Full text data of YBX3
YBX3
(CSDA, DBPA)
[Confidence: low (only semi-automatic identification from reviews)]
Y-box-binding protein 3 (Cold shock domain-containing protein A; DNA-binding protein A; Single-strand DNA-binding protein NF-GMB)
Note: presumably soluble (membrane word is not in UniProt keywords or features)
Y-box-binding protein 3 (Cold shock domain-containing protein A; DNA-binding protein A; Single-strand DNA-binding protein NF-GMB)
Note: presumably soluble (membrane word is not in UniProt keywords or features)
UniProt
P16989
ID YBOX3_HUMAN Reviewed; 372 AA.
AC P16989; B2RBW6; Q14121; Q969N6; Q96B76;
DT 01-AUG-1990, integrated into UniProtKB/Swiss-Prot.
read moreDT 16-MAY-2006, sequence version 4.
DT 22-JAN-2014, entry version 147.
DE RecName: Full=Y-box-binding protein 3;
DE AltName: Full=Cold shock domain-containing protein A;
DE AltName: Full=DNA-binding protein A;
DE AltName: Full=Single-strand DNA-binding protein NF-GMB;
GN Name=YBX3; Synonyms=CSDA, DBPA;
OS Homo sapiens (Human).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
OC Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
OC Catarrhini; Hominidae; Homo.
OX NCBI_TaxID=9606;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 3), AND VARIANT ALA-75.
RX PubMed=2977358; DOI=10.1016/0378-1119(88)90514-8;
RA Sakura H., Maekawa T., Imamoto F., Yasuda K., Ishii S.;
RT "Two human genes isolated by a novel method encode DNA-binding
RT proteins containing a common region of homology.";
RL Gene 73:499-507(1988).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], ALTERNATIVE SPLICING, AND VARIANT
RP ALA-75.
RC TISSUE=Placenta;
RX PubMed=7628487; DOI=10.1111/j.1432-1033.1995.tb20672.x;
RA Kudo S., Mattei M.-G., Fukuda M.;
RT "Characterization of the gene for dbpA, a family member of the
RT nucleic-acid-binding proteins containing a cold-shock domain.";
RL Eur. J. Biochem. 231:72-82(1995).
RN [3]
RP NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1).
RX PubMed=8710501; DOI=10.1093/nar/24.12.2311;
RA Coles L.S., Diamond P., Occhiodoro F., Vadas M.A., Shannon M.F.;
RT "Cold shock domain proteins repress transcription from the GM-CSF
RT promoter.";
RL Nucleic Acids Res. 24:2311-2317(1996).
RN [4]
RP NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1).
RC TISSUE=Blood;
RA Moschonas N.K.;
RL Submitted (MAR-1993) to the EMBL/GenBank/DDBJ databases.
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
RX PubMed=14702039; DOI=10.1038/ng1285;
RA Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R.,
RA Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H.,
RA Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S.,
RA Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K.,
RA Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A.,
RA Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M.,
RA Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y.,
RA Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M.,
RA Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K.,
RA Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S.,
RA Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J.,
RA Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.-O., Nomura Y.,
RA Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N.,
RA Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S.,
RA Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S.,
RA Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O.,
RA Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H.,
RA Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B.,
RA Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y.,
RA Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T.,
RA Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y.,
RA Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S.,
RA Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T.,
RA Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M.,
RA Togashi T., Oyama M., Hata H., Watanabe M., Komatsu T.,
RA Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K.,
RA Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R.,
RA Nakai K., Yada T., Nakamura Y., Ohara O., Isogai T., Sugano S.;
RT "Complete sequencing and characterization of 21,243 full-length human
RT cDNAs.";
RL Nat. Genet. 36:40-45(2004).
RN [6]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RA Mural R.J., Istrail S., Sutton G.G., Florea L., Halpern A.L.,
RA Mobarry C.M., Lippert R., Walenz B., Shatkay H., Dew I., Miller J.R.,
RA Flanigan M.J., Edwards N.J., Bolanos R., Fasulo D., Halldorsson B.V.,
RA Hannenhalli S., Turner R., Yooseph S., Lu F., Nusskern D.R.,
RA Shue B.C., Zheng X.H., Zhong F., Delcher A.L., Huson D.H.,
RA Kravitz S.A., Mouchard L., Reinert K., Remington K.A., Clark A.G.,
RA Waterman M.S., Eichler E.E., Adams M.D., Hunkapiller M.W., Myers E.W.,
RA Venter J.C.;
RL Submitted (JUL-2005) to the EMBL/GenBank/DDBJ databases.
RN [7]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 1 AND 2), AND VARIANT
RP ALA-75.
RC TISSUE=Kidney, Lung, Lymph, and Muscle;
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
RT project: the Mammalian Gene Collection (MGC).";
RL Genome Res. 14:2121-2127(2004).
RN [8]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-201; SER-203 AND
RP SER-204, AND MASS SPECTROMETRY.
RC TISSUE=Cervix carcinoma;
RX PubMed=18669648; DOI=10.1073/pnas.0805139105;
RA Dephoure N., Zhou C., Villen J., Beausoleil S.A., Bakalarski C.E.,
RA Elledge S.J., Gygi S.P.;
RT "A quantitative atlas of mitotic phosphorylation.";
RL Proc. Natl. Acad. Sci. U.S.A. 105:10762-10767(2008).
