SOX6_RAT
ID SOX6_RAT Reviewed; 827 AA.
AC A0A0G2JTZ2; F1MAJ5; Q4V8G3;
DT 17-JUN-2020, integrated into UniProtKB/Swiss-Prot.
DT 17-JUN-2020, sequence version 2.
DT 03-AUG-2022, entry version 54.
DE RecName: Full=Transcription factor SOX-6 {ECO:0000305};
GN Name=Sox6 {ECO:0000303|PubMed:26150426, ECO:0000312|RGD:1309000};
GN Synonyms=Sox-6;
OS Rattus norvegicus (Rat).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae;
OC Murinae; Rattus.
OX NCBI_TaxID=10116;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Brown Norway;
RX PubMed=15057822; DOI=10.1038/nature02426;
RA Gibbs R.A., Weinstock G.M., Metzker M.L., Muzny D.M., Sodergren E.J.,
RA Scherer S., Scott G., Steffen D., Worley K.C., Burch P.E., Okwuonu G.,
RA Hines S., Lewis L., Deramo C., Delgado O., Dugan-Rocha S., Miner G.,
RA Morgan M., Hawes A., Gill R., Holt R.A., Adams M.D., Amanatides P.G.,
RA Baden-Tillson H., Barnstead M., Chin S., Evans C.A., Ferriera S.,
RA Fosler C., Glodek A., Gu Z., Jennings D., Kraft C.L., Nguyen T.,
RA Pfannkoch C.M., Sitter C., Sutton G.G., Venter J.C., Woodage T., Smith D.,
RA Lee H.-M., Gustafson E., Cahill P., Kana A., Doucette-Stamm L.,
RA Weinstock K., Fechtel K., Weiss R.B., Dunn D.M., Green E.D.,
RA Blakesley R.W., Bouffard G.G., De Jong P.J., Osoegawa K., Zhu B., Marra M.,
RA Schein J., Bosdet I., Fjell C., Jones S., Krzywinski M., Mathewson C.,
RA Siddiqui A., Wye N., McPherson J., Zhao S., Fraser C.M., Shetty J.,
RA Shatsman S., Geer K., Chen Y., Abramzon S., Nierman W.C., Havlak P.H.,
RA Chen R., Durbin K.J., Egan A., Ren Y., Song X.-Z., Li B., Liu Y., Qin X.,
RA Cawley S., Cooney A.J., D'Souza L.M., Martin K., Wu J.Q.,
RA Gonzalez-Garay M.L., Jackson A.R., Kalafus K.J., McLeod M.P.,
RA Milosavljevic A., Virk D., Volkov A., Wheeler D.A., Zhang Z., Bailey J.A.,
RA Eichler E.E., Tuzun E., Birney E., Mongin E., Ureta-Vidal A., Woodwark C.,
RA Zdobnov E., Bork P., Suyama M., Torrents D., Alexandersson M., Trask B.J.,
RA Young J.M., Huang H., Wang H., Xing H., Daniels S., Gietzen D., Schmidt J.,
RA Stevens K., Vitt U., Wingrove J., Camara F., Mar Alba M., Abril J.F.,
RA Guigo R., Smit A., Dubchak I., Rubin E.M., Couronne O., Poliakov A.,
RA Huebner N., Ganten D., Goesele C., Hummel O., Kreitler T., Lee Y.-A.,
RA Monti J., Schulz H., Zimdahl H., Himmelbauer H., Lehrach H., Jacob H.J.,
RA Bromberg S., Gullings-Handley J., Jensen-Seaman M.I., Kwitek A.E.,
RA Lazar J., Pasko D., Tonellato P.J., Twigger S., Ponting C.P., Duarte J.M.,
RA Rice S., Goodstadt L., Beatson S.A., Emes R.D., Winter E.E., Webber C.,
RA Brandt P., Nyakatura G., Adetobi M., Chiaromonte F., Elnitski L.,
RA Eswara P., Hardison R.C., Hou M., Kolbe D., Makova K., Miller W.,
RA Nekrutenko A., Riemer C., Schwartz S., Taylor J., Yang S., Zhang Y.,
RA Lindpaintner K., Andrews T.D., Caccamo M., Clamp M., Clarke L., Curwen V.,
RA Durbin R.M., Eyras E., Searle S.M., Cooper G.M., Batzoglou S., Brudno M.,
RA Sidow A., Stone E.A., Payseur B.A., Bourque G., Lopez-Otin C., Puente X.S.,
RA Chakrabarti K., Chatterji S., Dewey C., Pachter L., Bray N., Yap V.B.,
RA Caspi A., Tesler G., Pevzner P.A., Haussler D., Roskin K.M., Baertsch R.,
RA Clawson H., Furey T.S., Hinrichs A.S., Karolchik D., Kent W.J.,
RA Rosenbloom K.R., Trumbower H., Weirauch M., Cooper D.N., Stenson P.D.,
RA Ma B., Brent M., Arumugam M., Shteynberg D., Copley R.R., Taylor M.S.,
RA Riethman H., Mudunuri U., Peterson J., Guyer M., Felsenfeld A., Old S.,
RA Mockrin S., Collins F.S.;
RT "Genome sequence of the Brown Norway rat yields insights into mammalian
RT evolution.";
RL Nature 428:493-521(2004).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Brown Norway;
RA Mural R.J., Adams M.D., Myers E.W., Smith H.O., Venter J.C.;
RL Submitted (SEP-2005) to the EMBL/GenBank/DDBJ databases.
