six1a (six1,six1b,LOC108263091,LOC108414064,LOC108257556,LOC107697302,LOC107589069,LOC108434988)


Basic Information

Item Value
gene id six1a
gene name six1,six1b,LOC108263091,LOC108414064,LOC108257556,LOC107697302,LOC107589069,LOC108434988
gene type coding
species striped catfish (Pangasianodon hypophthalmus)
category of species economic fish

Chromosome Information

Item Value
chromosome id NC_047597.1
NCBI id CM018543.1
chromosome length 33776708
location 33385114 ~ 33387819 (-)
genome version GENO_Phyp_1.0_2019_striped_catfish_Genome

Sequence

>XM_026939310.2
taaAGGGGGTCTCCGGTTTCAGGATCCGCCCTCCAGTGTAGAAGTGGATCTGCACACTTTCGTTCTGCTCAGTCTGCTCAGAGCAAATCGactaaaaatcacacacacacacacacacacacacacacacacacacacacacacacgcgcacacacacactacatcgaAGTCCAAAACCAGTTTAAATCAGCGATAGACATcactgcaggaggagaaaatCACTTCTAAGCGCTTGAAGGAGTTCAGAGGTTTCACATTCAGGAAGTTCATCATTTCTTCTAACCTAAAGACCCttcagttttctgtaaatattgtaaacgGAGATGTTTGGATAGTTGTGATGTTGGAAGAATGTCTAATTTAGGAGGAGCCTTGATTCTGAATCACATCATCCTGAAGGAATTGCTCATGTCTGGAGATTTGTATCATTTATCTGGAGCTCTAGTTgtccttttcttttaattttccaggatttttttcttcttagaaGCACTGATTTGGAAATTTGATTGCTCTTCTTGCTCTTCTCGGAATCTTTCTGACTGGCGCTCCACTGGAAACTCCAAATCCCCTGAAGGAACTGAGAGAGCTTTGTTCCAGTGTTTGGAGgagctgctgctctgctctgctggGGGAAAAGTCCAACGGTTCCTTCGCCTCTGTTGAGAAGAACAGCTTCATGTTCTGGAGCTTGTGGGTTTGTGAAGATCTGCCCAATTCGGAGTCACTGATCTTCTCAGGGTCTCAGAGGAGCTTCGGTTTTGGGGATGGTTATCGTACCGCGGTTGGATATCGCGCTGTAGAGTAGAGTATCATCACCACGATGTCGACTTCACCGAGCTTCGGCTTCACGCAGGAGCaggtggcgtgtgtgtgtgaggtcctTCAGCAGGGCGGAGATCTCGAGCGACTCGGTCGCTTCCTGTGGTCGCTTCCGGCGTGCGACCGCCTGCACAAGAACGAGTCGGTGCTCCAGGCCAAAGCGGCGGTGGCTTTCCACCGAGGAGACTTCCGCGAGCTCTACCGGATCCTCGAGAGCCACCAGTTCTCCGCGCAGAACCACGCCGGCCTGCAGCAGCTGTGGCTCAGGGCGCACTACGCGGAGGCGGAGAGGCTGCGCGGCCGCCCGCTCGGGGCCGTGGGGAAGTACCGCGTGCGACGGAAGTTCCCGCTGCCGCGCACCATCTGGGACGGAGAAGAGACGAGCTACTGCTTCAAGGAGAAGTCGCGCTCCGTGCTGCGGGACTGGTACACACACAACCCCTACCCGTCCCCGCGAGAGAAGCGGCAGCTGGCCGACGCCACCGGACTGACCACCACACAGGTCAGCAACTGGTTCAAGAACCGCAGACAGAGAGACCGAGCCGCCGAGGCCAAGGACAGAGACAGTGGAGATGTCAGCACTAATAAACCTCTTCAGCTCTGCAGCtctgaggaggaggatgaagagcagCTCTCTCCACCaagaagccccgcccccagacCAACCCCAAACCCCGCCCATCGACTGCTTCACCAAGTCAACCCGAACCTGAGACCCACCAGGAACCTGAACCCGGACCCACACGGTACCCAGACCCGGTACACACACGAGCCGCTGCTAAGAGCCTTAACAGAGACCCTCAGTGAGCCGGGACCttaaagcttattattattattattagtattattattatgtattacagCTTGtgtcactgcaacacacacacacacacacacacacacacacacggtattTTGCACTCCAGTTGATTGTGTggattttataaaaa
>XM_034301294.1
