six3 (six3,six3a,LOC107733790)


Basic Information

Item Value
gene id six3
gene name six3,six3a,LOC107733790
gene type coding
species mexican tetra (Astyanax mexicanus)
category of species ornamental fish

Chromosome Information

Item Value
chromosome id NC_035921.1
NCBI id CM008324.1
chromosome length 46505145
location 27840844 ~ 27844241 (+)
genome version Astyanax_mexicanus-2.0_2017_mexican_tetra_Genome

Sequence

>XM_007255772.3
GAAAAGCgaaacaaaatatttcaatgCTACACTCACGGCGGATTTTAGGGGGAGATATTATGAGGCTTGGTGTCATTAGGCGATAGCTATTGAATCATTCAATCTGCACTTCGGCGTTCCCCTTTTTTCCTCGgtaattttctttctctctcaggtcATTTCCATGGTTTTCAGATCGCCTTTAGAGCTTTATCCCTCCCATTTATTCCTGCCAAACTTCGCTGATCGCCCCCTGCTCCTGGCGAACAGCGCGCCCAGCGCCAGGTCTCCCGAAGACTTGTCCATGTTTCAGCTACCGACCCTCAACTTCTCTGCGGAGCAGGTGGCGAGCGTCTGCGAGACGCTGGAGGAGACGGGCGACATCGAGCGGCTCGGGCGCTTCCTGTGGTCGCTGCCCGTAGCGCCGGGCGCATGCGAGGCCATCAACAAACACGAGTCCATCCTGCGCGCGCGGGCCGTGGTTGCTTTCCACACAGGAAACTTCCGCGACCTCTACCACATACTAGAGAACCACAAGTTCACCAAGGACTCACACGGAAAGCTGCAGGCGATGTGGCTCGAAGCGCATTACCAGGAGGCCGAGAAGCTGCGCGGGCGCCCGCTCGGTCCGGTTGACAAGTACCGCGTGCGAAAGAAGTTCCCGCTCCCTCGAACCATCTGGGACGGCGAGCAGAAGACGCACTGTTTCAAGGAGCGGACGCGCAGCCTCTTGCGGGAGTGGTACCTACAGGACCCGTACCCGAACCCGAGCAAGAAAAGGGAACTGGCGCAAGCCACTGGACTCACTCCTACACAAGTCGGGAATTGGTTTAAAAACCGGAGGCAAAGAGACAGAGCGGCGGCAGCCAAAAACAGGCTCCAGCACCAAGCAATAGGGCAGAACGGCATGCGCTCTCTGTCGGAGGCCGGCTGCACCCCCCACAGCTCGGCAGAGTCCCCATCCACCGCGGCCAGTCCCACTACCAGCGTGTCCAGCATGACGGAGCGCGTGGACACGGCCACGTCCATCCTCTCAGTAACGTCGAGTGACTCCGAGTGCGACGTATGATACGCAAAGAGAGTTATTTTGCAGGGAATATGGACCTGaataaactttataaaatatcgggaagatttaaaaaatggacCAAGTGATAattattaagagaaaaaaagaaaagaacaacaaaaaagaaaagcacgTCTTTTTTTCAAGCGCTTTCAATGGACCCCACGCCTTTCCCTACCCCCATCACTTGCATGATTTATCAAtagccttttttctttttttatatgaagGAAACTCCCTTCGCTTGATTTCTGCCAGGACCACCGAGAAGAGGGAATTACTAATTCGGTGTCCATCGCCTGTgtttacacacacgcacacacacacacacacacacacacacacacaaacattcgttttaatttatttttttattttatttatttttttttttgtctgagtgATGACACGCAGCCAGGATGCAAttcctttttccttttactTTCATCAGACAATCATTTGAGTCGTAAGCACCTTTTTATTACACTTCTGTCACTGCCTGTGTGGGGTACTGGTTTAAAAAATGTGGAACTGAATCGTTATGACTgtatcagatttttatttttatttcgaGATTTTATATTGAATTATGTATATCTTAAATGATGCGATCATTCTCCCAGTCTGTAATATATGTGTAGAAATATGCCTGTATATAATATTGCTCTACGTCTCCATTGTCTTTTCTATCCCTGTTCACTTTTCTTGACTTGGTGTTCATAAACTCTTTGTCAAAAGCGTAACTATTAAGTGCTCTAGGCGTTtggtttctctgtttttatacCTTGGAAGAACGTGACGATAATGGATTTTCAGTCGAGAATTTatgcaaaaagaaaagtaacaaaaaagagggaaaaacacatgGGGATATTGTCGACTGATCCAGCCAACTTCGTGTTTAGCTTCGAGCGCTTATTATTCACTGTTTCTTTCTTGCGTGTTTATgttaatgtatacatttttaagctaaaatacagtatttcattTTGCTA

