XLOC_004736 (six3b)


Basic Information

Item Value
gene id XLOC_004736
gene name six3b
gene type coding
species zebrafish (Danio rerio)
category of species model fish

Chromosome Information

Item Value
chromosome id NC_007123.7
NCBI id CM002896.2
chromosome length 49182954
location 25600685 ~ 25603341 (+)
genome version GRCz11_2017_zebrafish_Genome

Sequence

>TCONS_00009381
GTGATTGGCAGGGCTGCCATGACAACCACAGCACGACACCAGGAAGACCAATAGAAAAGCGAAACAAAATGTTTCACCGTTGCACTCTAAGTTGATTAAGGGTAGATATTCGCGCTCGGTGGCACTGCGGCGATAGCAGCGCAAACACGACGTCGGGTTTTCCGTCTTTCCCCGTCGTTTTGTCTCTGTCCGGCGACTCCATGGTTTTCAGGTCTCCTTTAGAGCTTTATCCCTCACatcttttcctgcccaatttcgcGGATCGCCCTCTGCTTCTGGCGGGCAGCATTCCCAGAGCGAGGTCCCCGGAGGACTTACCGATGTTTCAGCTGCCCACCCTAAACTTCTCGGCGGAACAGGTGGCCAGCGTGTGCGAGACGCTGGAGGAAACCGGGGACATCGAGAGGCTCGGACGTTTCCTTTGGTCGTTGCCCGTAGCACCCGGAGCCTGCGATGCCATCAACAAGCACGAGTCCATCCAGCGAGCCCGAGCGGTGGTCGCGTATCACACGGGAAGCTTCCGTGAATTATACCACATCCTGGAAACCCACAAGTTCACCAAAGACTCTCATGGAAAGCTGCAAGCGATGTGGCTGGAAGCGCACTACCAAGAAGCAGAGAAGCTGCGCGGCCGTCCCCTTGGACCCGTTGATAAATACCGGGTCCGCAAGAAGTTTCCTTTGCCACGGACCATCTGGGATGGCGAACAGAAGACGCACTGTTTCAAGGAACGAACTCGCGGTTTGTTGAGGGAGTGGTACCTACAGGACCCTTACCCCAATCCGAGCAAGAAAAGGGAACTGGCACAAGCCACTGGACTGACTCCCACTCAAGTGGGCAATTGGTTTAAAAATCGAAGACAGAGGGACAGGGCGGCAGCTGCCAAAAACAGGCTTCAGCATCACGGACTGGGCCAAAGCAGTCTGCGCTCCATGTCAGAATCGGGCTGCACACCGCACAGCTCGGCAGAATCCCCGTGCGCGGCCGCCAGTCCCACGACCAGCGTCTCCAGTATGAATGAACGAGGCGACGGTGGGACAATTCTCTCAGTTACAGACAGTGACTCTGATTTCGATGTATGATGCACCGTCggacaaatataaaacatttttttgcccAGAGAAAAATGAACTTGTGAAAATGTGGGCAACATGGGGGCCGGCCATTTTGCCagcttgtgttcaacaaaaggagAAAAGCATGCTGTTTTTCCAGCGCTTCAACGGACTGACGCCCTTACCTTTTTATTTCCAAGGCCTATACACGACCATTTTGCATGTTCATTTGTGAatattttgcaattttaaaaGGCATTTATGAAGTGGAGTCCGAAAAGGTAGAACTCGATGCTCGATGAAATGAGTGAACCGGAGAggcaattttattattttgtgtttatcagaCAATCGTTGAAGTCCAAAAGCACCTTTATTCCCCCTCGTCTTTTACTCGACTGGAGATGTTCATACTAATTTTATCTCAAGATTTATATTGAATTGTCCATGTCTGATTCAAAGTTTTCCTTAGGTCTAGGCTTGTCTAGATATGCTTGTATATGGTATCGCAATTACGCCACTCTCTTTCCTGCAAATTTCTTTATGTTGTGTCCATAAAGCGTGAGTAACTGTCTGTTAAGTGCTTGGAGATTTTAAGTGTCTATTCATTCTGCTcgtttttatactgtaaatggGTTAATGGCGCTGAAAACACAGTGTTATGGGTCActtttatgcaaataaatataatttaatataacgaC

