CI01000063_05466326_05468126 (SIX3, SIX3A, SIX3B, SIX3.L)


Basic Information

Item Value
gene id CI01000063_05466326_05468126
gene name SIX3, SIX3A, SIX3B, SIX3.L
gene type coding
species grasscarp (Ctenopharyngodon idella)
category of species economic fish

Chromosome Information

Item Value
chromosome id CI01000063
NCBI id null
chromosome length 7808773
location 5466052 ~ 5469282 (+)
genome version v1_2015/06_NatureGenetics_grasscarp_Genome

Sequence

>CI01000063_05466326_05468126.mRNA
CGATAAAACCCTGCGCGCGAAGCAAATGTGCAGAAGGGCAGCGCGCACTGGCTAATGACGGGCAAGCTTGACAGTGATTGGCAGGGCTGCCATGACAACCACAGCACGACTCAAGGAAGACCAATAGAAAAGCGAAACAAAATGTTTCACCGTTGCACTCGAAGTTGATTAAGGGTAGATATTACGCGTTCGGTAGTACTGCAGCGATAGCAGCGCAAACACGACGTCAGTTTTACCGTCTTTTCCCGTCTGTTTGTCTCTGTCCGGCGACTCCATGGTGTTCAGGTCTCCTTTAGAGCTTTATCCCTCACATCTTTTCCTGCCCAATTTCGCGGATCGCCCTCTGCTTCTAGCGGGCAGCATTCCCAGAGCGAGGTCCCCGGAGGACTTACCGATGTTTCAACTGCCCACCCTAAACTTCTCGGCGGAACAGGTGGCCAGCGTGTGCGAGACGCTGGAGGAAACCGGGGACATCGAGAGACTCGGACGTTTCCTTTGGTCCTTGCCCGTGGCACCCGGAGCCTGCGATGCCATCAACAAGCACGAGTCCATCCAGCGAGCCCGAGCGGTGGTCGCGTATCACACTGGAAGCTTCCGCGAATTGTACCACATCCTGGAAAACCACAAGTTCACCAAAGACTCTCATGGAAAGCTGCAAGCGATGTGGCTCGAGGCACACTACCAAGAGGCAGAGAAGCTGCGCGGTCGTCCCCTCGGACCCGTTGATAAATACCGGGTCCGCAAGAAGTTCCCCTTGCCACGGACCATCTGGGATGGTGAACAGAAGACGCACTGTTTCAAGGAACGGACTCGCGGCTTGTTGAGGGAGTGGTACCTACAGGATCCTTACCCCAATCCGAGCAAGAAAAGGGAACTGGCACAAGCCACTGGACTGACTCCCACTCAAGCTTCAACATCACGGACTGGGTCAAAGCGGCCTGCGCTCCATGTCAGAGTCCGGGTGCACACCGCACAGCTCGGCCGAATCCCCGTGCGCGGCCGCCAGTCCCACTACCAGCGTCTCCAGTATGAATGAACGAGGCGACGGCGGGACCATCCTCTCAGTTACAGACAGTGACTCTGATTTCGATGTATGATGCACCGTCAGACAAATATGGAACATTTTTGCCCAGAGAAAAATGAACTTGTGAGAAAATGTGGGCAACATGAGGACCGGCCATTTTGCCACCTTGTGTTTGACAAAAGCATGCTGTTTTTCCAGCGCTTCAACGGACTGACGCCCTTTCCTTTCATTTCCAAGGCCTACACGACCATTTTGCATGTTCATTTGTGAATATTTTGCATTTTTAAAAGGCATTTATGAAGTGGAGTCTCAGAAAGTAGAACTCGATGCTCAAAGAAACGAGTGAACCCGAGAGGCAGTTTTGTTGTTTTGTGTTTATCAGACAATCGTTGAAGTCAAAAGCACCTTTATTCCCCATCGTCTTTTACTCGGCAGCAGATGTTCATACTAATTTTATCTCGAGATTTATATTGAATTGTCCATGTCTGATTCAAAGTTTTCCTTAGGTCTAGGCTTGTCTAGATATGCTTGTATGATATCGCAATTACGCCACTCTCTTTCCTGCAAATTTCTTTATGTTGTGTCCATAAAGCGTGAGTAACTGTCTGTTAAGTGCTTGGAGATTTTAAGTGTCTATTCATTCTGCTCGTTTTTATACTGTAAATGGGTTAATGGCGCTGAAAACACAGTGTTATGGGTCACTTTTATGCAAATAAATATAATTTAATATAACGACTATCAGAGTATTATTTGTTTATTTAAGTATTATGTCAGAAAATACAGGGGGAAAAAATCGATATTTCTATTCTGTACATTAATTTCTTCGTTTTTATTTTCATTTCAGGAGTGTTAATCATTTGTCTTATACTGAAAGAGAACTTAATTACGTTCAAATCGCACTTAAAAAAGAAAGGTGACGAATATGTGTTCTTTTATTTGTTTTGCCTTTTTTTTTTTTTAAATATACTATTATTAGGTTATTATTATTATTATTGTTAAAGAGTTGAACATTGGCGCACATACGGTTCTGAAATAACACGAGTTTTATTTCCGGTATAAATCAAATGGGAGAGTAATACAGCTTTTGTGTTGCCAGTGATTGTGCGTTTATTTTATTTTATTTTTTGTGATAATTATTGTAAATGTTTTATGCTTTAGGTAGAGAGCA

