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BEND2 BEN domain containing 2 [ Homo sapiens (human) ]

Gene ID: 139105, updated on 3-Apr-2024

Summary

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Official Symbol
BEND2provided by HGNC
Official Full Name
BEN domain containing 2provided by HGNC
Primary source
HGNC:HGNC:28509
See related
Ensembl:ENSG00000177324 AllianceGenome:HGNC:28509
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
CXorf20
Summary
This gene encodes a protein which has two BEN domains in the C-terminus. These domains are found in proteins which participate in protein and DNA interactions which occur during chromatin restructuring or transcription. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2011]
Expression
Restricted expression toward testis (RPKM 2.6) See more
Orthologs
all
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Genomic context

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Location:
Xp22.13
Exon count:
14
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (18162931..18220886, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (17745567..17803511, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (18181051..18239006, complement)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene MDM4 pseudogene 1 Neighboring gene long intergenic non-protein coding RNA 1456 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:18244195-18244696 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:18247834-18248500 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:18296901-18297401 Neighboring gene Scm polycomb group protein like 2 Neighboring gene uncharacterized LOC124905253 Neighboring gene thymosin beta 10 pseudogene 2

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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

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Related articles in PubMed

  1. The ten-year evolutionary trajectory of a highly recurrent paediatric high grade neuroepithelial tumour with MN1:BEND2 fusion. Burford A, et al. Sci Rep, 2018 Jan 18. PMID 29348602, Free PMC Article
  2. Epileptic encephalopathy in a girl with an interstitial deletion of Xp22 comprising promoter and exon 1 of the CDKL5 gene. Bahi-Buisson N, et al. Am J Med Genet B Neuropsychiatr Genet, 2010 Jan 5. PMID 19455595
  3. Early ependymal tumor with MN1-BEND2 fusion: a mostly cerebral tumor of female children with a good prognosis that is distinct from classical astroblastoma. Lehman NL. J Neurooncol, 2023 Feb. PMID 36604386, Free PMC Article
  4. EWSR1-BEND2 fusion defines an epigenetically distinct subtype of astroblastoma. Lucas CG, et al. Acta Neuropathol, 2022 Jan. PMID 34825267, Free PMC Article
  5. Spinal cord astroblastoma with an EWSR1-BEND2 fusion classified as a high-grade neuroepithelial tumour with MN1 alteration. Yamasaki K, et al. Neuropathol Appl Neurobiol, 2020 Feb. PMID 31863478

See all (11) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Early ependymal tumor with MN1-BEND2 fusion: a mostly cerebral tumor of female children with a good prognosis that is distinct from classical astroblastoma.
    Title: Early ependymal tumor with MN1-BEND2 fusion: a mostly cerebral tumor of female children with a good prognosis that is distinct from classical astroblastoma.
  2. EWSR1-BEND2 fusion defines an epigenetically distinct subtype of astroblastoma.
    Title: EWSR1-BEND2 fusion defines an epigenetically distinct subtype of astroblastoma.
  3. Spinal cord astroblastoma with an EWSR1-BEND2 fusion classified as a high-grade neuroepithelial tumour with MN1 alteration.
    Title: Spinal cord astroblastoma with an EWSR1-BEND2 fusion classified as a high-grade neuroepithelial tumour with MN1 alteration.
Submit: New GeneRIF Correction

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)

Genotypes

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Homology

Clone Names

  • MGC33653

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables DNA binding IEA
Inferred from Electronic Annotation
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 

General protein information

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Preferred Names
BEN domain-containing protein 2

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.

Genomic

  1. NG_021323.1 RefSeqGene

    Range
    5019..62974
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001184767.2 → NP_001171696.1  BEN domain-containing protein 2 isoform 2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) differs in the 3' UTR and has multiple coding region differences, compared to variant 1, one of which results in a frameshift. The resulting protein (isoform 2) has a distinct C-terminus and is shorter than isoform 1.
    Source sequence(s)
    AL096763, BC096745, BX952865
    Consensus CDS
    CCDS55375.1
    UniProtKB/TrEMBL
    B3KXX8
    Related
    ENSP00000369369.3, ENST00000380030.4
    Conserved Domains (2) summary
    smart01025
    Location:414 → 489
    BEN; The BEN domain is found in diverse animal proteins
    pfam13900
    Location:84 → 126
    GVQW; Putative domain of unknown function

  2. NM_153346.5 → NP_699177.2  BEN domain-containing protein 2 isoform 1

    See identical proteins and their annotated locations for NP_699177.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
    Source sequence(s)
    AK128155, AL096763, BC037301, BX952865
    Consensus CDS
    CCDS14184.1
    UniProtKB/Swiss-Prot
    E9PFY2, Q4V9S2, Q5JXE5, Q8NDZ0
    UniProtKB/TrEMBL
    B3KXX8
    Related
    ENSP00000369372.4, ENST00000380033.9
    Conserved Domains (2) summary
    smart01025
    Location:687 → 763
    BEN; The BEN domain is found in diverse animal proteins
    pfam13900
    Location:84 → 126
    GVQW; Putative domain of unknown function

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_000023.11 Reference GRCh38.p14 Primary Assembly

    Range
    18162931..18220886 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017029266.2 → XP_016884755.1  BEN domain-containing protein 2 isoform X2

    UniProtKB/TrEMBL
    B3KXX8

  2. XM_011545447.2 → XP_011543749.1  BEN domain-containing protein 2 isoform X1

    UniProtKB/TrEMBL
    B3KXX8
    Conserved Domains (2) summary
    smart01025
    Location:701 → 777
    BEN; The BEN domain is found in diverse animal proteins
    pfam13900
    Location:84 → 126
    GVQW; Putative domain of unknown function

  3. XM_017029267.2 → XP_016884756.1  BEN domain-containing protein 2 isoform X3

    UniProtKB/TrEMBL
    B3KXX8

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060947.1 Alternate T2T-CHM13v2.0

    Range
    17745567..17803511 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054326457.1 → XP_054182432.1  BEN domain-containing protein 2 isoform X2

  2. XM_054326456.1 → XP_054182431.1  BEN domain-containing protein 2 isoform X1

  3. XM_054326458.1 → XP_054182433.1  BEN domain-containing protein 2 isoform X3

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8NDZ0.2 GenPept UniProtKB/Swiss-Prot:Q8NDZ0

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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