XLOC_006470 (six3a)


Basic Information

Item Value
gene id XLOC_006470
gene name six3a
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 10258007 ~ 10261383 (-)
genome version GRCz11_2017_zebrafish_Genome

Sequence

>TCONS_00012549
ATTTAGGGGGAGATATTATGAGGCTGGTGTCATTAGGCGATAGCTATTGAATCATTCAATCTGAATTCGTCGTTCTTTTTTCCTTCGCAAATTTCACTCTCTCTCAGGTCATTTCCATGGTTTTCAGATCGCCTTTAGAGCTTTATCCCTCTCATTTCTTCCTGCCAAACTTTGCTGATCGCCCTTTGCTCTTGGCGAGCAGTGCGCCCAGCACCAGGTCTCCCGAAGACTTGTCAATGTTTCAGCTACCGACCCTAAACTTCTCTCCAGAGCAAGTGGCGAGCGTCTGCGAGACGCTGGAGGAGACCGGGGACATCGAGCGGCTGGGTCGCTTCCTATGGTCGCTTCCAGTGGCACCGGGTGCTTGCGAGGCGATCAacaagcatgaatccatcctacGCGCCCGGGCTGTTGTCGCCTTTCACACCGGCAATTTTCGCGATCTCTACCACATTTTGGAGAACCACAAGTTTACCAAGGACTCGCATGGTAAACTACAAGCGATGTGGCTAGAGGCTCACTATCAGGAGGCCGAGAAACTACGCGGGCGTCCCCTAGGACCGGTTGATAAGTACAGGGTGCGAAAGAAGTTTCCCCTGCCTAGAACCATCTGGGACGGTGAGCAGAAGACGCATTGTTTCAAGGAGCGAACGCGGAGTCTGTTACGAGAGTGGTACCTTCAGGACCCCTACCCAAACCCCAGCAAGAAAAGGGAACTGGCTCAAGCCACTGGACTCACTCCTACACAGGTCGGAAATTGGTTTAAAAACAGGAGACAACGAGACAGGGCAGCGGCAGCAAAAAACAGGCTCCAGCATCAAGCAATAGGGCAGAATGGCATGCGGTCCCTTTCAGAATCCGGCTGCACCCCACGGAGTTCGGCGGAGTCGCCATCAACTGCGGCTAGTCCAACAACCAGTGTCTCGAGTATGACAGAACGAGTCGACACGGGCACGTCAATTCTTTCAGTAACATCAAGTGACTCGGAATGCGACGTATGATACGCACACAGAGAAATATATAAAGGAGAATGGACCTGAAAAACTTTATTAATTATCGGGGAAGATGAAAAAGGACCAattgatattactattataaaAAGAAAAGCATAAAAGCACGTCTTTTTTCAAGCGCTTTCAATGGACCCCACACCTTTCCCCCACCCCACCACttgcatgatatatatatatctaaatatattttttctcatttttgtATATGGGGAAATGCCCCACGTTATTATGTCTACCAGGACCACCGTGAAGAGGGAATTACCAGAAAGCGGTGTCCAAcgcctttttttctgttttagtcCGAGTGACGACGAGCAGCCAGGATGcaatcctttttttcttttatgttcatCAGACAATCATTTGAGTCGTAAGCACCTTTTTACTACACTTCTGTCACTGCCTGTGTGGGGTACTGGTCAAATGTGGAACTGAATCGTTATGACtgtatcagatttttatttttatttcgagattttatattgaattatGTATATCTTAAATAATGCGATCATTCTCCCAGTCTGTAATATATGTGTAGAAATACGTCTGTAAATAATATTGCTATTCCCATTCTCTTTTCTATCCCTGTTCACTTTTCTTGGCTTGGTGTCCCTACATAAACTATTCGTCAAAACGTAACTATTAAGTGCTAGGCGTTTTGTTTCTCTGTTTTATGCCATGAAAAGAACGCTAGTGACTATGAAATATCAGTCGAGattaatgcaaaagaaaataTTGGATATCATCATCGACTGACCAAGTCTACTTCATGTTTCCAGTCCAGCGCTTATAATTCAATACTACTTTCTTGCGTGTTTCTGTTAATGTATACGTTTCTAAACTGAAAATACAGTATTCAATTTTGttataaaa

Function

symbol description
six3a 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 brain development and optic nerve morphogenesis. Predicted to be part of transcription regulator complex. Predicted to be active in nucleus. Is expressed in several structures, including anterior neural keel; central nervous system; eye; neural plate; and optic vesicle. 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:0045892 negative regulation of transcription, DNA-templated 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-990415-127 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 brain development and optic nerve morphogenesis. Predicted to be part of transcription regulator complex. Predicted to be active in nucleus. Is expressed in several structures, including anterior neural keel; central nervous system; eye; neural plate; and optic vesicle. Human ortholog(s) of this gene implicated in holoprosencephaly and holoprosencephaly 2. Orthologous to human SIX3 (SIX homeobox 3).

Ensembl:

ensembl_id ENSDARG00000058008

RNA

RNA id representative length rna type GC content exon number start site end site
TCONS_00012549 True 1889 mRNA 0.44 2 10258007 10261383

Neighbor

gene id symbol gene type direction distance location
XLOC_006469 NA coding downstream 4973 10250174 ~ 10253034 (-)
XLOC_006468 NA coding downstream 25929 10150919 ~ 10232078 (-)
XLOC_006467 NA coding downstream 139072 10077215 ~ 10118935 (-)
XLOC_006466 si:ch211-117n7.6 coding downstream 362379 9889676 ~ 9895628 (-)
XLOC_006465 si:ch211-117n7.7 coding downstream 371428 9878544 ~ 9886579 (-)
XLOC_006472 NA coding upstream 13903 10275286 ~ 10346890 (-)
XLOC_006473 camkmt coding upstream 99061 10360444 ~ 10620794 (-)
XLOC_006474 slc3a1 coding upstream 387686 10649069 ~ 10672538 (-)
XLOC_006475 ppm1ba coding upstream 421044 10682427 ~ 10731325 (-)
XLOC_006476 AL928999.1 coding upstream 651103 10912486 ~ 10912602 (-)
XLOC_006338 rn7sk misc downstream 9431782 825904 ~ 826225 (-)
XLOC_006471 BX537274.2 misc upstream 3358 10264741 ~ 10264905 (-)
XLOC_006458 NA non-coding downstream 699582 9501767 ~ 9558425 (-)
XLOC_006437 NA non-coding downstream 1481530 8760694 ~ 8776477 (-)
XLOC_006480 NA non-coding upstream 1181455 11442838 ~ 11445780 (-)
XLOC_006482 CR556710.1 non-coding upstream 1304353 11565736 ~ 11565863 (-)
XLOC_006492 CR792443.2 non-coding upstream 1713069 11974452 ~ 11974568 (-)

Expression


Co-expression Network

Homologous

species gene id symbol gene type chromosome NCBI id location
grasscarp (Ctenopharyngodon idella) G684905 NA non-coding CI01180000 null 9694434 ~ 9697780 (-)
bowfin (Amia calva) AMCG00001877 six3a,six3,LOC107733790,LOC107585256,LOC107602501 coding CM030143.1 CM030143.1 18536853 ~ 18539797 (+)