XLOC_006720 (six4a)


Basic Information

Item Value
gene id XLOC_006720
gene name six4a
gene type coding
species zebrafish (Danio rerio)
category of species model fish

Chromosome Information

Item Value
chromosome id NC_007124.7
NCBI id CM002897.2
chromosome length 52186027
location 31636732 ~ 31647323 (-)
genome version GRCz11_2017_zebrafish_Genome

Sequence

>TCONS_00012944
CCACTTACAAAGACACCCGATATCACTCGCATGGCGCACGGGTAACCTGATCAGCTTGGGCAGAAACGAGGCGGGGTGACGGACTAAAGGAATCTGAGGTGAAGAACAAAAACAATGTCTGTTTCCTCTAGTGAAGTGACAGTGCCAGGCGACATCAAAAAGGAAAATGTGAAGTACACGGAGCTTCTCGAGAGCTCCACGGCCAATCAGGAGCACGTCAAACTCCTGACTCTGGACAGTCCGGTGGCCACTGGGATGCGCGTGGGCCAGCAGACCTCTCCACCGGCGCGCAAGATGCCAACTATGGACTCTTTGTTTGCGCACAGTTCGCCCGCAGTAACCGCGACCTCTTTGGCTTTCTCACCGGAGCAGGTTGCGTGTGTTTGCGAGGCGCTTCAGCAGGGGGGCAACGTGGACCGACTCGCCCGTTTTCTGTGGTCTCTCCCGCAGAGCGACTTATTGCGCGGTAACGAGAGTATCCTCCGCGCTCAGGCACTCGTGGCTTTCCACCAGGCGCGCTACCAGGAGCTTTACAGCATCTTGGAGAGCCACAGCTTCAGCCCCTCGTGTCACTCTGCCCTGCAGGACTTATGGTACAAAGCCCGGTACACGGAGGCGGAGAAGGCCCGCGGTAGACCGCTGGGAGCAGTAGATAAATATCGCCTCCGACGAAAGTTTCCCCTACCCCGGACCATCTGGGATGGAGAGGAGACGGTGTACTGCTTCAAAGAGCGCTCCAGGAACGCGCTGAAGGATCTCTATAAGCAGAACCGGTACCCGTCCCCGGCCGAGAAGAGGAATCTGGCCAAGATCACAGGACTGTCCTTGACACAAGTCAGCAACTGGTTCAAAAACAGGAGGCAGCGAGACAGAAACCCATCAGAGACGCAGTCCAAAAGGTGAGCGAGTCGGATGGAAATCACAGTACGGAGGATGAGAGCAGTAAAGGTCAGGAGTCTCTCTCTCCATGCCCGATGTCCACCTGCGCTGATGGGCCAGTGAGTAACACAGCTCTGCCTCTCTGCTCCGGCTCTCTGGACGCCGGAGTGATCGTCCAGCAGGTTGCAGACAGCAGGACCTCTATCTCTCCACCCTCCGTCATCTTCAACGGAGTCTCAGTTCACTCACCTGCCTCTGTTTTCCACAACGGCACCCCTTCATTTCTCTCCTCCACGGGACACGTCTTGTTCAGTGGCATGAATTTGGGACTCCAGTCTTTGGCTTGCAGACCTACAGATGTGGAGATGGACGGTGCAGCACAGGAGAAAGGGGGAACGGCAGACCCTGCACTGGCCTACTCTTCATTTCATTGCAGTGTCAATGGGACGGATGTAGAGGTGAAAGAAGAAGATTTGAGGAAGGACGTTTCGGTGCAGGACCAAGCACCGTCTATTGGTTCAGCATTCAGCATCACTCCATCTAATGGCTTGCAGATTGATAGTTATAGTTTGGTTACTGAAGGAAACAAGGTTGTACTTCCCTCCCTGCAACTCACAGTATCTTCTTCACCCTCATCAGTCACACAGGGTGTTGTTGACTGCAGTTCTCCAGTGTGTCAGGAGCGGCTCCAGCTCACCTCTTTGGAGCCCAGCAGCACACTCTACAGCCTGGGCAACATTCACACATTGTCTGCCGTCAAGAAGGAGCCACTGGAGCCTCCTGGAGGATTCCTTTACCACCTGGGTTACTCATCTGACCCCACGCACAGCTCGCCCTTACTGGCCCAAACGGACCTGCCCACAGAGTTCAGAGGTCACACTGACCACATGACCTCCAGCGTAAATGGAGACTTCCTATGTGCTGTTTCTGAGGGAGGAAAgggagaaatggaggaagaagagGAAAAACAACTGACAAAACTAAAAACTGTGCATTTAGAGGAAGAGATGACCGACCTTTGAACTTAAGAGGAGAAGAAGGTAAAATACTGAAAATCATTATTTGGAAAACATTAACTCAAACATTATTTTGGATTATTGATTGagattttttatgttttcagaCTCTTGTTTTGTGTATTGTAAAGTATTAAATTATTTTGGTGAA