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
RC TISSUE=Testis;
RX PubMed=15489334; DOI=10.1101/gr.2596504;
RG The MGC Project Team;
RT "The status, quality, and expansion of the NIH full-length cDNA project:
RT the Mammalian Gene Collection (MGC).";
RL Genome Res. 14:2121-2127(2004).
RN [4]
RP FUNCTION, AND DNA-BINDING.
RX PubMed=26150426; DOI=10.1093/nar/gkv688;
RA Liu C.F., Lefebvre V.;
RT "The transcription factors SOX9 and SOX5/SOX6 cooperate genome-wide through
RT super-enhancers to drive chondrogenesis.";
RL Nucleic Acids Res. 43:8183-8203(2015).
CC -!- FUNCTION: Transcription factor that plays a key role in several
CC developmental processes, including neurogenesis, chondrocytes
CC differentiation and cartilage formation (By similarity). Specifically
CC binds the 5'-AACAAT-3' DNA motif present in enhancers and super-
CC enhancers and promotes expression of genes important for chondrogenesis
CC (By similarity). Required for overt chondrogenesis when condensed
CC prechondrocytes differentiate into early stage chondrocytes: SOX5 and
CC SOX6 cooperatively bind with SOX9 on active enhancers and super-
CC enhancers associated with cartilage-specific genes, and thereby
CC potentiate SOX9's ability to transactivate (PubMed:26150426). Not
CC involved in precartilaginous condensation, the first step in
CC chondrogenesis, during which skeletal progenitors differentiate into
CC prechondrocytes (By similarity). Together with SOX5, required to form
CC and maintain a pool of highly proliferating chondroblasts between
CC epiphyses and metaphyses, to form columnar chondroblasts, delay
CC chondrocyte prehypertrophy but promote hypertrophy, and to delay
CC terminal differentiation of chondrocytes on contact with ossification
CC fronts (By similarity). Binds to the proximal promoter region of the
CC myelin protein MPZ gene, and is thereby involved in the differentiation
CC of oligodendroglia in the developing spinal tube (By similarity). Binds
CC to the gene promoter of MBP and acts as a transcriptional repressor (By
CC similarity). {ECO:0000250|UniProtKB:P40645,
CC ECO:0000269|PubMed:26150426}.
CC -!- SUBUNIT: Homodimer (By similarity). Interacts with DAZAP2 (By
CC similarity). May interact with CENPK (By similarity).
CC {ECO:0000250|UniProtKB:P40645}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000250|UniProtKB:P40645,
CC ECO:0000255|PROSITE-ProRule:PRU00267}. Cytoplasm
CC {ECO:0000250|UniProtKB:P40645}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=1;
CC IsoId=A0A0G2JTZ2-1; Sequence=Displayed;
CC Name=2;
CC IsoId=A0A0G2JTZ2-2; Sequence=VSP_060589;
CC -!- PTM: Sumoylation inhibits the transcriptional activity.
CC {ECO:0000250|UniProtKB:P35712}.
CC -!- SEQUENCE CAUTION:
CC Sequence=EDM17752.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AABR07005536; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; AABR07005537; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; AABR07005538; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; AABR07071973; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; AC128610; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; CH473956; EDM17752.1; ALT_SEQ; Genomic_DNA.
DR EMBL; BC097403; AAH97403.1; -; mRNA.
DR RefSeq; NP_001019922.1; NM_001024751.1.
DR RefSeq; XP_006230149.1; XM_006230087.3.
DR RefSeq; XP_017444458.1; XM_017588969.1.
DR AlphaFoldDB; A0A0G2JTZ2; -.
DR SMR; A0A0G2JTZ2; -.
DR STRING; 10116.ENSRNOP00000044088; -.
