ENSDARG00000003293


Danio rerio

Features
Gene ID: ENSDARG00000003293
  
Biological name :sox9a
  
Synonyms : sox9a / SRY (sex determining region Y)-box 9a
  
Possible biological names infered from orthology : P48436 / Q04887 / SOX9 / SRY-box 9 / Transcription factor SOX-9
  
Species: Danio rerio
  
Chr. number: 12
Strand: -1
Band:
Gene start: 1947593
Gene end: 1951284
  
Corresponding Affymetrix probe sets: Dr.10460.1.S1_at (Zebrafish Array)   NM_131643_at (Zebrafish Genome Array with custom cdf files)   
  
Cross references: Ensembl peptide - ENSDARP00000006945
Ensembl peptide - ENSDARP00000106978
NCBI entrez gene - 60641     See in Manteia.
RefSeq - NM_131643
RefSeq Peptide - NP_571718
swissprot - F1Q8I8
swissprot - Q9DFH2
ZFIN ID - ZDB-GENE-001103-1
Ensembl - ENSDARG00000003293
  
See expression report in BioGPS
See gene description in Wikigenes
See co-cited genes in PubMed


Ortholog prediction (from Ensembl)
Ortholog nameID Species
 SOX9ENSGALG00000004386Gallus gallus
 SOX9ENSG00000125398Homo sapiens
 Sox9ENSMUSG00000000567Mus musculus


Paralog prediction (from Ensembl)
Paralog nameIDSimilarity(%)
sox9b / SRY (sex determining region Y)-box 9b / SOX8* / P57073* / SRY-box 8*ENSDARG0000004392361
sox10 / SRY (sex determining region Y)-box 10 / Q04888* / P56693* / SRY-box 10* / Transcription factor SOX-10 *ENSDARG0000007746751
sox8a / SRY (sex determining region Y)-box 8a / SOX8* / P57073* / SRY-box 8*ENSDARG0000010530145
sox8b / SRY (sex determining region Y)-box 8b / SOX8* / P57073* / SRY-box 8*ENSDARG0000003778243
sox18 / SRY (sex determining region Y)-box 18 / P43680* / P35713* / SRY-box 18* / Transcription factor SOX-18 *ENSDARG0000005859821
sox17 / SRY (sex determining region Y)-box 17 / Q9H6I2* / SRY-box 17*ENSDARG0000010171720
sox7 / SRY (sex determining region Y)-box 7 / Q9BT81* / P40646* / SRY-box 7* / AC105001.2*ENSDARG0000003012519
sox1b / Q2Z1R2 / SRY (sex determining region Y)-box 1b / SOX1* / P53783* / O00570* / SRY-box 1* / Transcription factor SOX-1 *ENSDARG0000000813118
sox4b / SRY (sex determining region Y)-box 4b / SOX4* / Q06945* / SRY-box 4*ENSDARG0000009883418
sox4a / SRY (sex determining region Y)-box 4a / SOX4* / Q06945* / Q06831* / SRY-box 4* / Transcription factor SOX-4 *ENSDARG0000000458817
sox12 / SRY (sex determining region Y)-box 12 / Q04890* / O15370* / SRY-box 12* / Transcription factor SOX-12 *ENSDARG0000002584717
sox1a / Q6DGL6 / SRY (sex determining region Y)-box 1a / SOX1* / P53783* / O00570* / SRY-box 1* / Transcription factor SOX-1 *ENSDARG0000006986617
sox19b / SRY (sex determining region Y)-box 19bENSDARG0000004026616
sox11a / SRY (sex determining region Y)-box 11a / SOX11* / Q7M6Y2* / P35716* / SRY-box 11* / Transcription factor SOX-11 *ENSDARG0000007781116
sox11b / SRY (sex determining region Y)-box 11b / SOX11* / Q7M6Y2* / P35716* / SRY-box 11* / Transcription factor SOX-11 *ENSDARG0000009574316
sox2 / Q6P0E1 / SRY (sex determining region Y)-box 2 / P48431* / SRY-box 2*ENSDARG0000007091316
P47792 / sox19a / SRY (sex determining region Y)-box 19aENSDARG0000001077015
sox3 / Q6EJB7 / SRY (sex determining region Y)-box 3 / P41225* / SRY-box 3*ENSDARG0000005356915
sox32 / SRY (sex determining region Y)-box 32 / SOX17* / Q9H6I2* / SRY-box 17*ENSDARG0000010059115
sox14 / Q32PP9 / SRY (sex determining region Y)-box 14 / Q04892* / O95416* / SRY-box 14* / Transcription factor SOX-14 *ENSDARG0000007092914


Protein motifs (from Interpro)
Interpro ID Name
 IPR009071  High mobility group box domain
 IPR022151  Sox developmental protein N-terminal
 IPR029548  Transcription factor SOX-9


