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P16989

- YBOX3_HUMAN

UniProt

P16989 - YBOX3_HUMAN

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Protein

Y-box-binding protein 3

Gene

YBX3

Organism
Homo sapiens (Human)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli

Functioni

Binds to the GM-CSF promoter. Seems to act as a repressor. Binds also to full length mRNA and to short RNA sequences containing the consensus site 5'-UCCAUCA-3'. May have a role in translation repression (By similarity).By similarity

GO - Molecular functioni

  1. double-stranded DNA binding Source: ProtInc
  2. mRNA 3'-UTR binding Source: BHF-UCL
  3. poly(A) RNA binding Source: UniProtKB
  4. Rho GTPase binding Source: BHF-UCL
  5. RNA polymerase II regulatory region sequence-specific DNA binding Source: Ensembl
  6. RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription Source: Ensembl
  7. sequence-specific DNA binding transcription factor activity Source: ProtInc
  8. single-stranded DNA binding Source: Ensembl
  9. transcription corepressor activity Source: ProtInc

GO - Biological processi

  1. 3'-UTR-mediated mRNA stabilization Source: BHF-UCL
  2. cellular hyperosmotic response Source: BHF-UCL
  3. cellular response to tumor necrosis factor Source: BHF-UCL
  4. fertilization Source: Ensembl
  5. in utero embryonic development Source: Ensembl
  6. male gonad development Source: Ensembl
  7. negative regulation of apoptotic process Source: Ensembl
  8. negative regulation of intrinsic apoptotic signaling pathway in response to osmotic stress Source: BHF-UCL
  9. negative regulation of necroptotic process Source: BHF-UCL
  10. negative regulation of skeletal muscle tissue development Source: Ensembl
  11. negative regulation of transcription from RNA polymerase II promoter Source: ProtInc
  12. positive regulation of cytoplasmic translation Source: BHF-UCL
  13. positive regulation of organ growth Source: Ensembl
  14. response to cold Source: ProtInc
  15. spermatogenesis Source: Ensembl
Complete GO annotation...

Keywords - Molecular functioni

Repressor

Keywords - Biological processi

Transcription, Transcription regulation

Keywords - Ligandi

DNA-binding

Names & Taxonomyi

Protein namesi
Recommended name:
Y-box-binding protein 3
Alternative name(s):
Cold shock domain-containing protein A
DNA-binding protein A
Single-strand DNA-binding protein NF-GMB
Gene namesi
Name:YBX3
Synonyms:CSDA, DBPA
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
ProteomesiUP000005640: Chromosome 12

Organism-specific databases

HGNCiHGNC:2428. YBX3.

Subcellular locationi

GO - Cellular componenti

  1. cytoplasm Source: HPA
  2. nucleus Source: BHF-UCL
  3. perinuclear region of cytoplasm Source: BHF-UCL
  4. polysome Source: Ensembl
  5. tight junction Source: BHF-UCL
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Nucleus

Pathology & Biotechi

Organism-specific databases

PharmGKBiPA26929.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methioninei1 – 11Removed2 Publications
Chaini2 – 372371Y-box-binding protein 3PRO_0000100214Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei2 – 21N-acetylserine2 Publications
Modified residuei134 – 1341Phosphoserine1 Publication
Modified residuei201 – 2011Phosphoserine2 Publications
Modified residuei203 – 2031Phosphoserine2 Publications
Modified residuei204 – 2041Phosphoserine3 Publications
Modified residuei324 – 3241Phosphoserine1 Publication

Keywords - PTMi

Acetylation, Phosphoprotein

Proteomic databases

MaxQBiP16989.
PaxDbiP16989.
PRIDEiP16989.

PTM databases

PhosphoSiteiP16989.

Miscellaneous databases

PMAP-CutDBP16989.

Expressioni

Tissue specificityi

Highly expressed in skeletal muscle and heart.

Gene expression databases

BgeeiP16989.
CleanExiHS_CSDA.
GenevestigatoriP16989.

Organism-specific databases

HPAiHPA034838.

Interactioni

Subunit structurei

Found in a mRNP complex with YBX2.By similarity

Protein-protein interaction databases

BioGridi114101. 64 interactions.
DIPiDIP-42489N.
IntActiP16989. 27 interactions.
MINTiMINT-1152000.
STRINGi9606.ENSP00000228251.