RN [9]
RP ACETYLATION [LARGE SCALE ANALYSIS] AT SER-2, MASS SPECTROMETRY, AND
RP CLEAVAGE OF INITIATOR METHIONINE.
RX PubMed=19413330; DOI=10.1021/ac9004309;
RA Gauci S., Helbig A.O., Slijper M., Krijgsveld J., Heck A.J.,
RA Mohammed S.;
RT "Lys-N and trypsin cover complementary parts of the phosphoproteome in
RT a refined SCX-based approach.";
RL Anal. Chem. 81:4493-4501(2009).
RN [10]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-134; SER-201; SER-203
RP AND SER-204, AND MASS SPECTROMETRY.
RC TISSUE=Leukemic T-cell;
RX PubMed=19690332; DOI=10.1126/scisignal.2000007;
RA Mayya V., Lundgren D.H., Hwang S.-I., Rezaul K., Wu L., Eng J.K.,
RA Rodionov V., Han D.K.;
RT "Quantitative phosphoproteomic analysis of T cell receptor signaling
RT reveals system-wide modulation of protein-protein interactions.";
RL Sci. Signal. 2:RA46-RA46(2009).
RN [11]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-204, AND MASS
RP SPECTROMETRY.
RC TISSUE=Cervix carcinoma;
RX PubMed=20068231; DOI=10.1126/scisignal.2000475;
RA Olsen J.V., Vermeulen M., Santamaria A., Kumar C., Miller M.L.,
RA Jensen L.J., Gnad F., Cox J., Jensen T.S., Nigg E.A., Brunak S.,
RA Mann M.;
RT "Quantitative phosphoproteomics reveals widespread full
RT phosphorylation site occupancy during mitosis.";
RL Sci. Signal. 3:RA3-RA3(2010).
RN [12]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=21269460; DOI=10.1186/1752-0509-5-17;
RA Burkard T.R., Planyavsky M., Kaupe I., Breitwieser F.P.,
RA Buerckstuemmer T., Bennett K.L., Superti-Furga G., Colinge J.;
RT "Initial characterization of the human central proteome.";
RL BMC Syst. Biol. 5:17-17(2011).
RN [13]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-324, AND MASS
RP SPECTROMETRY.
RX PubMed=21406692; DOI=10.1126/scisignal.2001570;
RA Rigbolt K.T., Prokhorova T.A., Akimov V., Henningsen J.,
RA Johansen P.T., Kratchmarova I., Kassem M., Mann M., Olsen J.V.,
RA Blagoev B.;
RT "System-wide temporal characterization of the proteome and
RT phosphoproteome of human embryonic stem cell differentiation.";
RL Sci. Signal. 4:RS3-RS3(2011).
CC -!- FUNCTION: Binds to the GM-CSF promoter. Seems to act as a
CC repressor. Binds also to full length mRNA and to short RNA
CC sequences containing the consensus site 5'-UCCAUCA-3'. May have a
CC role in translation repression (By similarity).
CC -!- SUBUNIT: Found in a mRNP complex with YBX2 (By similarity).
CC -!- SUBCELLULAR LOCATION: Cytoplasm. Nucleus.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=3;
CC Comment=Additional isoforms seem to exist;
CC Name=1;
CC IsoId=P16989-1; Sequence=Displayed;
CC Name=2;
CC IsoId=P16989-2; Sequence=VSP_001135;
CC Name=3;
CC IsoId=P16989-3; Sequence=VSP_001136;
CC -!- TISSUE SPECIFICITY: Highly expressed in skeletal muscle and heart.
CC -!- SIMILARITY: Contains 1 CSD (cold-shock) domain.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAA35749.1; Type=Erroneous initiation; Note=Translation N-terminally shortened;
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DR EMBL; M24069; AAA35749.1; ALT_INIT; mRNA.
DR EMBL; L29071; AAA79243.1; -; Genomic_DNA.
DR EMBL; L29064; AAA79243.1; JOINED; Genomic_DNA.
DR EMBL; L29065; AAA79243.1; JOINED; Genomic_DNA.
DR EMBL; L29066; AAA79243.1; JOINED; Genomic_DNA.
DR EMBL; L29067; AAA79243.1; JOINED; Genomic_DNA.
DR EMBL; L29068; AAA79243.1; JOINED; Genomic_DNA.
DR EMBL; L29069; AAA79243.1; JOINED; Genomic_DNA.
DR EMBL; L29070; AAA79243.1; JOINED; Genomic_DNA.
DR EMBL; X95325; CAA64631.1; -; mRNA.
DR EMBL; X72712; CAA51261.1; -; mRNA.
DR EMBL; AK314846; BAG37363.1; -; mRNA.
DR EMBL; CH471094; EAW96201.1; -; Genomic_DNA.
DR EMBL; CH471094; EAW96203.1; -; Genomic_DNA.
DR EMBL; BC008801; AAH08801.1; -; mRNA.
DR EMBL; BC015564; AAH15564.1; -; mRNA.
DR EMBL; BC015913; AAH15913.1; -; mRNA.
