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

    Gene ID: 139105, updated on 28-Oct-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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    See BEND2 in Genome Data Viewer
    Location:
    Xp22.13
    Exon count:
    14
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (18162931..18220886, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (17745567..17803511, complement)
    RS_2024_09 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 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_2024_08

    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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