Structurei

3D structure databases

ProteinModelPortaliP16989.
SMRiP16989. Positions 84-160.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini93 – 15765CSDAdd
BLAST

Sequence similaritiesi

Contains 1 CSD (cold-shock) domain.Curated

Phylogenomic databases

eggNOGiCOG1278.
GeneTreeiENSGT00390000009256.
HOGENOMiHOG000116439.
HOVERGENiHBG008757.
InParanoidiP16989.
KOiK06099.
OMAiLSFNRND.
OrthoDBiEOG7TBC44.
PhylomeDBiP16989.
TreeFamiTF317306.

Family and domain databases

Gene3Di2.40.50.140. 1 hit.
InterProiIPR019844. Cold-shock_CS.
IPR011129. Cold_shock_prot.
IPR002059. CSP_DNA-bd.
IPR012340. NA-bd_OB-fold.
[Graphical view]
PfamiPF00313. CSD. 1 hit.
[Graphical view]
PRINTSiPR00050. COLDSHOCK.
SMARTiSM00357. CSP. 1 hit.
[Graphical view]
SUPFAMiSSF50249. SSF50249. 1 hit.
PROSITEiPS00352. COLD_SHOCK. 1 hit.
[Graphical view]

Sequences (3)i

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

This entry describes 3 isoformsi produced by alternative splicing. Align

Note: Additional isoforms seem to exist.

Isoform 1 (identifier: P16989-1) [UniParc]FASTAAdd to Basket

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide

        10         20         30         40         50
MSEAGEATTT TTTTLPQAPT EAAAAAPQDP APKSPVGSGA PQAAAPAPAA
60 70 80 90 100
HVAGNPGGDA APAATGTAAA ASLATAAGSE DAEKKVLATK VLGTVKWFNV
110 120 130 140 150
RNGYGFINRN DTKEDVFVHQ TAIKKNNPRK YLRSVGDGET VEFDVVEGEK
160 170 180 190 200
GAEAANVTGP DGVPVEGSRY AADRRRYRRG YYGRRRGPPR NYAGEEEEEG
210 220 230 240 250
SGSSEGFDPP ATDRQFSGAR NQLRRPQYRP QYRQRRFPPY HVGQTFDRRS
260 270 280 290 300
RVLPHPNRIQ AGEIGEMKDG VPEGAQLQGP VHRNPTYRPR YRSRGPPRPR
310 320 330 340 350
PAPAVGEAED KENQQATSGP NQPSVRRGYR RPYNYRRRPR PPNAPSQDGK
360 370
EAKAGEAPTE NPAPPTQQSS AE
Length:372
Mass (Da):40,090
Last modified:May 16, 2006 - v4
Checksum:iAA8517AC3B7D35CC
GO
Isoform 2 (identifier: P16989-2) [UniParc]FASTAAdd to Basket

The sequence of this isoform differs from the canonical sequence as follows:
     192-260: Missing.

Show »
Length:303
Mass (Da):31,947
Checksum:i29E708D6FCB442CD
GO
Isoform 3 (identifier: P16989-3) [UniParc]FASTAAdd to Basket

The sequence of this isoform differs from the canonical sequence as follows:
     340-372: RPPNAPSQDGKEAKAGEAPTENPAPPTQQSSAE → PSS

Show »
Length:342
Mass (Da):37,021
Checksum:i255258C4B4E80A4F
GO

Sequence cautioni

The sequence AAA35749.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti75 – 751T → A.3 Publications
Corresponds to variant rs1126501 [ dbSNP | Ensembl ].
VAR_013114

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei192 – 26069Missing in isoform 2. 1 PublicationVSP_001135Add
BLAST
Alternative sequencei340 – 37233RPPNA…QSSAE → PSS in isoform 3. 1 PublicationVSP_001136Add
BLAST

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
M24069 mRNA. Translation: AAA35749.1. Different initiation.
L29071
, L29064, L29065, L29066, L29067, L29068, L29069, L29070 Genomic DNA. Translation: AAA79243.1.
X95325 mRNA. Translation: CAA64631.1.
X72712 mRNA. Translation: CAA51261.1.
AK314846 mRNA. Translation: BAG37363.1.
CH471094 Genomic DNA. Translation: EAW96201.1.
CH471094 Genomic DNA. Translation: EAW96203.1.
BC008801 mRNA. Translation: AAH08801.1.
BC015564 mRNA. Translation: AAH15564.1.
BC015913 mRNA. Translation: AAH15913.1.
BC021926 mRNA. Translation: AAH21926.1.
CCDSiCCDS44831.1. [P16989-2]
CCDS8630.1. [P16989-1]
PIRiI53354.
S69501.
RefSeqiNP_001138898.1. NM_001145426.1. [P16989-2]
NP_003642.3. NM_003651.4. [P16989-1]
UniGeneiHs.221889.