DR EMBL; BC021926; AAH21926.1; -; mRNA.
DR PIR; I53354; I53354.
DR PIR; S69501; S69501.
DR RefSeq; NP_001138898.1; NM_001145426.1.
DR RefSeq; NP_003642.3; NM_003651.4.
DR UniGene; Hs.221889; -.
DR ProteinModelPortal; P16989; -.
DR SMR; P16989; 84-160.
DR DIP; DIP-42489N; -.
DR IntAct; P16989; 26.
DR MINT; MINT-1152000; -.
DR STRING; 9606.ENSP00000228251; -.
DR PhosphoSite; P16989; -.
DR DMDM; 97536050; -.
DR PaxDb; P16989; -.
DR PRIDE; P16989; -.
DR DNASU; 8531; -.
DR Ensembl; ENST00000228251; ENSP00000228251; ENSG00000060138.
DR Ensembl; ENST00000279550; ENSP00000279550; ENSG00000060138.
DR GeneID; 8531; -.
DR KEGG; hsa:8531; -.
DR UCSC; uc001qyt.3; human.
DR CTD; 8531; -.
DR GeneCards; GC12M010852; -.
DR HGNC; HGNC:2428; YBX3.
DR HPA; HPA034838; -.
DR MIM; 603437; gene.
DR neXtProt; NX_P16989; -.
DR PharmGKB; PA26929; -.
DR eggNOG; COG1278; -.
DR HOGENOM; HOG000116439; -.
DR HOVERGEN; HBG008757; -.
DR InParanoid; P16989; -.
DR KO; K06099; -.
DR OMA; NQPPARR; -.
DR OrthoDB; EOG7TBC44; -.
DR PhylomeDB; P16989; -.
DR ChiTaRS; CSDA; human.
DR GeneWiki; CSDA_(gene); -.
DR GenomeRNAi; 8531; -.
DR NextBio; 31948; -.
DR PMAP-CutDB; P16989; -.
DR PRO; PR:P16989; -.
DR Bgee; P16989; -.
DR CleanEx; HS_CSDA; -.
DR Genevestigator; P16989; -.
DR GO; GO:0005634; C:nucleus; ISS:BHF-UCL.
DR GO; GO:0048471; C:perinuclear region of cytoplasm; ISS:BHF-UCL.
DR GO; GO:0005844; C:polysome; IEA:Ensembl.
DR GO; GO:0005923; C:tight junction; ISS:BHF-UCL.
DR GO; GO:0003690; F:double-stranded DNA binding; TAS:ProtInc.
DR GO; GO:0003730; F:mRNA 3'-UTR binding; ISS:BHF-UCL.
DR GO; GO:0017048; F:Rho GTPase binding; ISS:BHF-UCL.
DR GO; GO:0003700; F:sequence-specific DNA binding transcription factor activity; NAS:ProtInc.
DR GO; GO:0003697; F:single-stranded DNA binding; IEA:Ensembl.
DR GO; GO:0003714; F:transcription corepressor activity; TAS:ProtInc.
DR GO; GO:0070935; P:3'-UTR-mediated mRNA stabilization; IC:BHF-UCL.
DR GO; GO:0071474; P:cellular hyperosmotic response; IMP:BHF-UCL.
DR GO; GO:0071356; P:cellular response to tumor necrosis factor; IMP:BHF-UCL.
DR GO; GO:0009566; P:fertilization; IEA:Ensembl.
DR GO; GO:0001701; P:in utero embryonic development; IEA:Ensembl.
DR GO; GO:0008584; P:male gonad development; IEA:Ensembl.
DR GO; GO:0043066; P:negative regulation of apoptotic process; IEA:Ensembl.
DR GO; GO:1902219; P:negative regulation of intrinsic apoptotic signaling pathway in response to osmotic stress; IMP:BHF-UCL.
DR GO; GO:0060547; P:negative regulation of necrotic cell death; IMP:BHF-UCL.
DR GO; GO:0048642; P:negative regulation of skeletal muscle tissue development; IEA:Ensembl.
DR GO; GO:0000122; P:negative regulation of transcription from RNA polymerase II promoter; TAS:ProtInc.
DR GO; GO:2000767; P:positive regulation of cytoplasmic translation; ISS:BHF-UCL.
DR GO; GO:0046622; P:positive regulation of organ growth; IEA:Ensembl.
DR GO; GO:0009409; P:response to cold; TAS:ProtInc.
DR GO; GO:0007283; P:spermatogenesis; IEA:Ensembl.
DR GO; GO:0006351; P:transcription, DNA-dependent; IEA:UniProtKB-KW.
DR Gene3D; 2.40.50.140; -; 1.
DR InterPro; IPR019844; Cold-shock_CS.
DR InterPro; IPR011129; Cold_shock_prot.
DR InterPro; IPR002059; CSP_DNA-bd.
DR InterPro; IPR012340; NA-bd_OB-fold.
DR Pfam; PF00313; CSD; 1.
DR PRINTS; PR00050; COLDSHOCK.
DR SMART; SM00357; CSP; 1.
DR SUPFAM; SSF50249; SSF50249; 1.
DR PROSITE; PS00352; COLD_SHOCK; 1.
