AMCG00000553 (six6,six6a,LOC107743981,LOC106598791,LOC107588601)


Basic Information

Item Value
gene id AMCG00000553
gene name six6,six6a,LOC107743981,LOC106598791,LOC107588601
gene type coding
species bowfin (Amia calva)
category of species ecological fish

Chromosome Information

Item Value
chromosome id CM030141.1
NCBI id CM030141.1
chromosome length 22147039
location 18480371 ~ 18483206 (+)
genome version AmiCal1_2021_bowfin_Genome

Sequence

>AMCG00000553
ATGCCACAGCACCGCGCCTTTCCCAGCGCCAGGACCGTGAGCTCCAAAAGGCACcagagccgagccgagccgagccgagccgaggcGCAGGTGGCGGGGGTGTGTGAGACTCTGGAGGAGAGCGGGGATATCGAGCGTCTCGGCCGTTTCCTCTGGTCGCTGCCCGTGGCCCCGGCCGCCTGCGAGGTCCTCAACAAGAACGAGTCGGTCCTGAGGGCCCGGGCCATCGTGGCCTTCCACACGGGCAACTTCCGAGAGCTCTACCACATCCTGGAGAACCACAAGTTCACCAAGGACTCGCACGCCAAGCTGCAGGCCCTGTGGCTGGAGGCGCACTATCAGGAGGCGGAGAAACTGAGGGGCCGCCCGCTCGGACCGGTGGACAAATACAGGGTGCGCAAGAAGTTCCCGCTGCCCAGGACCATTTGGGACGGGGAGCAGAAGACGCACTGCTTCAAGGAGCGGACCCGGCACTTGCTCAGGGAGTGGTACCTGCAGGACCCGTATCCCAATCCCAGCAAGAAGAGGGAACTGGCGCAAGCCACTGGACTCACACCCACACAAGTGGGGAACTGGTTCAAAAACCGCAGACAAAGGGACAGAGCGGCCGCGGCGAAAAACAGGCTACAGCAGCAGGTTCTGTCCCAGGGCTCGGTCCGGTCTCTGACGGAGGAGGACAGCGCGGTGGACCGGCTCGGCACCGCCTCCAGCCCCGAGGCCAGCCTGTCCAGCAAAGCCGTGGTCTCCGCCATCTCCATCACCTCCAGCGACAGCGAATGTGACATCTGA

Function

symbol description
six6a 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 gene expression and neural retina development. Predicted to be part of transcription regulator complex. Predicted to be active in nucleus. Is expressed in several structures, including eye; gill; heart; integument; and kidney. Human ortholog(s) of this gene implicated in optic disc anomalies with retinal and/or macular dystrophy. Orthologous to human SIX6 (SIX homeobox 6).
six6 Enables RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in eye development and regulation of transcription by RNA polymerase II. Predicted to be part of chromatin and transcription regulator complex. Predicted to be active in nucleus. Implicated in optic disc anomalies with retinal and/or macular dystrophy.

NR:

description
PREDICTED: homeobox protein SIX6 isoform X2

GO:

id name namespace
GO:0006355 regulation of transcription, DNA-templated 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
AMCG00000553 True 789 mRNA 0.65 3 18480371 18483206

Neighbor

gene id symbol gene type direction distance location
AMCG00000552 ppm1a,LOC106610975 coding upstream 46770 18428915 ~ 18433601 (+)
AMCG00000551 NA coding upstream 75574 18392416 ~ 18404797 (+)
AMCG00000555 LOC104966444 coding upstream 143924 18308336 ~ 18336447 (+)
AMCG00000562 zfyve21,LOC106610961 coding upstream 228707 18245088 ~ 18251664 (+)
AMCG00000563 klc1 coding upstream 239429 18222486 ~ 18240942 (+)
AMCG00000571 NA coding downstream 85959 18569165 ~ 18583738 (+)
AMCG00000579 prkch,LOC100380676,LOC107675581,LOC107548619 coding downstream 119344 18602550 ~ 18606788 (+)
AMCG00000580 NA coding downstream 127701 18610907 ~ 18613346 (+)
AMCG00000581 NA coding downstream 139196 18622402 ~ 18623132 (+)
AMCG00000577 NA coding downstream 152919 18636125 ~ 18652518 (+)
G151052 NA non-coding upstream 95325 18384600 ~ 18385046 (+)
G151050 NA non-coding upstream 120079 18359247 ~ 18360292 (+)
G150953 NA non-coding upstream 395684 18084460 ~ 18084687 (+)
G150951 NA non-coding upstream 399030 18078114 ~ 18081341 (+)
G150913 NA non-coding upstream 417025 17994559 ~ 18063346 (+)
G151217 NA non-coding downstream 376057 18859263 ~ 18859464 (+)
G151219 NA non-coding downstream 379818 18863024 ~ 18868044 (+)
G151226 NA non-coding downstream 436715 18919921 ~ 18921366 (+)
G151310 NA non-coding downstream 647419 19130625 ~ 19130890 (+)
G151339 NA non-coding downstream 822040 19305246 ~ 19307462 (+)
AMCG00000550 NA other upstream 60795 18411443 ~ 18419576 (+)
G150976 NA other upstream 321050 18153864 ~ 18159321 (+)
AMCG00000525 NA other upstream 720789 17748510 ~ 17759582 (+)
G150811 NA other upstream 931863 17545454 ~ 17548508 (+)
G150750 NA other upstream 1542089 16935993 ~ 16938282 (+)
AMCG00000573 NA other downstream 6645 18489851 ~ 18530757 (+)
AMCG00000572 mnat1,LOC107757134,LOC107675563 other downstream 51263 18534469 ~ 18565627 (+)
G151522 gpr135,LOC107564991 other downstream 1486133 19969339 ~ 19972015 (+)
G151676 NA other downstream 2358732 20841938 ~ 20843463 (+)
AMCG00000661 NA other downstream 3043664 21526870 ~ 21533538 (+)

Expression


Co-expression Network

Homologous

species gene id symbol gene type chromosome NCBI id location
zebrafish (Danio rerio) XLOC_006096 six6a coding NC_007124.7 CM002897.2 31583034 ~ 31606247 (+)
grasscarp (Ctenopharyngodon idella) CI01000012_08489570_08491016 SIX6, SIX6A, SIX6B, SIX6.L coding CI01000012 null 8489098 ~ 8492326 (-)