)
XLOC_006471 BX537274.2 misc downstream 30144310 10264741 ~ 10264905 (-)
XLOC_006338 rn7sk misc downstream 39582990 825904 ~ 826225 (-)
XLOC_006850 NA non-coding downstream 904722 39499592 ~ 39504493 (-)
XLOC_006848 BX324188.2 non-coding downstream 1166543 39242555 ~ 39242672 (-)
XLOC_006846 BX323574.1 non-coding downstream 1555963 38853137 ~ 38853252 (-)
XLOC_006843 NA non-coding downstream 1789496 38613225 ~ 38619719 (-)
XLOC_006842 NA non-coding downstream 2214001 38190521 ~ 38195214 (-)
XLOC_006864 NA non-coding upstream 599915 41011832 ~ 41114062 (-)
XLOC_006866 BX548002.1 non-coding upstream 818376 41230293 ~ 41230409 (-)
XLOC_006867 CABZ01117863.1 non-coding upstream 1251055 41662972 ~ 41663088 (-)

Expression


Co-expression Network