PE 1: Evidence at protein level;
KW Acetylation; Alternative splicing; Complete proteome; Cytoplasm;
KW DNA-binding; Nucleus; Phosphoprotein; Polymorphism;
KW Reference proteome; Repressor; Transcription;
KW Transcription regulation.
FT INIT_MET 1 1 Removed.
FT CHAIN 2 372 Y-box-binding protein 3.
FT /FTId=PRO_0000100214.
FT DOMAIN 93 157 CSD.
FT MOD_RES 2 2 N-acetylserine.
FT MOD_RES 134 134 Phosphoserine.
FT MOD_RES 201 201 Phosphoserine.
FT MOD_RES 203 203 Phosphoserine.
FT MOD_RES 204 204 Phosphoserine.
FT MOD_RES 324 324 Phosphoserine.
FT VAR_SEQ 192 260 Missing (in isoform 2).
FT /FTId=VSP_001135.
FT VAR_SEQ 340 372 RPPNAPSQDGKEAKAGEAPTENPAPPTQQSSAE -> PSS
FT (in isoform 3).
FT /FTId=VSP_001136.
FT VARIANT 75 75 T -> A (in dbSNP:rs1126501).
FT /FTId=VAR_013114.
SQ SEQUENCE 372 AA; 40090 MW; AA8517AC3B7D35CC CRC64;
MSEAGEATTT TTTTLPQAPT EAAAAAPQDP APKSPVGSGA PQAAAPAPAA HVAGNPGGDA
APAATGTAAA ASLATAAGSE DAEKKVLATK VLGTVKWFNV RNGYGFINRN DTKEDVFVHQ
TAIKKNNPRK YLRSVGDGET VEFDVVEGEK GAEAANVTGP DGVPVEGSRY AADRRRYRRG
YYGRRRGPPR NYAGEEEEEG SGSSEGFDPP ATDRQFSGAR NQLRRPQYRP QYRQRRFPPY
HVGQTFDRRS RVLPHPNRIQ AGEIGEMKDG VPEGAQLQGP VHRNPTYRPR YRSRGPPRPR
PAPAVGEAED KENQQATSGP NQPSVRRGYR RPYNYRRRPR PPNAPSQDGK EAKAGEAPTE
NPAPPTQQSS AE
//
ID YBOX3_HUMAN Reviewed; 372 AA.
AC P16989; B2RBW6; Q14121; Q969N6; Q96B76;
DT 01-AUG-1990, integrated into UniProtKB/Swiss-Prot.
read moreDT 16-MAY-2006, sequence version 4.
DT 22-JAN-2014, entry version 147.
DE RecName: Full=Y-box-binding protein 3;
DE AltName: Full=Cold shock domain-containing protein A;
DE AltName: Full=DNA-binding protein A;
DE AltName: Full=Single-strand DNA-binding protein NF-GMB;
GN Name=YBX3; Synonyms=CSDA, DBPA;
OS Homo sapiens (Human).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
OC Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
OC Catarrhini; Hominidae; Homo.
OX NCBI_TaxID=9606;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 3), AND VARIANT ALA-75.
RX PubMed=2977358; DOI=10.1016/0378-1119(88)90514-8;
RA Sakura H., Maekawa T., Imamoto F., Yasuda K., Ishii S.;
RT "Two human genes isolated by a novel method encode DNA-binding
RT proteins containing a common region of homology.";
RL Gene 73:499-507(1988).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], ALTERNATIVE SPLICING, AND VARIANT
RP ALA-75.
RC TISSUE=Placenta;
RX PubMed=7628487; DOI=10.1111/j.1432-1033.1995.tb20672.x;
RA Kudo S., Mattei M.-G., Fukuda M.;
RT "Characterization of the gene for dbpA, a family member of the
RT nucleic-acid-binding proteins containing a cold-shock domain.";
RL Eur. J. Biochem. 231:72-82(1995).
RN [3]
RP NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1).
RX PubMed=8710501; DOI=10.1093/nar/24.12.2311;
RA Coles L.S., Diamond P., Occhiodoro F., Vadas M.A., Shannon M.F.;
RT "Cold shock domain proteins repress transcription from the GM-CSF
RT promoter.";
RL Nucleic Acids Res. 24:2311-2317(1996).
RN [4]
RP NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1).
RC TISSUE=Blood;
RA Moschonas N.K.;
RL Submitted (MAR-1993) to the EMBL/GenBank/DDBJ databases.
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
RX PubMed=14702039; DOI=10.1038/ng1285;
RA Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R.,
RA Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H.,
RA Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S.,
RA Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K.,
RA Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A.,
RA Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M.,
RA Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y.,
RA Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M.,
RA Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K.,
RA Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S.,
RA Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J.,
RA Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.-O., Nomura Y.,
RA Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N.,
RA Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S.,
RA Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S.,
RA Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O.,
RA Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H.,
RA Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B.,
RA Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y.,
RA Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T.,
RA Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y.,
RA Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S.,
RA Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T.,
RA Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M.,
RA Togashi T., Oyama M., Hata H., Watanabe M., Komatsu T.,
RA Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K.,
RA Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R.,
RA Nakai K., Yada T., Nakamura Y., Ohara O., Isogai T., Sugano S.;
RT "Complete sequencing and characterization of 21,243 full-length human
RT cDNAs.";
RL Nat. Genet. 36:40-45(2004).
