XLOC_006857 (nkx3.3)


Basic Information

Item Value
gene id XLOC_006857
gene name nkx3.3
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 40397517 ~ 40401870 (-)
genome version GRCz11_2017_zebrafish_Genome

Sequence

>TCONS_00013187
GGAAAGAGAAGAGAGGGAACTGATGTGCACATGACATTCTCTGACACTGCCTGTTGATTGGGTCGGAAGAAGTTTTGCCGCAATTAAATGACACGCAGAGAGGAAAGCAATTACACTGCGGACTAATTTATTGTCATGAACGCGCAGGAGCTTCCCAGATAGACGCGCAAAACTCCATCGACATAAAACCGGCGAGAAGGATaggtaaatgttttaaatggcGAATAACCGAACCTCCTTTTCCATCCACAATATTTTAAACCAAGGACATGAATGTGGGAAAAACGGCAGTTTTGATGAGGAATACGAGGGAGAGAAAAGGACACAGGACTCAGGCTCATCTGTGCCGGTGAACCGCGGAGCCGAAAGCGCACAGACGCGCATCTCTTCCTGCGTGCTCGTGCTCGAGTCTTTATCATCAGACCAGCATTCATGCGAGGAAGAATCAACAGGAGAAGATAATTCACTGGAAAGGCGACATGATCATGAAATGGACCAACAGAAACCCCAGAGCTGCAGCTTTGAAGACAGCAACCCTAAATCCAGCAAGAAAAGATCTCGGGCAGCATTTTCCCACGCACAGGTGTACGAGCTAGAGCGACGCTTTAACCTGCAGAGATATCTGTCTGGCCCAGAGCGAGCAGACCTAGCTGGAGCCCTCAAACTGACCGAGACTCAGGTCAAGATCTGGTTCCAGAACAGGAGATACAAAACCAAACGGCGACAAATGGCAGCTGAACTCGCCACAACTCCCACAACAACCCTTGCAAAGAGAGTGGCCGTGAAGGTACTAGTGAGAAATGACCAAAGGCAATATAACACAGAAGATCTGCCCAGTCCTTCTGTTCCTCCTTTATACCAATCATTCCCTTATTATCCCTACATGTTCTGCTTCCAGCCATGGATCTCAGGAAACACTTTAAGCGGTGGGATGTACTGATTTAATGGAGTTATGAATGATTCTGGAGAAACAAAGAGTCATAAACAACTGCTATTCATCCAGAGGGattaaaaatgttgaatattAAACTGAACAAGATGCAAATAAAAGAACTATGGGGTATATTGATGATCGATATCAATAATTTCCACAAATGATCATTAAGCCAAAGCAAAGacaatttattatattgttaGTCATTTGTTGAACGGTGGCCTATAAAATGTATCTGGACAGGTAATGCACACTTAAAATTTGAGGCGTGTTTGCTTTAGctaacaaaatatgaaaaccaAAGAGTGGCTGCAAACAAATTTGGTGGATCTACGTGATTTATTGACATTTGACAAAGTCAGAAAGAGCACGGATGATTTACAACCTAACAAGCTTCtgtttgtaaaatgttgtttGGCATGACTTgatatttgttcattaattcaaAGGCAGTCTTACACTTTTAAGTGTGGCTGAAAATGTTAGTTTTTTTAAGTGCAGGTGAATCGTTTTATGGAGTGTGTTTTAGCTATAGTTTGGGGAGTTTTTCTGTTATTACTTTTTCACAGATTAAAGTTGTTTATTTCCATCACCAT
>TCONS_00013188
ATGGACCAACAGAAACCCCAGAGCTGCAGCTTTGAAGACAGCAACCCTAAATCCAGCAAGAAAAGATCTCGGGCAGCATTTTCCCACGCACAGGTGTACGAGCTAGAGCGACGCTTTAACCTGCAGAGATATCTGTCTGGCCCAGAGCGAGCAGACCTAGCTGGAGCCCTCAAACTGACCGAGACTCAGGTCAAGATCTGGTTCCAGAACAGGAGATACAAAACCAAACGGCGACAAATGGCAGCTGAACTCGCCACAACTCCCACAACAACCCTTGCAAAGAGAGTGGCCGTGAAGGTACTAGTGAGAAATGACCAAAGGCAATATAACACAGAAGATCTGCCCAGTCCTTCTGTTCCTCCTTTATACCAATCATTCCCTTATTATCCCTACATGTTCTGCTTCCAGCCATGGATCTCAGGAAACACTTTAAGCGGTGGGATGTACTGATT

Function

symbol description
nkx3.3 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 heart and pharyngeal arch.

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-050306-27 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 heart and pharyngeal arch.

Ensembl:

ensembl_id ENSDARG00000069327

RNA

RNA id representative length rna type GC content exon number start site end site
TCONS_00013187 False 1530 mRNA 0.42 2 40397517 40401870
TCONS_00013188 True 452 mRNA 0.49 1 40398105 40398556

Neighbor

gene id symbol gene type direction distance location
XLOC_006856 pyroxd2 coding downstream 81150 40284872 ~ 40316367 (-)
XLOC_006855 zgc:123010 coding downstream 114747 40247379 ~ 40282770 (-)
XLOC_006854 loxl4 coding downstream 158704 40182487 ~ 40238813 (-)
XLOC_006853 crtac1b coding downstream 255887 40064481 ~ 40141630 (-)
XLOC_006852 sfrp5 coding downstream 450182 39911551 ~ 39947335 (-)
XLOC_006858 nkx2.3 coding upstream 7345 40409215 ~ 40411917 (-)
XLOC_006859 NA coding upstream 16446 40418316 ~ 40419308 (-)
XLOC_006860 CNNM1 coding upstream 60496 40462366 ~ 40499296 (-)
XLOC_006861 st3gal7 coding upstream 314449 40716319 ~ 40726865 (-)
XLOC_006862 morn4 coding upstream 344411 40746281 ~ 40754499 (-)
XLOC_006471 BX537274.2 misc downstream 30132612 10264741 ~ 10264905 (-)
XLOC_006338 rn7sk misc downstream 39571292 825904 ~ 826225 (-)
XLOC_006850 NA non-coding downstream 893024 39499592 ~ 39504493 (-)
XLOC_006848 BX324188.2 non-coding downstream 1154845 39242555 ~ 39242672 (-)
XLOC_006846 BX323574.1 non-coding downstream 1544265 38853137 ~ 38853252 (-)
XLOC_006843 NA non-coding downstream 1777798 38613225 ~ 38619719 (-)
XLOC_006842 NA non-coding downstream 2202303 38190521 ~ 38195214 (-)
XLOC_006863 NA non-coding upstream 559865 40961735 ~ 40977410 (-)
XLOC_006864 NA non-coding upstream 609962 41011832 ~ 41114062 (-)
XLOC_006866 BX548002.1 non-coding upstream 828423 41230293 ~ 41230409 (-)
XLOC_006867 CABZ01117863.1 non-coding upstream 1261102 41662972 ~ 41663088 (-)

Expression


Co-expression Network

Homologous

species gene id symbol gene type chromosome NCBI id location
bowfin (Amia calva) AMCG00003068 NA coding CM030139.1 CM030139.1 10730942 ~ 10743690 (-)