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

Gene ID: 389206, updated on 7-Apr-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

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
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q6ZU67.3 GenPept UniProtKB/Swiss-Prot:Q6ZU67

Gene LinkOut

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