YBX3 Y-box binding protein 3 [Homo sapiens (human)] - Gene

Summary

Official Symbol: YBX3provided by HGNC
Official Full Name: Y-box binding protein 3provided by HGNC
Primary source: HGNC:HGNC:2428
See related: Ensembl:ENSG00000060138 MIM:603437; AllianceGenome:HGNC:2428
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: CSDA; DBPA; CSDA1; ZONAB
Summary: 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, Dec 2024]
Expression: Broad expression in testis (RPKM 175.4), skin (RPKM 131.9) and 23 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 12p13.2

Exon count:: 11

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	12	NC_000012.12 (10699089..10723323, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	12	NC_060936.1 (10572193..10596426, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	12	NC_000012.11 (10851688..10875922, complement)

Chromosome 12 - NC_000012.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Tissue-specific circular RNA induction during human fetal development
Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
BioProject: PRJNA270632
Publication: PMID 26076956
Analysis date: Mon Apr 2 22:54:59 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

The YBX3 RNA-binding protein posttranscriptionally controls SLC1A5 mRNA in proliferating and differentiating skeletal muscle cells.
Title: The YBX3 RNA-binding protein posttranscriptionally controls SLC1A5 mRNA in proliferating and differentiating skeletal muscle cells.
M6A-mediated-upregulation of lncRNA BLACAT3 promotes bladder cancer angiogenesis and hematogenous metastasis through YBX3 nuclear shuttling and enhancing NCF2 transcription.
Title: M6A-mediated-upregulation of lncRNA BLACAT3 promotes bladder cancer angiogenesis and hematogenous metastasis through YBX3 nuclear shuttling and enhancing NCF2 transcription.
Identification of RNA-binding protein YBX3 as an oncogene in clear cell renal cell carcinoma.
Title: Identification of RNA-binding protein YBX3 as an oncogene in clear cell renal cell carcinoma.
Identification and verification of YBX3 and its regulatory gene HEIH as an oncogenic system: A multidimensional analysis in colon cancer.
Title: Identification and verification of YBX3 and its regulatory gene HEIH as an oncogenic system: A multidimensional analysis in colon cancer.
Knockdown of DNA-binding protein A enhances the chemotherapy sensitivity of colorectal cancer via suppressing the Wnt/beta-catenin/Chk1 pathway.
Title: Knockdown of DNA-binding protein A enhances the chemotherapy sensitivity of colorectal cancer via suppressing the Wnt/β-catenin/Chk1 pathway.
YB-3 substitutes YB-1 in global mRNA binding.
Title: YB-3 substitutes YB-1 in global mRNA binding.
Y-Box-Binding Protein 3 (YBX3) Restricts Influenza A Virus by Interacting with Viral Ribonucleoprotein Complex and Imparing its Function.
Title: Y-Box-Binding Protein 3 (YBX3) Restricts Influenza A Virus by Interacting with Viral Ribonucleoprotein Complex and Imparing its Function.
YBX3 binds within the 3' UTR of SLC7A5 to stabilize the transcript.
Title: The RNA-Binding Protein YBX3 Controls Amino Acid Levels by Regulating SLC mRNA Abundance.
ZONAB is up-regulated in bladder cancer cell lines, which promotes invasion, demonstrating the important role it plays in tumorogenesis and cancer progression
Title: Zonula occludens-1 associated nucleic acid binding protein plays an invasion-promoting role in bladder cancer.
Authors examined, for the first time in a Turkish population, the association between protamine gene alleles (PRM1 c.-190C>A, PRM1 c.197G>T, and PRM2 c.248C>T), and YBX2 (c.187T>C and c.1095 + 16A>G) and male infertility.
Title: Genetic Polymorphisms in PRM1, PRM2, and YBX2 Genes are Associated with Male Factor Infertility.

Submit: New GeneRIF Correction See all GeneRIFs (24)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

ha2919 (e-PCR)
- UniSTS:515610

IB391 (e-PCR)
- UniSTS:20001

G07129 (e-PCR)
- UniSTS:47410

D16S2544E (e-PCR)
- UniSTS:151633

G62320 (e-PCR)
- UniSTS:139377

RH92531 (e-PCR)
- UniSTS:87194

G61989 (e-PCR)
- UniSTS:139208

WI-20104 (e-PCR)
- UniSTS:62197

RH69102 (e-PCR)
- UniSTS:89854

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables RNA binding	HDA more info	PubMed
enables RNA polymerase II transcription regulatory region sequence-specific DNA binding	IEA Inferred from Electronic Annotation more info
enables mRNA 3'-UTR binding	ISS Inferred from Sequence or Structural Similarity more info	PubMed
enables nucleic acid binding	IBA Inferred from Biological aspect of Ancestor more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables ribonucleoprotein complex binding	IEA Inferred from Electronic Annotation more info
enables small GTPase binding	ISS Inferred from Sequence or Structural Similarity more info

