YBX3

Protein identityUniProt · HPA

UniProt accession

P16989

Gene

YBX3

Ensembl

ENSG00000060138

Chromosome

12

Canonical length

372 aa

Protein class

Predicted intracellular proteins, Transcription factors

Subcellular location

Cytosol

OverviewNCBI Gene

Enables RNA binding activity. Involved in cellular hyperosmotic response; cellular response to tumor necrosis factor; and negative regulation of programmed cell death. Located in cytosol. [provided by Alliance of Genome Resources, Jul 2025]

Canonical amino-acid sequenceUniProt

372 residues, UniProt reviewed canonical sequence.

>P16989|YBX3
     1  MSEAGEATTT TTTTLPQAPT EAAAAAPQDP APKSPVGSGA PQAAAPAPAA HVAGNPGGDA
    61  APAATGTAAA ASLATAAGSE DAEKKVLATK VLGTVKWFNV RNGYGFINRN DTKEDVFVHQ
   121  TAIKKNNPRK YLRSVGDGET VEFDVVEGEK GAEAANVTGP DGVPVEGSRY AADRRRYRRG
   181  YYGRRRGPPR NYAGEEEEEG SGSSEGFDPP ATDRQFSGAR NQLRRPQYRP QYRQRRFPPY
   241  HVGQTFDRRS RVLPHPNRIQ AGEIGEMKDG VPEGAQLQGP VHRNPTYRPR YRSRGPPRPR
   301  PAPAVGEAED KENQQATSGP NQPSVRRGYR RPYNYRRRPR PPNAPSQDGK EAKAGEAPTE
   361  NPAPPTQQSS AE

LocalizationUniProt · AlphaFold · HPA

Whether an antibody against YBX3 can act on the native protein depends on physical access: surface and secreted proteins are reachable by circulating antibodies, intracellular proteins usually are not.

Antibody reachability

Intracellular

Secreted

No

Transmembrane segments

0

Mean surface accessibility (rSASA)

0.63

Highest tissue expression

4,495 nTPM

Expression across tissuesHPA

Genetic constraint and essentialitygnomAD · DepMap

Does the body need this protein intact? Low LOEUF or a strong DepMap dependency means loss or blockade of the protein is likely to be felt.

gnomAD LOEUF (loss-of-function intolerance)

0.96

gnomAD pLI

0

gnomAD missense Z

0.11

DepMap mean gene effect

-0.18

DepMap dependency class

selective

Cancer expressionTCGA

Across TCGA tumor cohorts, this protein is over-expressed in roughly 7% of surveyed tumor types (aggregate summary; per-cohort expression, alteration, and survival load in the interactive view).

OntologyGO

Biological processes

• 3'-UTR-mediated mRNA stabilization
• apoptotic process
• cellular hyperosmotic response
• cellular response to tumor necrosis factor
• ectopic germ cell programmed cell death
• fertilization
• in utero embryonic development
• male gonad development
• negative regulation of intrinsic apoptotic signaling pathway in response to osmotic stress
• negative regulation of necroptotic process
• negative regulation of reproductive process
• negative regulation of skeletal muscle tissue development
• negative regulation of transcription by RNA polymerase II
• positive regulation of cytoplasmic translation
• positive regulation of organ growth
• regulation of gene expression
• spermatogenesis

Molecular functions

• mRNA 3'-UTR binding
• nucleic acid binding
• ribonucleoprotein complex binding
• RNA binding
• RNA polymerase II transcription regulatory region sequence-specific DNA binding
• small GTPase binding

Cellular components

• bicellular tight junction
• cytoplasm
• cytosol
• nucleus
• perinuclear region of cytoplasm
• synapse

Protein domainsUniProt · Pfam · InterPro

• Cold-shock protein Csp, DNA-binding
• Cold-shock domain
• Nucleic acid-binding, OB-fold
• Cold-shock domain, conserved site
• Cold shock domain-containing protein
• 'Cold-shock' DNA-binding domain

KeywordsUniProt

• Acetylation
• Cytoplasm
• DNA-binding
• Methylation
• Nucleus
• Phosphoprotein
• Repressor
• Transcription
• Transcription regulation

InteractionsUniProt · HPA

Protein binding partners of YBX3 in the human serome: UniProt-annotated complex subunits plus reported interactors. Each links to its own Seroatlas record.

• RRP1B
• YBX1