RN [6]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RA Mural R.J., Istrail S., Sutton G.G., Florea L., Halpern A.L.,
RA Mobarry C.M., Lippert R., Walenz B., Shatkay H., Dew I., Miller J.R.,
RA Flanigan M.J., Edwards N.J., Bolanos R., Fasulo D., Halldorsson B.V.,
RA Hannenhalli S., Turner R., Yooseph S., Lu F., Nusskern D.R.,
RA Shue B.C., Zheng X.H., Zhong F., Delcher A.L., Huson D.H.,
RA Kravitz S.A., Mouchard L., Reinert K., Remington K.A., Clark A.G.,
RA Waterman M.S., Eichler E.E., Adams M.D., Hunkapiller M.W., Myers E.W.,
RA Venter J.C.;
RL Submitted (JUL-2005) to the EMBL/GenBank/DDBJ databases.
RN [7]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 1 AND 2), AND VARIANT
RP ALA-75.
RC TISSUE=Kidney, Lung, Lymph, and Muscle;
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
RT project: the Mammalian Gene Collection (MGC).";
RL Genome Res. 14:2121-2127(2004).
RN [8]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-201; SER-203 AND
RP SER-204, AND MASS SPECTROMETRY.
RC TISSUE=Cervix carcinoma;
RX PubMed=18669648; DOI=10.1073/pnas.0805139105;
RA Dephoure N., Zhou C., Villen J., Beausoleil S.A., Bakalarski C.E.,
RA Elledge S.J., Gygi S.P.;
RT "A quantitative atlas of mitotic phosphorylation.";
RL Proc. Natl. Acad. Sci. U.S.A. 105:10762-10767(2008).
RN [9]
RP ACETYLATION [LARGE SCALE ANALYSIS] AT SER-2, MASS SPECTROMETRY, AND
RP CLEAVAGE OF INITIATOR METHIONINE.
RX PubMed=19413330; DOI=10.1021/ac9004309;
RA Gauci S., Helbig A.O., Slijper M., Krijgsveld J., Heck A.J.,
RA Mohammed S.;
RT "Lys-N and trypsin cover complementary parts of the phosphoproteome in
RT a refined SCX-based approach.";
RL Anal. Chem. 81:4493-4501(2009).
RN [10]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-134; SER-201; SER-203
RP AND SER-204, AND MASS SPECTROMETRY.
RC TISSUE=Leukemic T-cell;
RX PubMed=19690332; DOI=10.1126/scisignal.2000007;
RA Mayya V., Lundgren D.H., Hwang S.-I., Rezaul K., Wu L., Eng J.K.,
RA Rodionov V., Han D.K.;
RT "Quantitative phosphoproteomic analysis of T cell receptor signaling
RT reveals system-wide modulation of protein-protein interactions.";
RL Sci. Signal. 2:RA46-RA46(2009).
RN [11]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-204, AND MASS
RP SPECTROMETRY.
RC TISSUE=Cervix carcinoma;
RX PubMed=20068231; DOI=10.1126/scisignal.2000475;
RA Olsen J.V., Vermeulen M., Santamaria A., Kumar C., Miller M.L.,
RA Jensen L.J., Gnad F., Cox J., Jensen T.S., Nigg E.A., Brunak S.,
RA Mann M.;
RT "Quantitative phosphoproteomics reveals widespread full
RT phosphorylation site occupancy during mitosis.";
RL Sci. Signal. 3:RA3-RA3(2010).
RN [12]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=21269460; DOI=10.1186/1752-0509-5-17;
RA Burkard T.R., Planyavsky M., Kaupe I., Breitwieser F.P.,
RA Buerckstuemmer T., Bennett K.L., Superti-Furga G., Colinge J.;
RT "Initial characterization of the human central proteome.";
RL BMC Syst. Biol. 5:17-17(2011).
RN [13]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-324, AND MASS
RP SPECTROMETRY.
RX PubMed=21406692; DOI=10.1126/scisignal.2001570;
RA Rigbolt K.T., Prokhorova T.A., Akimov V., Henningsen J.,
RA Johansen P.T., Kratchmarova I., Kassem M., Mann M., Olsen J.V.,
RA Blagoev B.;
RT "System-wide temporal characterization of the proteome and
RT phosphoproteome of human embryonic stem cell differentiation.";
RL Sci. Signal. 4:RS3-RS3(2011).
CC -!- FUNCTION: Binds to the GM-CSF promoter. Seems to act as a
CC repressor. Binds also to full length mRNA and to short RNA
CC sequences containing the consensus site 5'-UCCAUCA-3'. May have a
CC role in translation repression (By similarity).
CC -!- SUBUNIT: Found in a mRNP complex with YBX2 (By similarity).
CC -!- SUBCELLULAR LOCATION: Cytoplasm. Nucleus.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=3;
CC Comment=Additional isoforms seem to exist;
CC Name=1;
CC IsoId=P16989-1; Sequence=Displayed;
CC Name=2;
CC IsoId=P16989-2; Sequence=VSP_001135;
CC Name=3;
CC IsoId=P16989-3; Sequence=VSP_001136;
CC -!- TISSUE SPECIFICITY: Highly expressed in skeletal muscle and heart.