taaAGGGGGTCTCCGGTTTCAGGATCCGCCCTCCAGTGTAGAAGTGGATCTGCACACTTTCGTTCTGCTCAGTCTGCTCAGAGCAAATCGactaaaaatcacacacacacacacacacacacacacacacacacacacacacacacgcgcacacacacactacatcgaAGTCCAAAACCAGTTTAAATCAGCGATAGACATcactgcaggaggagaaaatCACTTCTAAGCGCTTGAAGGAGTTCAGAGGTTTCACATTCAGGAAGTTCATCATTTCTTCTAACCTAAAGACCCttcagttttctgtaaatattgtaaacgGAGATGTTTGGATAGTTGTGATGTTGGAAGAATGTCTAATTTAGGAGGAGCCTTGATTCTGAATCACATCATCCTGAAGGAATTGCTCATGTCTGGAGATTTGTATCATTTATCTGGAGCTCTAGTTgtccttttcttttaattttccaggatttttttcttcttagaaGCACTGATTTGGAAATTTGATTGCTCTTCTTGCTCTTCTCGGAATCTTTCTGACTGGCGCTCCACTGGAAACTCCAAATCCCCTGAAGGAACTGAGAGAGCTTTGTTCCAGTGTTTGGAGgagctgctgctctgctctgctggGGGAAAAGTCCAACGGTTCCTTCGCCTCTGTTGAGAAGAACAGCTTCATGTTCTGGAGCTTGTGGGTTTGTGAAGATCTGCCCAATTCGGAGTCACTGATCTTCTCAGGGTCTCAGAGGAGCTTCGGTTTTGGGGATGGTTATCGTACCGCGGTTGGATATCGCGCTGTAGAGTAGAGTATCATCACCACGATGTCGACTTCACCGAGCTTCGGCTTCACGCAGGAGCaggtggcgtgtgtgtgtgaggtcctTCAGCAGGGCGGAGATCTCGAGCGACTCGGTCGCTTCCTGTGGTCGCTTCCGGCGTGCGACCGCCTGCACAAGAACGAGTCGGTGCTCCAGGCCAAAGCGGCGGTGGCTTTCCACCGAGGAGACTTCCGCGAGCTCTACCGGATCCTCGAGAGCCACCAGTTCTCCGCGCAGAACCACGCCGGCCTGCAGCAGCTGTGGCTCAGGGCGCACTACGCGGAGGCGGAGAGGCTGCGCGGCCGCCCGCTCGGGGCCGTGGGGAAGTACCGCGTGCGACGGAAGTTCCCGCTGCCGCGCACCATCTGGGACGGAGAAGAGACGAGCTACTGCTTCAAGGAGAAGTCGCGCTCCGTGCTGCGGGACTGGTACACACACAACCCCTACCCGTCCCCGCGAGAGAAGCGGCAGCTGGCCGACGCCACCGGACTGACCACCACACAGGTCAGCAACTGGTTCAAGAACCGCAGACAGAGAGACCGAGCCGCCGAGGCCAAGGACAGTGGAGATGTCAGCACTAATAAACCTCTTCAGCTCTGCAGCtctgaggaggaggatgaagagcagCTCTCTCCACCaagaagccccgcccccagacCAACCCCAAACCCCGCCCATCGACTGCTTCACCAAGTCAACCCGAACCTGAGACCCACCAGGAACCTGAACCCGGACCCACACGGTACCCAGACCCGGTACACACACGAGCCGCTGCTAAGAGCCTTAACAGAGACCCTCAGTGAGCCGGGACCttaaagcttattattattattattagtattattattatgtattacagCTTGtgtcactgcaacacacacacacacacacacacacacacacacggtattTTGCACTCCAGTTGATTGTGTggattttataaaaa

Function

symbol description
six1b 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 several processes, including muscle organ development; nervous system development; and regulation of skeletal muscle cell proliferation. Predicted to be located in cytoplasm. Predicted to be part of transcription regulator complex. Predicted to be active in nucleus. Is expressed in several structures, including ectoderm; musculature system; nervous system; pharyngeal arch; and trunk. Human ortholog(s) of this gene implicated in autosomal dominant nonsyndromic deafness 23; branchiootorenal syndrome; and nephroblastoma. Orthologous to human SIX1 (SIX homeobox 1).
six1 Enables DNA-binding transcription activator activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Involved in positive regulation of transcription by RNA polymerase II and protein localization to nucleus. Located in nucleolus and nucleoplasm. Implicated in autosomal dominant nonsyndromic deafness 23; branchiootorenal syndrome; and nephroblastoma. Biomarker of breast cancer; hepatocellular carcinoma; nephroblastoma; neurilemmoma; and ovarian carcinoma.

