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    BEND4 BEN domain containing 4 [ Homo sapiens (human) ]

    Gene ID: 389206, updated on 17-Jun-2024

    Summary

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    Official Symbol
    BEND4provided by HGNC
    Official Full Name
    BEN domain containing 4provided by HGNC
    Primary source
    HGNC:HGNC:23815
    See related
    Ensembl:ENSG00000188848 AllianceGenome:HGNC:23815
    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
    CCDC4
    Summary
    Predicted to enable DNA binding activity. [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Biased expression in testis (RPKM 7.9), prostate (RPKM 2.2) and 4 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See BEND4 in Genome Data Viewer
    Location:
    4p13
    Exon count:
    6
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (42110853..42152655, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (42084790..42126591, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (42112870..42154672, complement)

    Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr4:41983504-41984703 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21511 Neighboring gene ReSE screen-validated silencer GRCh37_chr4:41992428-41992647 Neighboring gene DDB1 and CUL4 associated factor 4 like 1 Neighboring gene solute carrier family 30 member 9 Neighboring gene ATPase Na+/K+ transporting subunit beta 1 pseudogene 1 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr4:42138326-42138861 Neighboring gene VISTA enhancer hs847 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:42153146-42153989 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15391 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:42263210-42263710 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21513 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:42287227-42287728 Neighboring gene uncharacterized LOC124900697 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr4:42295847-42296786 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr4:42296787-42297726 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21514 Neighboring gene uncharacterized LOC105374428 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:42304402-42304934 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr4:42312337-42312842 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr4:42315325-42316524 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:42316933-42317480 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:42317481-42318028 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21516 Neighboring gene Sharpr-MPRA regulatory region 6384

    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. Genetic Variants May Play Role in Opioid Dependence. . Am J Med Genet A, 2020 Jun. PMID 32453508
    2. Asbestos-associated genome-wide DNA methylation changes in lung cancer. Kettunen E, et al. Int J Cancer, 2017 Nov 15. PMID 28722770
    3. Proteomic analyses reveal distinct chromatin-associated and soluble transcription factor complexes. Li X, et al. Mol Syst Biol, 2015 Jan 21. PMID 25609649, Free PMC Article
    4. Complete sequencing and characterization of 21,243 full-length human cDNAs. Ota T, et al. Nat Genet, 2004 Jan. PMID 14702039
    5. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, et al. Proc Natl Acad Sci U S A, 2002 Dec 24. PMID 12477932, Free PMC Article

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Genetic Variants May Play Role in Opioid Dependence.
      Title: Genetic Variants May Play Role in Opioid Dependence.
    2. BEND4 hypermethylation is associated with lung cancer.
      Title: Asbestos-associated genome-wide DNA methylation changes in lung cancer.
    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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    Markers

    Homology

    Clone Names

    • FLJ35632, FLJ43965, MGC157807, MGC157808

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables DNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    BEN domain-containing protein 4
    Names
    coiled-coil domain containing 4
    coiled-coil domain-containing protein 4

    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_001159547.2 → NP_001153019.1  BEN domain-containing protein 4 isoform b

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) uses an alternate splice site in the 3' coding region, compared to variant 1, that results in a frameshift. It encodes isoform b which has a shorter and distinct C-terminus compared to isoform a.
      Source sequence(s)
      AA757195, AB126829
      UniProtKB/TrEMBL
      A0A0C4DGA9
      Related
      ENSP00000421160.1, ENST00000504360.5
      Conserved Domains (1) summary
      smart00338
      Location:325 → 362
      BRLZ; basic region leucin zipper

    2. NM_207406.4 → NP_997289.2  BEN domain-containing protein 4 isoform a

      See identical proteins and their annotated locations for NP_997289.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (a).
      Source sequence(s)
      AA757195, AB126828
      Consensus CDS
      CCDS47048.1
      UniProtKB/Swiss-Prot
      A1A5D6, A1A5D7, C9JQZ5, Q58A26, Q58A27, Q6ZU67
      UniProtKB/TrEMBL
      A0A0C4DGA9
      Related
      ENSP00000421169.1, ENST00000502486.6
      Conserved Domains (2) summary
      pfam10523
      Location:414 → 489
      BEN; BEN domain
      cl21462
      Location:325 → 362
      bZIP; Basic leucine zipper (bZIP) domain of bZIP transcription factors: a DNA-binding and dimerization domain

    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_000004.12 Reference GRCh38.p14 Primary Assembly

      Range
      42110853..42152655 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017008185.2 → XP_016863674.1  BEN domain-containing protein 4 isoform X1

      UniProtKB/Swiss-Prot
      A1A5D6, A1A5D7, C9JQZ5, Q58A26, Q58A27, Q6ZU67
      UniProtKB/TrEMBL
      A0A0C4DGA9
      Conserved Domains (2) summary
      pfam10523
      Location:414 → 489
      BEN; BEN domain
      cl21462
      Location:325 → 362
      bZIP; Basic leucine zipper (bZIP) domain of bZIP transcription factors: a DNA-binding and dimerization domain

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060928.1 Alternate T2T-CHM13v2.0

      Range
      42084790..42126591 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054349972.1 → XP_054205947.1  BEN domain-containing protein 4 isoform X1

      UniProtKB/Swiss-Prot
      A1A5D6, A1A5D7, C9JQZ5, Q58A26, Q58A27, Q6ZU67
      UniProtKB/TrEMBL
      A0A0C4DGA9
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q6ZU67.3 GenPept UniProtKB/Swiss-Prot:Q6ZU67

    Gene LinkOut

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

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