CC -!- SIMILARITY: Contains 1 CSD (cold-shock) domain.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAA35749.1; Type=Erroneous initiation; Note=Translation N-terminally shortened;
CC -----------------------------------------------------------------------
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DR EMBL; M24069; AAA35749.1; ALT_INIT; mRNA.
DR EMBL; L29071; AAA79243.1; -; Genomic_DNA.
DR EMBL; L29064; AAA79243.1; JOINED; Genomic_DNA.
DR EMBL; L29065; AAA79243.1; JOINED; Genomic_DNA.
DR EMBL; L29066; AAA79243.1; JOINED; Genomic_DNA.
DR EMBL; L29067; AAA79243.1; JOINED; Genomic_DNA.
DR EMBL; L29068; AAA79243.1; JOINED; Genomic_DNA.
DR EMBL; L29069; AAA79243.1; JOINED; Genomic_DNA.
DR EMBL; L29070; AAA79243.1; JOINED; Genomic_DNA.
DR EMBL; X95325; CAA64631.1; -; mRNA.
DR EMBL; X72712; CAA51261.1; -; mRNA.
DR EMBL; AK314846; BAG37363.1; -; mRNA.
DR EMBL; CH471094; EAW96201.1; -; Genomic_DNA.
DR EMBL; CH471094; EAW96203.1; -; Genomic_DNA.
DR EMBL; BC008801; AAH08801.1; -; mRNA.
DR EMBL; BC015564; AAH15564.1; -; mRNA.
DR EMBL; BC015913; AAH15913.1; -; mRNA.
DR EMBL; BC021926; AAH21926.1; -; mRNA.
DR PIR; I53354; I53354.
DR PIR; S69501; S69501.
DR RefSeq; NP_001138898.1; NM_001145426.1.
DR RefSeq; NP_003642.3; NM_003651.4.
DR UniGene; Hs.221889; -.
DR ProteinModelPortal; P16989; -.
DR SMR; P16989; 84-160.
DR DIP; DIP-42489N; -.
DR IntAct; P16989; 26.
DR MINT; MINT-1152000; -.
DR STRING; 9606.ENSP00000228251; -.
DR PhosphoSite; P16989; -.
DR DMDM; 97536050; -.
DR PaxDb; P16989; -.
DR PRIDE; P16989; -.
DR DNASU; 8531; -.
DR Ensembl; ENST00000228251; ENSP00000228251; ENSG00000060138.
DR Ensembl; ENST00000279550; ENSP00000279550; ENSG00000060138.
DR GeneID; 8531; -.
DR KEGG; hsa:8531; -.
DR UCSC; uc001qyt.3; human.
DR CTD; 8531; -.
DR GeneCards; GC12M010852; -.
DR HGNC; HGNC:2428; YBX3.
DR HPA; HPA034838; -.
DR MIM; 603437; gene.
DR neXtProt; NX_P16989; -.
DR PharmGKB; PA26929; -.
DR eggNOG; COG1278; -.
DR HOGENOM; HOG000116439; -.
DR HOVERGEN; HBG008757; -.
DR InParanoid; P16989; -.
DR KO; K06099; -.
DR OMA; NQPPARR; -.
DR OrthoDB; EOG7TBC44; -.
DR PhylomeDB; P16989; -.
DR ChiTaRS; CSDA; human.
DR GeneWiki; CSDA_(gene); -.
DR GenomeRNAi; 8531; -.
DR NextBio; 31948; -.
DR PMAP-CutDB; P16989; -.
DR PRO; PR:P16989; -.
DR Bgee; P16989; -.
DR CleanEx; HS_CSDA; -.
DR Genevestigator; P16989; -.
DR GO; GO:0005634; C:nucleus; ISS:BHF-UCL.
DR GO; GO:0048471; C:perinuclear region of cytoplasm; ISS:BHF-UCL.
DR GO; GO:0005844; C:polysome; IEA:Ensembl.
DR GO; GO:0005923; C:tight junction; ISS:BHF-UCL.
DR GO; GO:0003690; F:double-stranded DNA binding; TAS:ProtInc.
DR GO; GO:0003730; F:mRNA 3'-UTR binding; ISS:BHF-UCL.
DR GO; GO:0017048; F:Rho GTPase binding; ISS:BHF-UCL.
DR GO; GO:0003700; F:sequence-specific DNA binding transcription factor activity; NAS:ProtInc.
DR GO; GO:0003697; F:single-stranded DNA binding; IEA:Ensembl.
DR GO; GO:0003714; F:transcription corepressor activity; TAS:ProtInc.
DR GO; GO:0070935; P:3'-UTR-mediated mRNA stabilization; IC:BHF-UCL.
DR GO; GO:0071474; P:cellular hyperosmotic response; IMP:BHF-UCL.
DR GO; GO:0071356; P:cellular response to tumor necrosis factor; IMP:BHF-UCL.
DR GO; GO:0009566; P:fertilization; IEA:Ensembl.
DR GO; GO:0001701; P:in utero embryonic development; IEA:Ensembl.