Genome annotation databases

EnsembliENST00000228251; ENSP00000228251; ENSG00000060138. [P16989-1]
ENST00000279550; ENSP00000279550; ENSG00000060138. [P16989-2]
GeneIDi8531.
KEGGihsa:8531.
UCSCiuc001qyt.3. human. [P16989-1]
uc001qyu.3. human. [P16989-2]

Polymorphism databases

DMDMi97536050.

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
M24069 mRNA. Translation: AAA35749.1 . Different initiation.
L29071
, L29064 , L29065 , L29066 , L29067 , L29068 , L29069 , L29070 Genomic DNA. Translation: AAA79243.1 .
X95325 mRNA. Translation: CAA64631.1 .
X72712 mRNA. Translation: CAA51261.1 .
AK314846 mRNA. Translation: BAG37363.1 .
CH471094 Genomic DNA. Translation: EAW96201.1 .
CH471094 Genomic DNA. Translation: EAW96203.1 .
BC008801 mRNA. Translation: AAH08801.1 .
BC015564 mRNA. Translation: AAH15564.1 .
BC015913 mRNA. Translation: AAH15913.1 .
BC021926 mRNA. Translation: AAH21926.1 .
CCDSi CCDS44831.1. [P16989-2 ]
CCDS8630.1. [P16989-1 ]
PIRi I53354.
S69501.
RefSeqi NP_001138898.1. NM_001145426.1. [P16989-2 ]
NP_003642.3. NM_003651.4. [P16989-1 ]
UniGenei Hs.221889.

3D structure databases

ProteinModelPortali P16989.
SMRi P16989. Positions 84-160.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

BioGridi 114101. 64 interactions.
DIPi DIP-42489N.
IntActi P16989. 27 interactions.
MINTi MINT-1152000.
STRINGi 9606.ENSP00000228251.

PTM databases

PhosphoSitei P16989.

Polymorphism databases

DMDMi 97536050.

Proteomic databases

MaxQBi P16989.
PaxDbi P16989.
PRIDEi P16989.

Protocols and materials databases

DNASUi 8531.
Structural Biology Knowledgebase Search...

Genome annotation databases

Ensembli ENST00000228251 ; ENSP00000228251 ; ENSG00000060138 . [P16989-1 ]
ENST00000279550 ; ENSP00000279550 ; ENSG00000060138 . [P16989-2 ]
GeneIDi 8531.
KEGGi hsa:8531.
UCSCi uc001qyt.3. human. [P16989-1 ]
uc001qyu.3. human. [P16989-2 ]

Organism-specific databases

CTDi 8531.
GeneCardsi GC12M010852.
HGNCi HGNC:2428. YBX3.
HPAi HPA034838.
MIMi 603437. gene.
neXtProti NX_P16989.
PharmGKBi PA26929.
GenAtlasi Search...

Phylogenomic databases

eggNOGi COG1278.
GeneTreei ENSGT00390000009256.
HOGENOMi HOG000116439.
HOVERGENi HBG008757.
InParanoidi P16989.
KOi K06099.
OMAi LSFNRND.
OrthoDBi EOG7TBC44.
PhylomeDBi P16989.
TreeFami TF317306.

Miscellaneous databases

ChiTaRSi CSDA. human.
GeneWikii CSDA_(gene).
GenomeRNAii 8531.
NextBioi 31948.
PMAP-CutDB P16989.
PROi P16989.
SOURCEi Search...

Gene expression databases

Bgeei P16989.
CleanExi HS_CSDA.
Genevestigatori P16989.