>TCONS_00012945
AATGAACTAAGGGGTAGGGCTTGTCGTTTTGTTAATGTCTGTGTCGTTTGAAGTGTCTGTTGTATAAGCAGTCTGAGTCTGTTAAGCCCAGAGTAAACACTCAGCAGCGGACAAAAGCCTCGAATGAGATCTCACCTATAGCGCAGGTGAGCCGCGGCAGCGCGTCACGGCtgattgacagctttatttcAATGGATTCGCCTTGAAGCTAAGATCGCCCCGCCCCTTTTGAAATTCCGAGCAGCCAATCATGTGCGTCCCTCCAAACTATCGGACTGAGAACAAGTCACGCTGCTGGAGCGAAAGGGGAAAGCTATCCACTTACAAAGACACCCGATATCACTCGCATGGCGCACGGGTAACCTGATCAGCTTGGGCAGAAACGAGGCGGGGTGACGGACTAAAGGAATCTGAGGTGAAGAACAAAAACAATGTCTGTTTCCTCTAGTGAAGTGACAGTGCCAGGCGACATCAAAAAGGAAAATGTGAAGTACACGGAGCTTCTCGAGAGCTCCACGGCCAATCAGGAGCACGTCAAACTCCTGACTCTGGACAGTCCGGTGGCCACTGGGATGCGCGTGGGCCAGCAGACCTCTCCACCGGCGCGCAAGATGCCAACTATGGACTCTTTGTTTGCGCACAGTTCGCCCGCAGTAACCGCGACCTCTTTGGCTTTCTCACCGGAGCAGGTTGCGTGTGTTTGCGAGGCGCTTCAGCAGGGGGGCAACGTGGACCGACTCGCCCGTTTTCTGTGGTCTCTCCCGCAGAGCGACTTATTGCGCGGTAACGAGAGTATCCTCCGCGCTCAGGCACTCGTGGCTTTCCACCAGGCGCGCTACCAGGAGCTTTACAGCATCTTGGAGAGCCACAGCTTCAGCCCCTCGTGTCACTCTGCCCTGCAGGACTTATGGTACAAAGCCCGGTACACGGAGGCGGAGAAGGCCCGCGGTAGACCGCTGGGAGCAGTAGATAAATATCGCCTCCGACGAAAGTTTCCCCTACCCCGGACCATCTGGGATGGAGAGGAGACGGTGTACTGCTTCAAAGAGCGCTCCAGGAACGCGCTGAAGGATCTCTATAAGCAGAACCGGTACCCGTCCCCGGCCGAGAAGAGGAATCTGGCCAAGATCACAGGACTGTCCTTGACACAAGTCAGCAACTGGTTCAAAAACAGGAGGCAGCGAGACAGAAACCCATCAGAGACGCAGTCCAAAAGCGAGTCGGATGGAAATCACAGTACGGAGGATGAGAGCAGTAAAGGTCAGGAGTCTCTCTCTCCATGCCCGATGTCCACCTGCGCTGATGGGCCAGTGAGTAACACAGCTCTGCCTCTCTGCTCCGGCTCTCTGGACGCCGGAGTGATCGTCCAGCAGGTTGCAGACAGCAGGACCTCTATCTCTCCACCCTCCGTCATCTTCAACGGAGTCTCAGTTCACTCACCTGCCTCTGTTTTCCACAACGGCACCCCTTCATTTCTCTCCTCCACGGGACACGTCTTGTTCAGTGGCATGAATTTGGGACTCCAGTCTTTGGCTTGCAGACCTACAGATGTGGAGATGGACGGTGCAGCACAGGAGAAAGGGGGAACGGCAGACCCTGCACTGGCCTACTCTTCATTTCATTGCAGTGTCAATGGGACGGATGTAGAGGTGAAAGAAGAAGATTTGAGGAAGGACGTTTCGGTGCAGGACCAAGCACCGTCTATTGGTTCAGCATTCAGCATCACTCCATCTAATGGCTTGCAGATTGATAGTTATAGTTTGGTTACTGAAGGAAACAAGGTTGTACTTCCCTCCCTGCAACTCACAGTATCTTCTTCACCCTCATCAGTCACACAGGGTGTTGTTGACTGCAGTTCTCCAGTGTGTCAGGAGCGGCTCCAGCTCACCTCTTTGGAGCCCAGCAGCACACTCTACAGCCTGGGCAACATTCACACATTGTCTGCCGTCAAGAAGGAGCCACTGGAGCCTCCTGGAGGATTCCTTTACCACCTGGGTTACTCATCTGACCCCACGCACAGCTCGCCCTTACTGGCCCAAACGGACCTGCCCACAGAGTTCAGAGGTCACACTGACCACATGACCTCCAGCGTAAATGGAGACTTCCTATGTGCTGTTTCTGAGGGAGGAAAgggagaaatggaggaagaagagGAAAAACAACTGACAAAACTAAAAACTGTGCATTTAGAGGAAGAGATGACCGACCTTTGAACTTAAGAGGAGAAGAAGGTAAAATACTGAAAATCATTATTTGGAAAACATTAACTCAAACATTATTTTGGATTATTGATTGagattttttatgttttcagaCTCTTGTTTTGTGTATTGTAAAGTATTAAATTATTTTGGTGAA

