Gene: SIX4

Basic information

Tag Content
Uniprot ID Q9UIU6; Q4QQH5; Q4V764;
Entrez ID 51804
Genbank protein ID AAH98282.1; AAI01935.1; EAW80786.1; AAH99722.1; AAH98135.1; BAA86223.1;
Genbank nucleotide ID NM_017420.4
Ensembl protein ID ENSP00000216513
Ensembl nucleotide ID ENSG00000100625
Gene name Homeobox protein SIX4
Gene symbol SIX4
Organism Homo sapiens
NCBI taxa ID 9606
Cleft type
Developmental stage
Data sources Homology search
Reference
Functional description Transcriptional regulator which can act as both a transcriptional repressor and activator by binding a DNA sequence on these target genes and is involved in processes like cell differentiation, cell migration and cell survival. Transactivates gene expression by binding a 5'-[CAT]A[CT][CT][CTG]GA[GAT]-3' motif present in the Trex site and a 5'-TCA[AG][AG]TTNC-3' motif present in the MEF3 site of the muscle-specific genes enhancer. Acts cooperatively with EYA proteins to transactivate their target genes through interaction and nuclear translocation of EYA protein. Acts synergistically with SIX1 to regulate target genes involved in formation of various organs, including muscle, kidney, gonad, ganglia, olfactory epithelium and cranial skeleton. Plays a role in several important steps of muscle development. Controls the genesis of hypaxial myogenic progenitors in the dermomyotome by transactivating PAX3 and the delamination and migration of the hypaxial precursors from the ventral lip to the limb buds through the transactivation of PAX3, MET and LBX1. Controls myoblast determination by transactivating MYF5, MYOD1 and MYF6. Controls somitic differentiation in myocyte through MYOG transactivation. Plays a role in synaptogenesis and sarcomere organization by participating in myofiber specialization during embryogenesis by activating fast muscle program in the primary myotome resulting in an up-regulation of fast muscle genes, including ATP2A1, MYL1 and TNNT3. Simultaneously, is also able to activate inhibitors of slow muscle genes, such as SOX6, HRASLS, and HDAC4, thereby restricting the activation of the slow muscle genes. During muscle regeneration, negatively regulates differentiation of muscle satellite cells through down-regulation of MYOG expression. During kidney development regulates the early stages of metanephros development and ureteric bud formation through regulation of GDNF, SALL1, PAX8 and PAX2 expression. Plays a role in gonad development by regulating both testis determination and size determination. In gonadal sex determination, transactivates ZFPM2 by binding a MEF3 consensus sequence, resulting in SRY up-regulation. In gonadal size determination, transactivates NR5A1 by binding a MEF3 consensus sequence resulting in gonadal precursor cell formation regulation. During olfactory development mediates the specification and patterning of olfactory placode through fibroblast growth factor and BMP4 signaling pathways and also regulates epithelial cell proliferation during placode formation. Promotes survival of sensory neurons during early trigeminal gangliogenesis. In the developing dorsal root ganglia, up-regulates SLC12A2 transcription. Regulates early thymus/parathyroid organogenesis through regulation of GCM2 and FOXN1 expression. Forms gustatory papillae during development of the tongue. Also plays a role during embryonic cranial skeleton morphogenesis.
Sequence
MSSSSPTGQI ASAADIKQEN GMESASEGQE AHREVAGGAA VGLSPPAPAP FPLEPGDAAT 60
AAARVSGEEG AVAAAAAGAA ADQVQLHSEL LGRHHHAAAA AAQTPLAFSP DHVACVCEAL 120
QQGGNLDRLA RFLWSLPQSD LLRGNESLLK ARALVAFHQG IYPELYSILE SHSFESANHP 180
LLQQLWYKAR YTEAERARGR PLGAVDKYRL RRKFPLPRTI WDGEETVYCF KEKSRNALKE 240
LYKQNRYPSP AEKRHLAKIT GLSLTQVSNW FKNRRQRDRN PSETQSKSES DGNPSTEDES 300
SKGHEDLSPH PLSSSSDGIT NLSLSSHMEP VYMQQIGNAK ISLSSSGVLL NGSLVPASTS 360
PVFLNGNSFI QGPSGVILNG LNVGNTQAVA LNPPKMSSNI VSNGISMTDI LGSTSQDVKE 420
FKVLQSSANS ATTTSYSPSV PVSFPGLIPS TEVKREGIQT VASQDGGSVV TFTTPVQINQ 480
YGIVQIPNSG ANSQFLNGSI GFSPLQLPPV SVAASQGNIS VSSSTSDGST FTSESTTVQQ 540
GKVFLSSLAP SAVVYTVPNT GQTIGSVKQE GLERSLVFSQ LMPVNQNAQV NANLSSENIS 600
GSGLHPLASS LVNVSPTHNF SLSPSTLLNP TELNRDIADS QPMSAPVASK STVTSVSNTN 660
YATLQNCSLI TGQDLLSVPM TQAALGEIVP TAEDQVGHPS PAVHQDFVQE HRLVLQSVAN 720
MKENFLSNSE SKATSSLMML DSKSKYVLDG MVDTVCEDLE TDKKELAKLQ TVQLDEDMQD 780
L 781

Abbreviation :
CLO : cleft lip only. CPO : cleft palate only. CLP : cleft lip and palate. CL/P : cleft lip with/without cleft palate.
For humans: CL/P, CLO, CPO, and CLP. For mice: CLO, CLP, and CPO.

