XLOC_005979 (msx3)


Basic Information

Item Value
gene id XLOC_005979
gene name msx3
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 24662238 ~ 24664668 (+)
genome version GRCz11_2017_zebrafish_Genome

Sequence

>TCONS_00011812
GCGAGTGCGCTCTGCTTGGAGAGCGAGGCAAGCGTCGCAAAAGCGCGACGGCAGAAGGGAAGCGCTGCTGGACCAGAGTACAGTTCAGGACGACTCACATATTCTTGTTGTATGGCCCCTTTATCATCTATGATGAATTCTGAAGGGCCACTCTCCCAAGAAGGAAAACTACAGGAGCGCAAAAGCGCGGACAAAGAGGATGCTCAATCCAACGATAAAGCGGCTGTCAAAGGATGTAAAGGCAAAGCGCTGAGTCTCCCGTTCAGTGTGGAATCTTTAATATCAGACAGAACAAGCTCACGGACTTTATACACGTCTTCTGAAGCTGGTATTATATCTCCGACATCCGGTGCGGATGAGCGGCTGAAGCTCTCGCCCATGGCTCTTTACGCAGATAGGAAGATCCCAGTGGAGAGCGTCTCCAACCTCTCCGACTGCAAGAGAGGGGATATGGAAGAACTAAGTGACAAGGGACAGTCCGGCTGGTTTCAGACAACCTCGTACACTTCTCCGCCAAgGCATTCAAGTCCACCCCCCTGTACCCTCAGAAAGCACAAGAACAACCGAAAACCGCGGACCCCGTTTACCACCTCGCAGTTGCTCGCTTTGGAGAGAAAATTTCGTCAAAAACAGTATCTTTCTATTGCAGAGAGAGCGGAATTTTCCAATTCACTCAACCTCACAGAGACTCAAGTTAAAATCTGGTTTCAAAACAGACGGGCGAAGGCAAAAAGACTCCAGGAGGCCGAACTAGAGAAACTGAAACTTGCAACCAAGCCGTTATTACCTGCGTTCGCCTTTCCGTTCCCACTCGGAACACATGTTGGTTCTCCACCACTCTACGGACCGTCCAGCTCCTTTCCCAGACCTGCCTTACCAGTCCCGGGACTTTTCGGTGGGCCAGTGACCTACGGAATGTATTATTTGTCTTAACAGACTGAAGCACGTCCTTCAATTCACCGTCTGTAACTGCTGCAATTCTGCCAGTCAAAAGACGTGTGAAATTGCAAATATGTTTCCTTTATAGAACTTAAGCAAatgcaaaaatttaaaataaattatttttgtaatcCACACGGTTTATTCCAAAAGTAATAGTACCCAAATTGGTTTTAAAAGTGCAATGAATATTCCCCTTAATACAGAAGACTTTATGCTGTATTATACAAGTATAGCCTACAGACACACCGCTATGTGAATAATTGTCTTAGTCTCAGAGAAAATATTTCCAGTAGATTATTTCAAGGGCACAGCCGATCTAGAAAGTTTCTAGAGCAGCATCATTTGTTGATGTGTGATGCGAAAATAAACTCCTGGTTTGTGCCAGTTCCAAAAAGCTCTTAAAGAAGACcttataattactatttttttttaaattaaagtgctTGTTTCGACTGGCAGCAGAATAGGCCTATAccgtaaaaataaaagttttactgTGTCATTGCTACTTTCCATAGGTCTGCCCTAATTGGGGCCTAAATGGATTGTAAGAGccttttttaaattaatccaTGTATTTTCACTCAAACCAAATATTTTGTAGAATATTACAAAGATTGTGCTCAGATATCAAAATTAGCAAATTCTCTACTGCCAATCTggttacttgtttttatttctgcCCGCTATTAGTTTCAGATATTCGATTTGTTATTTGGTTGGTCTTTATTGAATATGATCAACGAGAAACAGCATCTTCAATTACTCTATACTTTTTCTTCCCAAACCTTTTGGGACACAGAGTATTTTGGCCTGTGTTTTTTGATTTTCGCCTGTTTAGCCATAATCCCTTCAGTAGACTACATGTATGCTAGTTTGCTAGGTTGTAAGAATAATgtctagatttttttattattgtaaatacacGTATATATTACAGATTTTGCATTCCCTttgaacaaaaatacaaacagaaTTGCTGATATTTatacactgtttacatttatcttctgtaaattattgtatattttatatgtatatacaaattAGAAATAATcttttgcattaaaataaatcttCACAGAA

Function

symbol description
msx3 Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II transcription regulatory region sequence-specific DNA binding activity. Acts upstream of or within otic placode formation. Predicted to be active in nucleus. Is expressed in several structures, including fin bud; germ ring; immature eye; median fin fold; and nervous system.

GO:

id name namespace
GO:0006355 regulation of transcription, DNA-templated biological_process
GO:0043049 otic placode formation biological_process
GO:0007275 multicellular organism development biological_process
GO:0048598 embryonic morphogenesis biological_process
GO:0005634 nucleus cellular_component
GO:0043565 sequence-specific DNA binding molecular_function
GO:0003677 DNA binding molecular_function
GO:0000977 RNA polymerase II 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-980526-306 Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II transcription regulatory region sequence-specific DNA binding activity. Acts upstream of or within otic placode formation. Predicted to be active in nucleus. Is expressed in several structures, including fin bud; germ ring; immature eye; median fin fold; and nervous system.

Ensembl:

ensembl_id ENSDARG00000015674

RNA

RNA id representative length rna type GC content exon number start site end site
TCONS_00011812 True 2028 mRNA 0.40 2 24662238 24664668

Neighbor

gene id symbol gene type direction distance location
XLOC_005978 NA coding upstream 12299 24597665 ~ 24649939 (+)
XLOC_005977 fuom coding upstream 75755 24584401 ~ 24586483 (+)
XLOC_005976 echs1 coding upstream 80002 24579108 ~ 24582236 (+)
XLOC_005975 NA coding upstream 89310 24570620 ~ 24572928 (+)
XLOC_005974 lgalslb coding upstream 108210 24552254 ~ 24554028 (+)
XLOC_005980 adam8a coding downstream 6813 24671481 ~ 24679636 (+)
XLOC_005981 zgc:66426 coding downstream 15006 24679674 ~ 24688122 (+)
XLOC_005982 cfap43 coding downstream 53212 24717880 ~ 24743151 (+)
XLOC_005983 col17a1b coding downstream 85410 24750078 ~ 24779692 (+)
XLOC_005984 AL929005.1 coding downstream 164085 24828753 ~ 24828869 (+)
XLOC_005962 CR352246.1 non-coding upstream 840938 23821186 ~ 23821300 (+)
XLOC_005959 NA non-coding upstream 1251728 23388493 ~ 23410510 (+)
XLOC_005957 CR356222.1 non-coding upstream 1421661 23227531 ~ 23240577 (+)
XLOC_005997 BX530079.1 non-coding downstream 779316 25443984 ~ 25444523 (+)
XLOC_006005 NA non-coding downstream 1105331 25769999 ~ 25782811 (+)
XLOC_006007 NA non-coding downstream 1279611 25944279 ~ 25961369 (+)
XLOC_006008 NA non-coding downstream 1301059 25965727 ~ 25983365 (+)

Expression


Co-expression Network

Homologous

species gene id symbol gene type chromosome NCBI id location
grasscarp (Ctenopharyngodon idella) CI01000012_12540676_12541954 MSX3 coding CI01000012 null 12540232 ~ 12542559 (-)