Function

symbol description
six4a Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to act upstream of or within regulation of transcription, DNA-templated. Predicted to be part of transcription regulator complex. Predicted to be active in nucleus. Is expressed in inner ear and trunk musculature. Orthologous to human SIX4 (SIX homeobox 4).

GO:

id name namespace
GO:0006355 regulation of transcription, DNA-templated biological_process
GO:0048856 anatomical structure development biological_process
GO:0045892 negative regulation of transcription, DNA-templated biological_process
GO:0005634 nucleus cellular_component
GO:0005667 transcription regulator complex cellular_component
GO:0043565 sequence-specific DNA binding molecular_function
GO:0003677 DNA binding 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: NA

ZFIN:

id description
ZDB-GENE-010201-2 Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to act upstream of or within regulation of transcription, DNA-templated. Predicted to be part of transcription regulator complex. Predicted to be active in nucleus. Is expressed in inner ear and trunk musculature. Orthologous to human SIX4 (SIX homeobox 4).

Ensembl:

ensembl_id ENSDARG00000004695

RNA

RNA id representative length rna type GC content exon number start site end site
TCONS_00012944 False 2046 nonsense_mediated_decay 0.52 3 31636732 31647006
TCONS_00012945 True 2358 mRNA 0.52 3 31636732 31647323

Neighbor

gene id symbol gene type direction distance location
XLOC_006719 six1a coding downstream 14537 31619961 ~ 31622195 (-)
XLOC_006718 BX537123.2 coding downstream 57168 31579448 ~ 31579564 (-)
XLOC_006717 dhrs7 coding downstream 92367 31536709 ~ 31544365 (-)
XLOC_006716 rtn1a coding downstream 166293 31424586 ~ 31470439 (-)
XLOC_006715 pgam1a coding downstream 238745 31393192 ~ 31397987 (-)
XLOC_006721 trmt5 coding upstream 34665 31681988 ~ 31687925 (-)
XLOC_006722 BX537123.1 coding upstream 47608 31694931 ~ 31695047 (-)
XLOC_006723 NA coding upstream 152709 31800032 ~ 31800406 (-)
XLOC_006724 sertad4 coding upstream 158501 31805824 ~ 31829786 (-)
XLOC_006725 syt14a coding upstream 196688 31844011 ~ 31888487 (-)
XLOC_006471 BX537274.2 misc downstream 21371827 10264741 ~ 10264905 (-)
XLOC_006338 rn7sk misc downstream 30810507 825904 ~ 826225 (-)
XLOC_006710 CR931802.1 non-coding downstream 431539 31193485 ~ 31205193 (-)
XLOC_006708 CR931802.2 non-coding downstream 509686 31126449 ~ 31127046 (-)
XLOC_006707 NA non-coding downstream 513894 31102907 ~ 31122838 (-)
XLOC_006706 NA non-coding downstream 544332 31089586 ~ 31092400 (-)
XLOC_006727 NA non-coding upstream 302834 31950157 ~ 31955798 (-)
XLOC_006728 NA non-coding upstream 335738 31983061 ~ 31999012 (-)
XLOC_006729 BX470107.1 non-coding upstream 376165 32023488 ~ 32063016 (-)

Expression


Co-expression Network

Homologous

species gene id symbol gene type chromosome NCBI id location
grasscarp (Ctenopharyngodon idella) CI01000012_08464015_08470633 NA coding CI01000012 null 8464015 ~ 8470764 (+)