Gene expression information

Gene expression in different tissues (GTEx V7)

  

Gene expression in different tissues (ENCODE)

  

Protein structural annotations

3D structure in PDB database

There is no related protein structure for this gene.

Protein disorder information

Orthologous information

Relation Gene symbol Entrez ID UniProt ID Cleft type Developmental stage Species Evidence Details
1:1 orthologSIX4490720F6XRS2Canis lupus familiarisPredictionMore>>
1:1 orthologSIX4102173941A0A452EBD2Capra hircusPredictionMore>>
1:1 orthologSIX451804Q9UIU6Homo sapiensPredictionMore>>
1:1 orthologSix420474Q61321CPOMus musculusPublicationMore>>
1:1 orthologSIX4452953K7A7J5Pan troglodytesPredictionMore>>
1:1 orthologSIX4F1SRW3Sus scrofaPredictionMore>>
1:1 orthologSix4299138D3ZAJ7Rattus norvegicusPredictionMore>>

Other genetic variants/mutations

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Disease or phenotype associated information

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Gene Ontology (GO)/biological pathways

GO:Molecular Function

GO ID GO Term Evidence
GO:0000976 transcription regulatory region sequence-specific DNA bindingIBA
GO:0000978 RNA polymerase II cis-regulatory region sequence-specific DNA bindingIEA
GO:0000981 DNA-binding transcription factor activity, RNA polymerase II-specificISA
GO:0000981 DNA-binding transcription factor activity, RNA polymerase II-specificISM
GO:0000981 DNA-binding transcription factor activity, RNA polymerase II-specificIBA
GO:0001228 DNA-binding transcription activator activity, RNA polymerase II-specificIEA

GO:Biological Process

GO ID GO Term Evidence
GO:0007519 skeletal muscle tissue developmentISS
GO:0008582 regulation of synaptic growth at neuromuscular junctionIEA
GO:0008584 male gonad developmentISS
GO:0009653 anatomical structure morphogenesisTAS
GO:0030238 male sex determinationISS
GO:0030910 olfactory placode formationISS
GO:0032880 regulation of protein localizationIEA
GO:0034504 protein localization to nucleusISS
GO:0042472 inner ear morphogenesisIEA
GO:0043066 negative regulation of apoptotic processISS
GO:0043524 negative regulation of neuron apoptotic processISS
GO:0043586 tongue developmentISS
GO:0045214 sarcomere organizationISS
GO:0045892 negative regulation of transcription, DNA-templatedISS
GO:0045892 negative regulation of transcription, DNA-templatedIBA
GO:0045893 positive regulation of transcription, DNA-templatedISS
GO:0045944 positive regulation of transcription by RNA polymerase IIIEA
GO:0046661 male sex differentiationISS
GO:0048538 thymus developmentIEA
GO:0048699 generation of neuronsISS
GO:0048701 embryonic cranial skeleton morphogenesisIEA
GO:0048856 anatomical structure developmentIBA
GO:0050678 regulation of epithelial cell proliferationISS
GO:0051451 myoblast migrationIEA
GO:0060037 pharyngeal system developmentISS
GO:0061055 myotome developmentISS
GO:0061197 fungiform papilla morphogenesisISS
GO:0061551 trigeminal ganglion developmentISS
GO:0072075 metanephric mesenchyme developmentISS
GO:0072095 regulation of branch elongation involved in ureteric bud branchingISS
GO:0072107 positive regulation of ureteric bud formationISS
GO:0090190 positive regulation of branching involved in ureteric bud morphogenesisISS
GO:0098528 skeletal muscle fiber differentiationISS
GO:1902725 negative regulation of satellite cell differentiationISS

GO:Cellular Component

GO ID GO Term Evidence
GO:0000790 nuclear chromatinISA
GO:0005634 nucleusISS
GO:0005634 nucleusIBA
GO:0005667 transcription factor complexIBA
GO:0005737 cytoplasmISS

Reactome Pathway

Reactome ID Reactome Term Evidence

Drugs and compounds information

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Functional annotations

Keywords

Keyword ID Keyword Term
KW-0007 Acetylation
KW-0963 Cytoplasm
KW-0217 Developmental protein
KW-0238 DNA-binding
KW-0371 Homeobox
KW-0539 Nucleus
KW-0597 Phosphoprotein
KW-0621 Polymorphism
KW-1185 Reference proteome
KW-0804 Transcription
KW-0805 Transcription regulation

Interpro

InterPro ID InterPro Term
IPR009057 Homeobox-like_sf
IPR017970 Homeobox_CS
IPR001356 Homeobox_dom
IPR031701 SIX1_SD

PROSITE

PROSITE ID PROSITE Term
PS00027 HOMEOBOX_1
PS50071 HOMEOBOX_2

Pfam

Pfam ID Pfam Term
PF00046 Homeodomain
PF16878 SIX1_SD

Protein-protein interaction

Protein-miRNA interaction