DR GeneID; 293165; -.
DR KEGG; rno:293165; -.
DR UCSC; RGD:1309000; rat.
DR CTD; 55553; -.
DR RGD; 1309000; Sox6.
DR eggNOG; KOG0528; Eukaryota.
DR HOGENOM; CLU_018522_0_1_1; -.
DR OrthoDB; 465521at2759; -.
DR Reactome; R-RNO-3769402; Deactivation of the beta-catenin transactivating complex.
DR PRO; PR:A0A0G2JTZ2; -.
DR Proteomes; UP000002494; Unplaced.
DR Proteomes; UP000234681; Chromosome 1.
DR ExpressionAtlas; A0A0G2JTZ2; baseline and differential.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0005634; C:nucleus; ISS:UniProtKB.
DR GO; GO:0000987; F:cis-regulatory region sequence-specific DNA binding; IDA:UniProtKB.
DR GO; GO:0003677; F:DNA binding; ISO:RGD.
DR GO; GO:0003700; F:DNA-binding transcription factor activity; ISS:UniProtKB.
DR GO; GO:0000981; F:DNA-binding transcription factor activity, RNA polymerase II-specific; IBA:GO_Central.
DR GO; GO:0001217; F:DNA-binding transcription repressor activity; ISO:RGD.
DR GO; GO:0001227; F:DNA-binding transcription repressor activity, RNA polymerase II-specific; ISO:RGD.
DR GO; GO:0042803; F:protein homodimerization activity; ISS:UniProtKB.
DR GO; GO:0000978; F:RNA polymerase II cis-regulatory region sequence-specific DNA binding; ISO:RGD.
DR GO; GO:0043565; F:sequence-specific DNA binding; ISO:RGD.
DR GO; GO:0000976; F:transcription cis-regulatory region binding; ISO:RGD.
DR GO; GO:0048708; P:astrocyte differentiation; IMP:RGD.
DR GO; GO:0007420; P:brain development; ISS:UniProtKB.
DR GO; GO:0055007; P:cardiac muscle cell differentiation; ISO:RGD.
DR GO; GO:0001502; P:cartilage condensation; ISS:UniProtKB.
DR GO; GO:0051216; P:cartilage development; ISS:UniProtKB.
DR GO; GO:0045165; P:cell fate commitment; ISO:RGD.
DR GO; GO:0000902; P:cell morphogenesis; ISO:RGD.
DR GO; GO:0071560; P:cellular response to transforming growth factor beta stimulus; ISO:RGD.
DR GO; GO:0007417; P:central nervous system development; IBA:GO_Central.
DR GO; GO:0002062; P:chondrocyte differentiation; ISS:UniProtKB.
DR GO; GO:0048821; P:erythrocyte development; ISO:RGD.
DR GO; GO:0030218; P:erythrocyte differentiation; ISO:RGD.
DR GO; GO:0030097; P:hemopoiesis; ISO:RGD.
DR GO; GO:0001701; P:in utero embryonic development; ISO:RGD.
DR GO; GO:0042692; P:muscle cell differentiation; ISO:RGD.
DR GO; GO:2000726; P:negative regulation of cardiac muscle cell differentiation; ISO:RGD.
DR GO; GO:0000122; P:negative regulation of transcription by RNA polymerase II; ISO:RGD.
DR GO; GO:0045892; P:negative regulation of transcription, DNA-templated; ISO:RGD.
DR GO; GO:0021778; P:oligodendrocyte cell fate specification; ISO:RGD.
DR GO; GO:0048709; P:oligodendrocyte differentiation; ISO:RGD.
DR GO; GO:0061036; P:positive regulation of cartilage development; ISO:RGD.
DR GO; GO:0032332; P:positive regulation of chondrocyte differentiation; ISO:RGD.
DR GO; GO:2000741; P:positive regulation of mesenchymal stem cell differentiation; ISO:RGD.
DR GO; GO:0045944; P:positive regulation of transcription by RNA polymerase II; ISO:RGD.
DR GO; GO:0045893; P:positive regulation of transcription, DNA-templated; ISO:RGD.
DR GO; GO:0009791; P:post-embryonic development; ISO:RGD.
DR GO; GO:0010468; P:regulation of gene expression; ISO:RGD.
DR GO; GO:0006357; P:regulation of transcription by RNA polymerase II; IBA:GO_Central.
DR GO; GO:0006355; P:regulation of transcription, DNA-templated; ISO:RGD.
DR GO; GO:0021529; P:spinal cord oligodendrocyte cell differentiation; ISO:RGD.
DR Gene3D; 1.10.30.10; -; 1.