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).
six3 Enables RNA polymerase II cis-regulatory region sequence-specific DNA binding activity and transcription corepressor binding activity. Involved in eye development; forebrain dorsal/ventral pattern formation; and negative regulation of transcription, DNA-templated. Predicted to be part of chromatin and transcription regulator complex. Predicted to be active in nucleus. Implicated in holoprosencephaly and holoprosencephaly 2.

NR:

description
homeobox protein SIX3

GO:

id name namespace
GO:0006355 regulation of transcription, DNA-templated biological_process
GO:0007420 brain development biological_process
GO:0005634 nucleus cellular_component
GO:0043565 sequence-specific DNA binding molecular_function
GO:0003700 DNA-binding transcription factor activity molecular_function

KEGG:

id description
K19473 SIX3_6, OPTIX; homeobox protein SIX3/6

RNA

RNA id representative length rna type GC content exon number start site end site
XM_007255772.3 True 2043 mRNA 0.47 2 27840844 27844241

Neighbor

gene id symbol gene type direction distance location
camkmt camkmt,si:ch73-54n14.2,LOC107585255,LOC107733780,LOC107602502,LOC107666367 coding upstream 129125 27510214 ~ 27711719 (+)
slc3a1 slc3a1,LOC107585281 coding upstream 348428 27473909 ~ 27492416 (+)
ppm1b ppm1b,ppm1ba,LOC107747533,LOC107666482,LOC107733761,LOC107585253 coding upstream 372860 27432862 ~ 27467984 (+)
abcg8 abcg8,LOC107666472 coding upstream 547759 27282600 ~ 27293085 (+)
cep170 cep170 coding upstream 658927 27094098 ~ 27181917 (+)
LOC103033108 LOC108420482 coding downstream 734415 28578656 ~ 28607913 (+)
LOC103028596 calm1,LOC102778633,LOC102293206,LOC107396020,LOC105896953,LOC107668515 coding downstream 771813 28616054 ~ 28621231 (+)
stpg4 NA coding downstream 780029 28624270 ~ 28631758 (+)
mcfd2 mcfd2 coding downstream 891518 28735759 ~ 28741543 (+)
LOC107197786 thada,LOC104958480 coding downstream 1029779 28874020 ~ 29005591 (+)
G219657 NA non-coding upstream 432754 27373876 ~ 27408090 (+)
G219620 NA non-coding upstream 498406 27264767 ~ 27342438 (+)
G219651 NA non-coding upstream 510636 27312708 ~ 27330208 (+)
G219643 NA non-coding upstream 536778 27295416 ~ 27304066 (+)
G219639 NA non-coding upstream 576969 27262554 ~ 27263875 (+)
G219891 NA non-coding downstream 84293 27928534 ~ 27928739 (+)
G219896 NA non-coding downstream 103620 27947861 ~ 27948095 (+)
G219917 NA non-coding downstream 338620 28182861 ~ 28185425 (+)
G219914 NA non-coding downstream 375454 28219695 ~ 28224612 (+)
G220032 LOC108422531 non-coding downstream 720774 28565015 ~ 28568032 (+)
LOC111196018 NA other upstream 604228 27200452 ~ 27236616 (+)
LOC103047652 NA other upstream 2398263 25438719 ~ 25442581 (+)
G219171 cunh4orf32,c3h4orf32 other upstream 2538257 25256950 ~ 25302587 (+)
dapp1 dapp1,LOC107579178,LOC107556904,LOC107667071,LOC107585227,LOC107733757 other upstream 2666136 25161727 ~ 25174708 (+)
G219050 NA other upstream 2998311 24842302 ~ 24842533 (+)
plekhh2 plekhh2 other downstream 646605 28490846 ~ 28551769 (+)
G220074 NA other downstream 875015 28719256 ~ 28720661 (+)
G220194 NA other downstream 1297126 29141367 ~ 29142018 (+)
LOC103047316 NA other downstream 1791820 29636061 ~ 29640401 (+)
G220336 NA other downstream 1943698 29787939 ~ 29793496 (+)

Expression


Co-expression Network