Family and domain databases

Gene3Di 2.40.50.140. 1 hit.
InterProi IPR019844. Cold-shock_CS.
IPR011129. Cold_shock_prot.
IPR002059. CSP_DNA-bd.
IPR012340. NA-bd_OB-fold.
[Graphical view ]
Pfami PF00313. CSD. 1 hit.
[Graphical view ]
PRINTSi PR00050. COLDSHOCK.
SMARTi SM00357. CSP. 1 hit.
[Graphical view ]
SUPFAMi SSF50249. SSF50249. 1 hit.
PROSITEi PS00352. COLD_SHOCK. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  1. "Two human genes isolated by a novel method encode DNA-binding proteins containing a common region of homology."
    Sakura H., Maekawa T., Imamoto F., Yasuda K., Ishii S.
    Gene 73:499-507(1988) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 3), VARIANT ALA-75.
  2. "Characterization of the gene for dbpA, a family member of the nucleic-acid-binding proteins containing a cold-shock domain."
    Kudo S., Mattei M.-G., Fukuda M.
    Eur. J. Biochem. 231:72-82(1995) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], ALTERNATIVE SPLICING, VARIANT ALA-75.
    Tissue: Placenta.
  3. "Cold shock domain proteins repress transcription from the GM-CSF promoter."
    Coles L.S., Diamond P., Occhiodoro F., Vadas M.A., Shannon M.F.
    Nucleic Acids Res. 24:2311-2317(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1).
  4. Moschonas N.K.
    Submitted (MAR-1993) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1).
    Tissue: Blood.
  5. "Complete sequencing and characterization of 21,243 full-length human cDNAs."
    Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R., Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H., Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S.
    , Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K., Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S., Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O., Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H., Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B., Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H., Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O., Isogai T., Sugano S.
    Nat. Genet. 36:40-45(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
  6. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  7. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
    The MGC Project Team
    Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 1 AND 2), VARIANT ALA-75.
    Tissue: Kidney, Lung, Lymph and Muscle.
  8. Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-201; SER-203 AND SER-204, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Cervix carcinoma.
  9. "Lys-N and trypsin cover complementary parts of the phosphoproteome in a refined SCX-based approach."
    Gauci S., Helbig A.O., Slijper M., Krijgsveld J., Heck A.J., Mohammed S.
    Anal. Chem. 81:4493-4501(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT SER-2, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS], CLEAVAGE OF INITIATOR METHIONINE [LARGE SCALE ANALYSIS].
  10. "Quantitative phosphoproteomic analysis of T cell receptor signaling reveals system-wide modulation of protein-protein interactions."
    Mayya V., Lundgren D.H., Hwang S.-I., Rezaul K., Wu L., Eng J.K., Rodionov V., Han D.K.
    Sci. Signal. 2:RA46-RA46(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-134; SER-201; SER-203 AND SER-204, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Leukemic T-cell.
  11. "Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis."
    Olsen J.V., Vermeulen M., Santamaria A., Kumar C., Miller M.L., Jensen L.J., Gnad F., Cox J., Jensen T.S., Nigg E.A., Brunak S., Mann M.
    Sci. Signal. 3:RA3-RA3(2010) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-204, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Cervix carcinoma.
  12. Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  13. "System-wide temporal characterization of the proteome and phosphoproteome of human embryonic stem cell differentiation."
    Rigbolt K.T., Prokhorova T.A., Akimov V., Henningsen J., Johansen P.T., Kratchmarova I., Kassem M., Mann M., Olsen J.V., Blagoev B.
    Sci. Signal. 4:RS3-RS3(2011) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-324, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  14. "Comparative large-scale characterisation of plant vs. mammal proteins reveals similar and idiosyncratic N-alpha acetylation features."
    Bienvenut W.V., Sumpton D., Martinez A., Lilla S., Espagne C., Meinnel T., Giglione C.
    Mol. Cell. Proteomics 11:M111.015131-M111.015131(2012) [PubMed] [Europe PMC] [Abstract]
    Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT SER-2, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].

Entry informationi

Entry nameiYBOX3_HUMAN
AccessioniPrimary (citable) accession number: P16989
Secondary accession number(s): B2RBW6
, Q14121, Q969N6, Q96B76
Entry historyi
Integrated into UniProtKB/Swiss-Prot: August 1, 1990
Last sequence update: May 16, 2006
Last modified: October 29, 2014
This is version 156 of the entry and version 4 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Human chromosome 12
    Human chromosome 12: entries, gene names and cross-references to MIM
  2. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  3. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  4. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  5. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3