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YBX2 Y-box binding protein 2 [ Homo sapiens (human) ]

Gene ID: 51087, updated on 17-Jun-2024

Summary

Official Symbol
YBX2provided by HGNC
Official Full Name
Y-box binding protein 2provided by HGNC
Primary source
HGNC:HGNC:17948
See related
Ensembl:ENSG00000006047 MIM:611447; AllianceGenome:HGNC:17948
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
DBPC; MSY2; CSDA3; CONTRIN
Summary
This gene encodes a nucleic acid binding protein which is highly expressed in germ cells. The encoded protein binds to a Y-box element in the promoters of certain genes but also binds to mRNA transcribed from these genes. Pseudogenes for this gene are located on chromosome 10 and 15. [provided by RefSeq, Feb 2012]
Expression
Restricted expression toward testis (RPKM 189.1) See more
Orthologs
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Genomic context

See YBX2 in Genome Data Viewer
Location:
17p13.1
Exon count:
10
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (7288263..7294639, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (7189206..7195582, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (7191582..7197958, complement)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene elongator acetyltransferase complex subunit 5 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11607 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8098 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:7164637-7165600 Neighboring gene Sharpr-MPRA regulatory region 7888 Neighboring gene claudin 7 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8100 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:7185283-7186270 Neighboring gene solute carrier family 2 member 4 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:7197310-7197485 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8101 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8102 Neighboring gene uncharacterized LOC124903912 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8103 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11608 Neighboring gene H3K27ac-H3K4me1 hESC enhancers GRCh37_chr17:7209261-7210072 and GRCh37_chr17:7210073-7210883 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8105 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8106 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11610 Neighboring gene eukaryotic translation initiation factor 5A

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Clone Names

  • MGC45104

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables DNA binding IEA
Inferred from Electronic Annotation
more info
 
enables RNA binding IEA
Inferred from Electronic Annotation
more info
 
enables nucleic acid binding IBA
Inferred from Biological aspect of Ancestor
more info
 
Process Evidence Code Pubs
involved_in oocyte development IEA
Inferred from Electronic Annotation
more info
 
involved_in positive regulation of cold-induced thermogenesis ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
involved_in regulation of gene expression IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in spermatogenesis TAS
Traceable Author Statement
more info
PubMed 
involved_in transcription by RNA polymerase II TAS
Traceable Author Statement
more info
PubMed 
involved_in translational attenuation TAS
Traceable Author Statement
more info
PubMed 
Component Evidence Code Pubs
located_in cytoplasm IEA
Inferred from Electronic Annotation
more info
 
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
 

General protein information

Preferred Names
Y-box-binding protein 2
Names
DNA-binding protein C
alternative protein YBX2
epididymis secretory sperm binding protein
germ cell specific Y-box binding protein

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)

  1. NM_015982.4NP_057066.2  Y-box-binding protein 2

    See identical proteins and their annotated locations for NP_057066.2

    Status: VALIDATED

    Source sequence(s)
    AC003688, AI805280, BC033800, DB065912
    Consensus CDS
    CCDS11098.1
    UniProtKB/Swiss-Prot
    D3DTP1, Q8N4P0, Q9Y2T7
    UniProtKB/TrEMBL
    A0A384MDP4, B2RCC2
    Related
    ENSP00000007699.5, ENST00000007699.10
    Conserved Domains (2) summary
    pfam00313
    Location:94163
    CSD; 'Cold-shock' DNA-binding domain
    cl26247
    Location:304352
    DNA_pol3_delta2; DNA polymerase III, delta subunit

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000017.11 Reference GRCh38.p14 Primary Assembly

    Range
    7288263..7294639 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017024713.3XP_016880202.1  Y-box-binding protein 2 isoform X1

    UniProtKB/TrEMBL
    B2RCC2

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_021160020.1 Reference GRCh38.p14 PATCHES

    Range
    43591..49967 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054332660.1XP_054188635.1  Y-box-binding protein 2 isoform X1

    UniProtKB/TrEMBL
    B2RCC2

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    7189206..7195582 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054316342.1XP_054172317.1  Y-box-binding protein 2 isoform X1

    UniProtKB/TrEMBL
    B2RCC2