Function

symbol description
six3b Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Acts upstream of or within embryonic camera-type eye morphogenesis; nervous system development; and sensory epithelium regeneration. Predicted to be part of transcription regulator complex. Predicted to be active in nucleus. Is expressed in several structures, including hypoblast; immature eye; nervous system; neural keel; and neural rod. Human ortholog(s) of this gene implicated in holoprosencephaly and holoprosencephaly 2. Orthologous to human SIX3 (SIX homeobox 3).

GO:

id name namespace
GO:0021554 optic nerve development biological_process
GO:0006355 regulation of transcription, DNA-templated biological_process
GO:0021631 optic nerve morphogenesis biological_process
GO:0048856 anatomical structure development biological_process
GO:0048596 embryonic camera-type eye morphogenesis biological_process
GO:0045892 negative regulation of transcription, DNA-templated biological_process
GO:0070654 sensory epithelium regeneration biological_process
GO:0001654 eye development biological_process
GO:0007420 brain development biological_process
GO:0005634 nucleus cellular_component
GO:0005667 transcription regulator complex cellular_component
GO:0003677 DNA binding molecular_function
GO:0000976 transcription 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-990415-128 Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Acts upstream of or within embryonic camera-type eye morphogenesis; nervous system development; and sensory epithelium regeneration. Predicted to be part of transcription regulator complex. Predicted to be active in nucleus. Is expressed in several structures, including hypoblast; immature eye; nervous system; neural keel; and neural rod. Human ortholog(s) of this gene implicated in holoprosencephaly and holoprosencephaly 2. Orthologous to human SIX3 (SIX homeobox 3).

Ensembl:

ensembl_id ENSDARG00000054879

RNA

RNA id representative length rna type GC content exon number start site end site
TCONS_00009381 True 1759 mRNA 0.49 2 25600685 25603341

Neighbor

gene id symbol gene type direction distance location
XLOC_004735 NA coding upstream 96305 25502406 ~ 25504380 (+)
XLOC_004734 ppm1bb coding upstream 113441 25432626 ~ 25487244 (+)
XLOC_004733 CR932077.1 coding upstream 170314 25312018 ~ 25430371 (+)
XLOC_004732 mta3 coding upstream 316175 25223799 ~ 25284510 (+)
XLOC_004731 CR848736.1 coding upstream 385958 25201543 ~ 25214727 (+)
XLOC_004737 prkcea coding downstream 37139 25640480 ~ 25770232 (+)
XLOC_004738 CR932018.1 coding downstream 44786 25648127 ~ 25648243 (+)
XLOC_004739 epas1a coding downstream 172393 25775734 ~ 25830268 (+)
XLOC_004740 glud1b coding downstream 242153 25845494 ~ 25881944 (+)
XLOC_004741 mmrn2b coding downstream 342219 25945560 ~ 25948479 (+)
XLOC_004728 CR385067.1 non-coding upstream 525565 25073305 ~ 25075120 (+)
XLOC_004726 NA non-coding upstream 656181 24944172 ~ 24944504 (+)
XLOC_004744 NA non-coding downstream 886012 26489353 ~ 26491973 (+)
XLOC_004748 NA non-coding downstream 986303 26589644 ~ 26593298 (+)
XLOC_004751 NA non-coding downstream 1088478 26691819 ~ 26692051 (+)
XLOC_004752 NA non-coding downstream 1134090 26737431 ~ 26834192 (+)

Expression


Co-expression Network

Homologous

species gene id symbol gene type chromosome NCBI id location
grasscarp (Ctenopharyngodon idella) CI01000063_05466326_05468126 SIX3, SIX3A, SIX3B, SIX3.L coding CI01000063 null 5466052 ~ 5469282 (+)