Gene Ontology (GO)
TypeGO IDTermEv.Code
 biological_processGO:0006355 regulation of transcription, DNA-templated IEA
 biological_processGO:0006357 regulation of transcription by RNA polymerase II IEA
 biological_processGO:0030916 otic vesicle formation IGI
 biological_processGO:0033339 pectoral fin development IMP
 biological_processGO:0035118 embryonic pectoral fin morphogenesis IMP
 biological_processGO:0043049 otic placode formation IGI
 biological_processGO:0048708 astrocyte differentiation IMP
 biological_processGO:0048709 oligodendrocyte differentiation IMP
 biological_processGO:0048839 inner ear development IMP
 biological_processGO:0051216 cartilage development IMP
 biological_processGO:0060536 cartilage morphogenesis IMP
 cellular_componentGO:0005634 nucleus IEA
 cellular_componentGO:0005737 cytoplasm IMP
 molecular_functionGO:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding IEA
 molecular_functionGO:0003677 DNA binding IEA
 molecular_functionGO:0003682 chromatin binding IDA
 molecular_functionGO:0005515 protein binding IPI


Pathways (from Reactome)
Pathway description
Deactivation of the beta-catenin transactivating complex
Transcriptional regulation by RUNX2


Phenotype (from MGI, Zfin or HPO)
IDPhenotypeDefinition Genetic BG
 ZFA:0000051 otic vesicle otic vesicle decreased size , abnormal
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 ZFA:0000095 pharyngeal arch 3-7 skeleton pharyngeal arch 3-7 skeleton quality , abnormal
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 ZFA:0000112 gut gut quality , abnormal
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 ZFA:0000123 liver liver increased size , abnormal
liver quality , abnormal
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 ZFA:0000191 dentary dentary decreased size , abnormal
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 ZFA:0000250 opercle opercle decreased size , abnormal
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 ZFA:0000270 maxilla maxilla decreased size , abnormal
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 ZFA:0000332 coracoid coracoid absent , abnormal
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 ZFA:0000422 retroarticular retroarticular aplastic , abnormal
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 ZFA:0000488 ceratobranchial bone ceratobranchial bone aplastic , abnormal
ceratobranchial bone decreased size , abnormal
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 ZFA:0000578 ceratohyal bone ceratohyal bone aplastic , abnormal
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 ZFA:0000588 statoacoustic (VIII) ganglion statoacoustic (VIII) ganglion anatomical region decreased size , abnormal
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 ZFA:0000657 entopterygoid entopterygoid aplastic , abnormal
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 ZFA:0000672 hyomandibula hyomandibula aplastic , abnormal
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 ZFA:0001094 whole organism whole organism decreased length , abnormal
whole organism lethal (sensu genetics) , abnormal
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 ZFA:0001114 head head circular , abnormal
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 ZFA:0001161 pectoral fin pectoral fin decreased size , abnormal
pectoral fin decreased length , abnormal
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 ZFA:0001205 Meckel s cartilage Meckels cartilage decreased size , abnormal
Meckels cartilage aplastic , abnormal
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 ZFA:0001227 mandibular arch skeleton mandibular arch skeleton morphology , abnormal
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 ZFA:0001239 ceratobranchial 5 bone ceratobranchial 5 bone decreased size , abnormal
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 ZFA:0001272 palatoquadrate arch palatoquadrate arch quality , abnormal
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 ZFA:0001321 neurocranial trabecula neurocranial trabecula aplastic , abnormal
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 ZFA:0001399 palatoquadrate cartilage palatoquadrate cartilage aplastic , abnormal
palatoquadrate cartilage decreased size , abnormal
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 ZFA:0001400 ceratohyal cartilage ceratohyal cartilage decreased size , abnormal
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 ZFA:0001405 ethmoid cartilage ethmoid cartilage aplastic , abnormal
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 ZFA:0001422 hyosymplectic cartilage hyosymplectic cartilage aplastic , abnormal
hyosymplectic cartilage decreased size , abnormal
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 ZFA:0001423 parachordal cartilage parachordal cartilage aplastic , abnormal
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 ZFA:0001425 basal plate cartilage basal plate cartilage aplastic , abnormal
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 ZFA:0001455 scapulocoracoid scapulocoracoid aplastic , abnormal
scapulocoracoid decreased size , abnormal
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 ZFA:0001458 cranial cartilage cranial cartilage aplastic , abnormal
cranial cartilage decreased amount , abnormal
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 ZFA:0001460 pharyngeal arch cartilage pharyngeal arch cartilage absent , abnormal
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 ZFA:0001510 basihyal cartilage basihyal cartilage aplastic , abnormal
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 ZFA:0001516 ceratobranchial cartilage ceratobranchial cartilage aplastic , abnormal
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 ZFA:0001580 neurocranium neurocranium absent , abnormal
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 ZFA:0001612 pharyngeal arch 1 pharyngeal arch 1 decreased size , abnormal
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 ZFA:0001613 pharyngeal arch 3-7 pharyngeal arch 3-7 decreased size , abnormal
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 ZFA:0009084 chondrocyte chondrocyte disorganized , abnormal
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Interacting proteins (from Reactome)
Interactor ID Name Interaction type
 ENSDARG00000040261 runx2a / runt-related transcription factor 2a / RUNX2* / Q08775* / Q13950* / runt related transcription factor 2*  / complex / reaction






 

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