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).
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.

GO:

id name namespace
GO:0021537 telencephalon development biological_process

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
CI01000063_05466326_05468126.mRNA True 2192 mRNA 0.45 2 5466052 5469282

Neighbor

gene id symbol gene type direction distance location
CI01000063_05400578_05406105 PPM1BB, PPM1B coding upstream 59775 5400578 ~ 5406277 (+)
CI01000063_05281800_05302429 NA coding upstream 163553 5280655 ~ 5302499 (+)
CI01000063_05271158_05276999 NA coding upstream 188947 5271158 ~ 5277105 (+)
CI01000063_05223875_05227171 NA coding upstream 238881 5223875 ~ 5227171 (+)
CI01000063_05191319_05197432 PIGF coding upstream 268492 5191319 ~ 5197560 (+)
CI01000063_05490285_05556254 PRKCEA, PRKCE, PRKCEB coding downstream 21003 5490285 ~ 5556462 (+)
CI01000063_05563124_05584474 NA coding downstream 93842 5563124 ~ 5585104 (+)
CI01000063_05597755_05613489 GDH1, GLUD1B, GLUD1A, GDH2, GDH3.2, GLUD1, GDH03, GDH01, GLUD1.S coding downstream 128042 5597324 ~ 5614654 (+)
CI01000063_05639341_05650366 NA coding downstream 170008 5639290 ~ 5650682 (+)
CI01000063_05673923_05678546 NA coding downstream 204547 5673829 ~ 5678725 (+)
G265173 NA non-coding upstream 30412 5435399 ~ 5435640 (+)
G265142 NA non-coding upstream 83128 5382707 ~ 5382924 (+)
G265141 NA non-coding upstream 83573 5382191 ~ 5382479 (+)
G265094 NA non-coding upstream 98786 5360934 ~ 5367266 (+)
G265133 NA non-coding upstream 115139 5350506 ~ 5350913 (+)
G265198 NA non-coding downstream 21295 5490577 ~ 5490806 (+)
G265156 NA non-coding downstream 199620 5668902 ~ 5689574 (+)
G265153 NA non-coding downstream 220934 5690216 ~ 5712916 (+)
G265246 NA non-coding downstream 235811 5705093 ~ 5706882 (+)
G262436 NA other upstream 2751535 2713615 ~ 2714517 (+)
G262423 NA other upstream 3223087 2241408 ~ 2242965 (+)
G262194 NA other upstream 4321045 1139352 ~ 1145007 (+)
G262060 NA other upstream 4755498 710110 ~ 710554 (+)
G261984 NA other upstream 4798670 665800 ~ 667382 (+)
G265391 NA other downstream 444501 5913783 ~ 5919029 (+)
CI01000063_06335618_06338138 HOXB8B other downstream 865996 6335618 ~ 6338283 (+)

Expression


Co-expression Network

Homologous

species gene id symbol gene type chromosome NCBI id location
zebrafish (Danio rerio) XLOC_004736 six3b coding NC_007123.7 CM002896.2 25600685 ~ 25603341 (+)