NR:

description
sine oculis homeobox like 1

GO:

id name namespace
GO:0051146 striated muscle cell differentiation biological_process
GO:0043282 pharyngeal muscle development biological_process
GO:0006915 apoptotic process biological_process
GO:0006355 regulation of transcription, DNA-templated biological_process
GO:0006357 regulation of transcription by RNA polymerase II biological_process
GO:2000980 regulation of inner ear receptor cell differentiation biological_process
GO:0002074 extraocular skeletal muscle development biological_process
GO:0048839 inner ear development biological_process
GO:0021984 adenohypophysis development biological_process
GO:0048935 peripheral nervous system neuron development biological_process
GO:0005634 nucleus cellular_component
GO:0005737 cytoplasm cellular_component
GO:0043565 sequence-specific DNA binding molecular_function
GO:0003700 DNA-binding transcription factor activity 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:

id description
K15614 SIX1; homeobox protein SIX1

RNA

RNA id representative length rna type GC content exon number start site end site
XM_026939310.2 True 1773 mRNA 0.53 2 33385114 33387819
XM_034301294.1 False 1767 mRNA 0.53 2 33385114 33387819

Neighbor

gene id symbol gene type direction distance location
dhrs7 dhrs7 coding downstream 23249 33357030 ~ 33361865 (-)
prkcha prkch,LOC107707065,LOC107675581,LOC107757130 coding downstream 48319 33329005 ~ 33336795 (-)
hif1aa hif1a coding downstream 63451 33306312 ~ 33321663 (-)
LOC113542112 NA coding downstream 91771 33286801 ~ 33293343 (-)
osr1 osr1,LOC108440809,LOC107548611,LOC107588719,LOC107668777,LOC107757107,LOC107675531 coding downstream 280871 33095656 ~ 33104243 (-)
six4a NA coding upstream 1674 33389493 ~ 33403724 (-)
tdrd9 tdrd9,LOC104966444 coding upstream 80204 33468023 ~ 33484082 (-)
kif15 kif15 coding upstream 97194 33485013 ~ 33505325 (-)
tacc3 tacc3,LOC108440911 coding upstream 119275 33507094 ~ 33516686 (-)
LOC113541868 NA coding upstream 200074 33587893 ~ 33592807 (-)
G57224 NA non-coding downstream 9613 33369860 ~ 33375501 (-)
G57300 NA non-coding downstream 20567 33363604 ~ 33364547 (-)
G57294 NA non-coding downstream 24423 33326080 ~ 33360691 (-)
G57292 NA non-coding downstream 79596 33303570 ~ 33305518 (-)
G57290 NA non-coding downstream 86801 33296819 ~ 33298313 (-)
G57223 NA non-coding upstream 22729 33410548 ~ 33411453 (-)
G57317 NA non-coding upstream 34005 33421824 ~ 33422474 (-)
G57220 NA non-coding upstream 77880 33465699 ~ 33467307 (-)
G57335 NA non-coding upstream 147659 33535478 ~ 33535975 (-)
G57354 NA non-coding upstream 183591 33571410 ~ 33572419 (-)
slc38a6 slc38a6 other downstream 40278 33337403 ~ 33344836 (-)
G57210 NA other downstream 285542 33019278 ~ 33099572 (-)
G57124 pdss2,LOC102782659 other downstream 656373 32715827 ~ 32728741 (-)
slc66a3 pqlc3 other downstream 723502 32653836 ~ 32661612 (-)
ndufaf1 ndufaf1,LOC107588570 other downstream 995970 32374336 ~ 32389144 (-)
lrrc9 LOC108262921 other upstream 35845 33423664 ~ 33442815 (-)
G57322 NA other upstream 67403 33455222 ~ 33462342 (-)
mycla LOC108263077 other upstream 92529 33480348 ~ 33524819 (-)
trnag-gcc_5 NA other upstream 142108 33529927 ~ 33529997 (-)
LOC113542143 LOC108263078 other upstream 174959 33562778 ~ 33570236 (-)

Expression


Co-expression Network