Process	Evidence Code	Pubs
involved_in 3'-UTR-mediated mRNA stabilization	IC Inferred by Curator more info	PubMed
involved_in apoptotic process	IEA Inferred from Electronic Annotation more info
involved_in cellular hyperosmotic response	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in cellular response to tumor necrosis factor	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in ectopic germ cell programmed cell death	IEA Inferred from Electronic Annotation more info
involved_in fertilization	IEA Inferred from Electronic Annotation more info
involved_in in utero embryonic development	IEA Inferred from Electronic Annotation more info
involved_in male gonad development	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of intrinsic apoptotic signaling pathway in response to osmotic stress	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of necroptotic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of reproductive process	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of skeletal muscle tissue development	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of transcription by RNA polymerase II	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of cytoplasmic translation	ISS Inferred from Sequence or Structural Similarity more info	PubMed
involved_in positive regulation of organ growth	IEA Inferred from Electronic Annotation more info
involved_in regulation of gene expression	IBA Inferred from Biological aspect of Ancestor more info
involved_in spermatogenesis	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in bicellular tight junction	ISS Inferred from Sequence or Structural Similarity more info	PubMed
located_in cytoplasm	TAS Traceable Author Statement more info	PubMed
located_in cytosol	IDA Inferred from Direct Assay more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	ISS Inferred from Sequence or Structural Similarity more info	PubMed
located_in perinuclear region of cytoplasm	ISS Inferred from Sequence or Structural Similarity more info	PubMed
located_in synapse	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: Y-box-binding protein 3

Names: DNA-binding protein A; ZO-1-associated nucleic acid-binding protein; cold shock domain-containing protein A; cold-shock domain containing A1; cold-shock domain protein A; single-strand DNA-binding protein NF-GMB

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

NM_001145426.2 → NP_001138898.1 Y-box-binding protein 3 isoform b

See identical proteins and their annotated locations for NP_001138898.1

Status: VALIDATED

Description

Transcript Variant: This variant (2) lacks an alternate in-frame exon compared to variant 1. The resulting protein (isoform b) is shorter compared to isoform a.

Source sequence(s)

AC021049

Consensus CDS

CCDS44831.1

UniProtKB/TrEMBL

Q96GD7

Related

ENSP00000279550.7, ENST00000279550.11

Conserved Domains (1) summary

pfam00313
Location:91 → 160

CSD; 'Cold-shock' DNA-binding domain
NM_003651.5 → NP_003642.3 Y-box-binding protein 3 isoform a

See identical proteins and their annotated locations for NP_003642.3

Status: VALIDATED

Description

Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (a).

Source sequence(s)

AC021049

Consensus CDS

CCDS8630.1

UniProtKB/Swiss-Prot

B2RBW6, P16989, Q14121, Q969N6, Q96B76

UniProtKB/TrEMBL

Q96GD7

Related

ENSP00000228251.4, ENST00000228251.9

Conserved Domains (1) summary

pfam00313
Location:91 → 160

CSD; 'Cold-shock' DNA-binding domain

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000012.12 Reference GRCh38.p14 Primary Assembly

Range

10699089..10723323 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_017020123.3 → XP_016875612.1 Y-box-binding protein 3 isoform X3

UniProtKB/TrEMBL

Q96GD7
XM_017020122.3 → XP_016875611.1 Y-box-binding protein 3 isoform X2
XM_047429799.1 → XP_047285755.1 Y-box-binding protein 3 isoform X1

UniProtKB/Swiss-Prot

B2RBW6, P16989, Q14121, Q969N6, Q96B76

UniProtKB/TrEMBL

Q96GD7
XM_011520871.4 → XP_011519173.1 Y-box-binding protein 3 isoform X4

Conserved Domains (1) summary

pfam00313
Location:91 → 160

CSD; 'Cold-shock' DNA-binding domain

Alternate T2T-CHM13v2.0

Genomic

NC_060936.1 Alternate T2T-CHM13v2.0

Range

10572193..10596426 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054373689.1 → XP_054229664.1 Y-box-binding protein 3 isoform X3

UniProtKB/TrEMBL

Q96GD7
XM_054373688.1 → XP_054229663.1 Y-box-binding protein 3 isoform X2
XM_054373687.1 → XP_054229662.1 Y-box-binding protein 3 isoform X1

UniProtKB/Swiss-Prot

B2RBW6, P16989, Q14121, Q969N6, Q96B76

UniProtKB/TrEMBL

Q96GD7
XM_054373690.1 → XP_054229665.1 Y-box-binding protein 3 isoform X4