AMCG00001877 (six3a,six3,LOC107733790,LOC107585256,LOC107602501)


Basic Information

Item Value
gene id AMCG00001877
gene name six3a,six3,LOC107733790,LOC107585256,LOC107602501
gene type coding
species bowfin (Amia calva)
category of species ecological fish

Chromosome Information

Item Value
chromosome id CM030143.1
NCBI id CM030143.1
chromosome length 20516281
location 18536853 ~ 18539797 (+)
genome version AmiCal1_2021_bowfin_Genome

Sequence

>AMCG00001877
ATGGTTTTCAGATCCCCTTTAGAGCTTTATCCCTCCCATTTCTTCCTGCCAAACTTCGCTGATCGCCCCTTGGTCCTGGCGAGCAGCGCGCCCAGCGCCCGGTCTCCAGAAGAGTTGTCCATGTTTCAGCTGCCCACCCTCAACTTCTCCCCGGAGCAGGTGGCCAGTGTCTGCGAGACGCTGGAGGAGACCGGGGACATCGAGCGCCTGGGACGCTTCCTCTGGTCCCTGCCGGTGGCCCCGGGCGCCTGCGAGGCCATCAACAAGCATGAGTCCATCCTGCGCGCCCGCGCCGTGGTGGCCTTCCACACGGGCAATTTCAGAGACCTGTACCACATCCTGGAGAATCACAAGTTCACCAAGGACTCCCACGGCAAACTACAGGCCATGTGGCTAGAAGCCCACTATCAGGAGGCCGAGAAGCTGCGCGGTCGCCCCCTAGGACCCGTCGACAAGTACAGGGTGCGGAAGAAGTTCCCTCTTCCCAGGACCATCTGGGACGGCGAGCAGAAGACCCACTGCTTCAAGGAGCGGACGCGCAGCCTCCTCAGGGAGTGGTATCTGCAGGACCCGTACCCCAACCCCAGCAAGAAAAGGGAACTGGCTCAGGCCACTGGACTCACTCCCACACAAGTCGGGAATTGGTTTAAAAATCGCAGGCAAAGAGACAGAGCCGCAGCTGCAAAGAACAGGCTCCAGCACCAAGCAATAGGGCAGAACGGCCTGCGGTCGCTGTCAGAGTCCGGCTGCACGCCCCACAGCTCGGCCGAGTCCCCGTCTACGGCGGCCAGTCCGACCACCAGTGTTTCCAGTATGACGGAGAGGGTGGACAATGGCACGTCCATCCTTTCTGTAACCTCCAGTGACTCGGAATGTGATGTATga

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
PREDICTED: 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
AMCG00001877 True 885 mRNA 0.61 2 18536853 18539797

Neighbor

gene id symbol gene type direction distance location
AMCG00001874 NA coding upstream 169617 18364302 ~ 18367236 (+)
AMCG00001873 NA coding upstream 177898 18347796 ~ 18358955 (+)
AMCG00001872 LOC108430462,LOC108273990,LOC107582773,LOC107749348,LOC107698817 coding upstream 195976 18328491 ~ 18340877 (+)
AMCG00001875 NA coding upstream 242163 18287712 ~ 18294690 (+)
AMCG00001882 abcg8 coding upstream 306588 18224054 ~ 18230265 (+)
AMCG00001888 prkcea,prkce,LOC107582817,LOC108274197,LOC107739250 coding downstream 186902 18726699 ~ 18727082 (+)
AMCG00001886 NA coding downstream 231283 18771080 ~ 18778684 (+)
AMCG00001897 prkcea,LOC107739250,LOC107582770,LOC107550054,LOC107698816 coding downstream 249969 18789766 ~ 18803912 (+)
AMCG00001895 NA coding downstream 290382 18830179 ~ 18850985 (+)
AMCG00001898 rhoq,LOC105900041 coding downstream 330039 18869836 ~ 18877697 (+)
G160985 NA non-coding upstream 317822 18218764 ~ 18219031 (+)
G160943 NA non-coding upstream 497479 18038704 ~ 18039374 (+)
G160939 NA non-coding upstream 507037 18024196 ~ 18029816 (+)
G160910 NA non-coding upstream 619799 17916795 ~ 17917054 (+)
G160895 NA non-coding upstream 675426 17860162 ~ 17861427 (+)
G161170 NA non-coding downstream 383652 18923449 ~ 18923672 (+)
G161282 NA non-coding downstream 915291 19455088 ~ 19457752 (+)
G161285 NA non-coding downstream 968446 19508243 ~ 19508522 (+)
G161392 NA non-coding downstream 1696380 20236177 ~ 20236391 (+)
G161469 NA non-coding downstream 1934874 20474671 ~ 20474889 (+)
AMCG00001883 NA other upstream 319715 18210009 ~ 18217138 (+)
AMCG00001881 NA other upstream 327462 18187902 ~ 18209391 (+)
AMCG00001846 NA other upstream 1073919 17417351 ~ 17462934 (+)
AMCG00001841 NA other upstream 1354252 17179594 ~ 17182601 (+)
AMCG00001814 ryr2,LOC106456445,LOC108410403,LOC106906861,LOC101062804,LOC103129799 other upstream 2158993 16237262 ~ 16377860 (+)
AMCG00001880 NA other downstream 124198 18663995 ~ 18673815 (+)
AMCG00001889 cript,LOC107582781,LOC107728714 other downstream 359540 18899337 ~ 18901718 (+)

Expression


Co-expression Network

Homologous

species gene id symbol gene type chromosome NCBI id location
zebrafish (Danio rerio) XLOC_006470 six3a coding NC_007124.7 CM002897.2 10258007 ~ 10261383 (-)
grasscarp (Ctenopharyngodon idella) G684905 NA non-coding CI01180000 null 9694434 ~ 9697780 (-)