DR GO; GO:0008584; P:male gonad development; IEA:Ensembl.
DR GO; GO:0043066; P:negative regulation of apoptotic process; IEA:Ensembl.
DR GO; GO:1902219; P:negative regulation of intrinsic apoptotic signaling pathway in response to osmotic stress; IMP:BHF-UCL.
DR GO; GO:0060547; P:negative regulation of necrotic cell death; IMP:BHF-UCL.
DR GO; GO:0048642; P:negative regulation of skeletal muscle tissue development; IEA:Ensembl.
DR GO; GO:0000122; P:negative regulation of transcription from RNA polymerase II promoter; TAS:ProtInc.
DR GO; GO:2000767; P:positive regulation of cytoplasmic translation; ISS:BHF-UCL.
DR GO; GO:0046622; P:positive regulation of organ growth; IEA:Ensembl.
DR GO; GO:0009409; P:response to cold; TAS:ProtInc.
DR GO; GO:0007283; P:spermatogenesis; IEA:Ensembl.
DR GO; GO:0006351; P:transcription, DNA-dependent; IEA:UniProtKB-KW.
DR Gene3D; 2.40.50.140; -; 1.
DR InterPro; IPR019844; Cold-shock_CS.
DR InterPro; IPR011129; Cold_shock_prot.
DR InterPro; IPR002059; CSP_DNA-bd.
DR InterPro; IPR012340; NA-bd_OB-fold.
DR Pfam; PF00313; CSD; 1.
DR PRINTS; PR00050; COLDSHOCK.
DR SMART; SM00357; CSP; 1.
DR SUPFAM; SSF50249; SSF50249; 1.
DR PROSITE; PS00352; COLD_SHOCK; 1.
PE 1: Evidence at protein level;
KW Acetylation; Alternative splicing; Complete proteome; Cytoplasm;
KW DNA-binding; Nucleus; Phosphoprotein; Polymorphism;
KW Reference proteome; Repressor; Transcription;
KW Transcription regulation.
FT INIT_MET 1 1 Removed.
FT CHAIN 2 372 Y-box-binding protein 3.
FT /FTId=PRO_0000100214.
FT DOMAIN 93 157 CSD.
FT MOD_RES 2 2 N-acetylserine.
FT MOD_RES 134 134 Phosphoserine.
FT MOD_RES 201 201 Phosphoserine.
FT MOD_RES 203 203 Phosphoserine.
FT MOD_RES 204 204 Phosphoserine.
FT MOD_RES 324 324 Phosphoserine.
FT VAR_SEQ 192 260 Missing (in isoform 2).
FT /FTId=VSP_001135.
FT VAR_SEQ 340 372 RPPNAPSQDGKEAKAGEAPTENPAPPTQQSSAE -> PSS
FT (in isoform 3).
FT /FTId=VSP_001136.
FT VARIANT 75 75 T -> A (in dbSNP:rs1126501).
FT /FTId=VAR_013114.
SQ SEQUENCE 372 AA; 40090 MW; AA8517AC3B7D35CC CRC64;
MSEAGEATTT TTTTLPQAPT EAAAAAPQDP APKSPVGSGA PQAAAPAPAA HVAGNPGGDA
APAATGTAAA ASLATAAGSE DAEKKVLATK VLGTVKWFNV RNGYGFINRN DTKEDVFVHQ
TAIKKNNPRK YLRSVGDGET VEFDVVEGEK GAEAANVTGP DGVPVEGSRY AADRRRYRRG
YYGRRRGPPR NYAGEEEEEG SGSSEGFDPP ATDRQFSGAR NQLRRPQYRP QYRQRRFPPY
HVGQTFDRRS RVLPHPNRIQ AGEIGEMKDG VPEGAQLQGP VHRNPTYRPR YRSRGPPRPR
PAPAVGEAED KENQQATSGP NQPSVRRGYR RPYNYRRRPR PPNAPSQDGK EAKAGEAPTE
NPAPPTQQSS AE
//
MIM
603437
*RECORD*
*FIELD* NO
603437
*FIELD* TI
*603437 COLD-SHOCK DOMAIN PROTEIN A; CSDA
;;DNA-BINDING PROTEIN A; DBPA
*FIELD* TX
read moreCold-shock domain (CSD) proteins are characterized by a highly conserved
central domain of approximately 100 amino acids that is homologous to
bacterial cold-shock proteins.
To identify cDNAs encoding DNA-binding proteins (DBPs), Sakura et al.
(1988) screened a human placenta cDNA expression library with DNA
fragments containing either the human epidermal growth factor receptor
(EGFR; 131550) enhancer or the human c-erbB2 (164870) promoter. They
isolated cDNAs encoding DBPA and DBPB (154030). The DBPA cDNAs consisted
of 2 forms that differ by an internal 207-bp deletion. Northern blot
analysis of HeLa cell RNA detected a major 2.5-kb DBPA transcript and a
minor 2.3-kb DBPA transcript. The deduced DBPA and DBPB proteins share a
central region in which 100 of 109 amino acids are identical between the
2 proteins.