DR InterPro; IPR009071; HMG_box_dom.
DR InterPro; IPR036910; HMG_box_dom_sf.
DR InterPro; IPR027153; SOX-6.
DR PANTHER; PTHR45789:SF1; PTHR45789:SF1; 1.
DR Pfam; PF00505; HMG_box; 1.
DR SMART; SM00398; HMG; 1.
DR SUPFAM; SSF47095; SSF47095; 1.
DR PROSITE; PS50118; HMG_BOX_2; 1.
PE 1: Evidence at protein level;
KW Activator; Alternative splicing; Coiled coil; Cytoplasm;
KW Developmental protein; Differentiation; DNA-binding; Isopeptide bond;
KW Nucleus; Phosphoprotein; Reference proteome; Repressor; Transcription;
KW Transcription regulation; Ubl conjugation.
FT CHAIN 1..827
FT /note="Transcription factor SOX-6"
FT /id="PRO_0000450218"
FT DNA_BIND 620..688
FT /note="HMG box"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00267"
FT REGION 1..51
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 329..360
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 380..470
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 752..772
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 786..827
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COILED 184..257
FT /evidence="ECO:0000255"
FT COMPBIAS 1..20
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 21..37
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 344..360
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 797..812
FT /note="Acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOD_RES 119
FT /note="Phosphothreonine"
FT /evidence="ECO:0000250|UniProtKB:P35712"
FT MOD_RES 399
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:P35712"
FT MOD_RES 401
FT /note="Phosphothreonine"
FT /evidence="ECO:0000250|UniProtKB:P40645"
FT MOD_RES 439
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:P35712"
FT MOD_RES 442
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:P40645"
FT CROSSLNK 404
FT /note="Glycyl lysine isopeptide (Lys-Gly) (interchain with
FT G-Cter in SUMO)"
FT /evidence="ECO:0000250|UniProtKB:P35712"
FT CROSSLNK 417
FT /note="Glycyl lysine isopeptide (Lys-Gly) (interchain with
FT G-Cter in SUMO)"
FT /evidence="ECO:0000250|UniProtKB:P35712"
FT VAR_SEQ 326..367
FT /note="QKGHVSHPQINPRLKGISDRLGRNLDPYEHGGGHSYNHKQIE -> Q (in
FT isoform 2)"
FT /id="VSP_060589"
FT CONFLICT 258
FT /note="I -> IQ (in Ref. 3; AABR07005536/AABR07005537/
FT AABR07005538/AABR07071973/AC128610/AAH97403)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 827 AA; 91816 MW; A9EA0E9A1DE55613 CRC64;
MSSKQATSPF ACTVDGEETM TQDLTSREKE EGSDQHPASH LPLHPIMHNK PHSEELPTLV
STIQQDADWD SVLSSQQRME SENNKLCSLY SFRNTSTSPH KPDEGSRERE IMNSVTFGTP
ERRKGSLADV VDTLKQKKLE EMTRTEQEDS SCMEKLLSKD WKEKMERLNT SELLGEIKGT
PESLAEKERQ LSTMITQLIS LREQLLAAHD EQKKLAASQI EKQRQQMDLA RQQQEQIARQ
QQQLLQQQHK INLLQQQIQV QGHMPPLMIP IFPHDQRTLA AAAAAQQGFL FPPGITYKPG
DNYPVQFIPS TMAAAAASGL SPLQLQKGHV SHPQINPRLK GISDRLGRNL DPYEHGGGHS
YNHKQIEQLY AAQLASMQVS PGAKMPSTPQ PPNSAGAVSP TGIKNEKRGT SPVTQVKDET
TAQPLNLSSR PKTAEPVKSP TSPTQSLFPA SKTSPVNLPN KSSIPSPIGG SLGRGSSLDI
LSSLNSPALF GDQDTVMKAI QEARKMREQI QREQQQQPHG VDGKLSSMNS MGLSNCRNEK
ERTRFENLGP QLTGKSSEDG KLGPGVIDLT RPEDAEGSKA MNGSAAKLQQ YYCWPTGGAT
VAEARVYRDA RGRASSEPHI KRPMNAFMVW AKDERRKILQ AFPDMHNSNI SKILGSRWKS
MSNQEKQPYY EEQARLSKIH LEKYPNYKYK PRPKRTCIVD GKKLRIGEYK QLMRSRRQEM
RQFFTVGQQP QIPITTGTGV VYPGAITMAT TTPSPQMTSD CSSTSASPEP SLPVIQSTYG
MKMDGASLAG NDMINGEDEM EAYDDYEDDP KSDYSSENEA PEPVSAN