Kudo et al. (1995) isolated full-length human cDNAs encoding DBPA and
DBPB by screening for proteins that bind to the human leukosialin
(182160) promoter. The deduced 342-amino acid DBPA protein has a
cold-shock domain and a DNA-binding domain. The authors isolated the
DBPA genomic sequence and found that it contains 10 exons spanning 24
kb; exon 6, which encodes 69 amino acids, is alternatively spliced.
Northern blot analysis of human tissues demonstrated highest levels of
DBPA transcription in skeletal muscle and heart. Immunofluorescence
detected DBPA protein expression in both the cytoplasm and nucleus of
HeLa cells.
Independently, Coles et al. (1996) isolated DBPA and DBPB cDNAs by
screening for proteins that are able to bind to the repressor element in
the human GMCSF (138960) promoter. They determined that their DBPA cDNA
has a variant sequence compared to the previously reported DBPA cDNA
sequences, resulting in a deduced 372-amino acid protein with 4 amino
acid substitutions and a 30-amino acid C-terminal extension.
Overexpression of this variant DBPA led to repression of the GMCSF
promoter.
Kudo et al. (1995) mapped the CSDA gene to 12p13.1 by in situ
hybridization.
*FIELD* RF
1. Coles, L. S.; Diamond, P.; Occhiodoro, F.; Vadas, M. A.; Shannon,
M. F.: Cold shock domain proteins repress transcription from the
GM-CSF promoter. Nucleic Acids Res. 24: 2311-2317, 1996.
2. Kudo, S.; Mattei, M.-G.; Fukuda, M.: Characterization of the gene
for dbpA, a family member of the nucleic-acid-binding proteins containing
a cold-shock domain. Europ. J. Biochem. 231: 72-82, 1995.
3. Sakura, H.; Maekawa, T.; Imamoto, F.; Yasuda, K.; Ishii, S.: Two
human genes isolated by a novel method encode DNA-binding proteins
containing a common region of homology. Gene 73: 499-507, 1988.
*FIELD* CD
Sheryl A. Jankowski: 1/15/1999
*FIELD* ED
psherman: 01/21/1999
*RECORD*
*FIELD* NO
603437
*FIELD* TI
*603437 COLD-SHOCK DOMAIN PROTEIN A; CSDA
;;DNA-BINDING PROTEIN A; DBPA
*FIELD* TX
read moreCold-shock domain (CSD) proteins are characterized by a highly conserved
central domain of approximately 100 amino acids that is homologous to
bacterial cold-shock proteins.
To identify cDNAs encoding DNA-binding proteins (DBPs), Sakura et al.
(1988) screened a human placenta cDNA expression library with DNA
fragments containing either the human epidermal growth factor receptor
(EGFR; 131550) enhancer or the human c-erbB2 (164870) promoter. They
isolated cDNAs encoding DBPA and DBPB (154030). The DBPA cDNAs consisted
of 2 forms that differ by an internal 207-bp deletion. Northern blot
analysis of HeLa cell RNA detected a major 2.5-kb DBPA transcript and a
minor 2.3-kb DBPA transcript. The deduced DBPA and DBPB proteins share a
central region in which 100 of 109 amino acids are identical between the
2 proteins.
Kudo et al. (1995) isolated full-length human cDNAs encoding DBPA and
DBPB by screening for proteins that bind to the human leukosialin
(182160) promoter. The deduced 342-amino acid DBPA protein has a
cold-shock domain and a DNA-binding domain. The authors isolated the
DBPA genomic sequence and found that it contains 10 exons spanning 24
kb; exon 6, which encodes 69 amino acids, is alternatively spliced.
Northern blot analysis of human tissues demonstrated highest levels of
DBPA transcription in skeletal muscle and heart. Immunofluorescence
detected DBPA protein expression in both the cytoplasm and nucleus of
HeLa cells.
Independently, Coles et al. (1996) isolated DBPA and DBPB cDNAs by
screening for proteins that are able to bind to the repressor element in
the human GMCSF (138960) promoter. They determined that their DBPA cDNA
has a variant sequence compared to the previously reported DBPA cDNA
sequences, resulting in a deduced 372-amino acid protein with 4 amino
acid substitutions and a 30-amino acid C-terminal extension.
Overexpression of this variant DBPA led to repression of the GMCSF
promoter.
Kudo et al. (1995) mapped the CSDA gene to 12p13.1 by in situ
hybridization.
*FIELD* RF
1. Coles, L. S.; Diamond, P.; Occhiodoro, F.; Vadas, M. A.; Shannon,
M. F.: Cold shock domain proteins repress transcription from the
GM-CSF promoter. Nucleic Acids Res. 24: 2311-2317, 1996.
2. Kudo, S.; Mattei, M.-G.; Fukuda, M.: Characterization of the gene
for dbpA, a family member of the nucleic-acid-binding proteins containing
a cold-shock domain. Europ. J. Biochem. 231: 72-82, 1995.
3. Sakura, H.; Maekawa, T.; Imamoto, F.; Yasuda, K.; Ishii, S.: Two
human genes isolated by a novel method encode DNA-binding proteins
containing a common region of homology. Gene 73: 499-507, 1988.
*FIELD* CD
Sheryl A. Jankowski: 1/15/1999
*FIELD* ED
psherman: 01/21/1999