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BEND6 BEN domain containing 6 [ Homo sapiens (human) ]

Gene ID: 221336, updated on 3-Apr-2024

Summary

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Official Symbol
BEND6provided by HGNC
Official Full Name
BEN domain containing 6provided by HGNC
Primary source
HGNC:HGNC:20871
See related
Ensembl:ENSG00000151917 AllianceGenome:HGNC:20871
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
C6orf65
Summary
Enables transcription corepressor activity. Predicted to be involved in negative regulation of Notch signaling pathway and positive regulation of neuron differentiation. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Biased expression in brain (RPKM 5.4), gall bladder (RPKM 1.0) and 7 other tissues See more
Orthologs
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Genomic context

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Location:
6p12.1
Exon count:
12
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (56955107..57027346)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (56794154..56866397)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (56819905..56892144)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene dystonin Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_92361 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24706 Neighboring gene ribosomal protein L17 pseudogene 26 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_92363 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_92364 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24707 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr6:56803197-56804396 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:56818611-56819242 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17300 Neighboring gene RNA, U6 small nuclear 626, pseudogene Neighboring gene oligosaccharyltransferase complex subunit pseudogene 6 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:56895065-56895565 Neighboring gene Sharpr-MPRA regulatory region 7771 Neighboring gene ferritin heavy chain 1 pseudogene 15 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24708 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:56912079-56912956 Neighboring gene mitochondrial ribosomal protein L30 pseudogene 1 Neighboring gene KIAA1586

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. BEND6 is a nuclear antagonist of Notch signaling during self-renewal of neural stem cells. Dai Q, et al. Development, 2013 May. PMID 23571214, Free PMC Article
  2. Parent-of-origin-specific allelic associations among 106 genomic loci for age at menarche. Perry JR, et al. Nature, 2014 Oct 2. PMID 25231870, Free PMC Article
  3. Systematic mapping of genetic interactions for de novo fatty acid synthesis identifies C12orf49 as a regulator of lipid metabolism. Aregger M, et al. Nat Metab, 2020 Jun. PMID 32694731, 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. Dual proteome-scale networks reveal cell-specific remodeling of the human interactome. Huttlin EL, et al. Cell, 2021 May 27. PMID 33961781, Free PMC Article

See all (7) citations in PubMed

GeneRIFs: Gene References Into Functions

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

EBI GWAS Catalog

Description
Parent-of-origin-specific allelic associations among 106 genomic loci for age at menarche.
EBI GWAS Catalog

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

  • FLJ30162

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables DNA binding IEA
Inferred from Electronic Annotation
more info
  
enables chromatin binding IEA
Inferred from Electronic Annotation
more info
  
enables transcription corepressor activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables transcription corepressor activity IGI
Inferred from Genetic Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in negative regulation of DNA-templated transcription IEA
Inferred from Electronic Annotation
more info
  
involved_in negative regulation of Notch signaling pathway IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in nervous system development IEA
Inferred from Electronic Annotation
more info
  
involved_in positive regulation of neuron differentiation IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
BEN domain-containing protein 6

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_001318539.2 → NP_001305468.1  BEN domain-containing protein 6 isoform 2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks multiple 3' coding exons and contains an alternate 3' coding region and 3' UTR compared to variant 1. The encoded isoform (2) has a shorter, distinct C-terminus compared to isoform 1.
    Source sequence(s)
    AL590037, BC036119
    Consensus CDS
    CCDS83102.1
    UniProtKB/Swiss-Prot
    Q5SZJ8
    Related
    ENSP00000359784.3, ENST00000370748.7

  2. NM_152731.3 → NP_689944.2  BEN domain-containing protein 6 isoform 1

    See identical proteins and their annotated locations for NP_689944.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
    Source sequence(s)
    AI803591, AK054724, AL590037, BC022988, DC411761
    Consensus CDS
    CCDS43476.1
    UniProtKB/Swiss-Prot
    Q4G0W8, Q5SZJ8, Q8N662, Q96NS6
    UniProtKB/TrEMBL
    B7Z8N8
    Related
    ENSP00000359782.3, ENST00000370746.8
    Conserved Domains (1) summary
    smart01025
    Location:190 → 271
    BEN; The BEN domain is found in diverse animal proteins

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_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    56955107..57027346
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017010406.2 → XP_016865895.1  BEN domain-containing protein 6 isoform X1

    UniProtKB/Swiss-Prot
    Q4G0W8, Q5SZJ8, Q8N662, Q96NS6
    UniProtKB/TrEMBL
    B7Z8N8
    Conserved Domains (1) summary
    smart01025
    Location:190 → 271
    BEN; The BEN domain is found in diverse animal proteins

  2. XM_047418320.1 → XP_047274276.1  BEN domain-containing protein 6 isoform X5

  3. XM_047418321.1 → XP_047274277.1  BEN domain-containing protein 6 isoform X6

    UniProtKB/TrEMBL
    Q5SZK0
    Related
    ENSP00000359781.1, ENST00000370745.1

  4. XM_047418322.1 → XP_047274278.1  BEN domain-containing protein 6 isoform X7

  5. XM_047418323.1 → XP_047274279.1  BEN domain-containing protein 6 isoform X3

  6. XM_047418324.1 → XP_047274280.1  BEN domain-containing protein 6 isoform X4

  7. XM_017010407.3 → XP_016865896.1  BEN domain-containing protein 6 isoform X1

    UniProtKB/Swiss-Prot
    Q4G0W8, Q5SZJ8, Q8N662, Q96NS6
    UniProtKB/TrEMBL
    B7Z8N8
    Conserved Domains (1) summary
    smart01025
    Location:190 → 271
    BEN; The BEN domain is found in diverse animal proteins

  8. XM_005248889.2 → XP_005248946.1  BEN domain-containing protein 6 isoform X2

    See identical proteins and their annotated locations for XP_005248946.1

    UniProtKB/Swiss-Prot
    Q5SZJ8
    Conserved Domains (1) summary
    smart01025
    Location:92 → 173
    BEN; The BEN domain is found in diverse animal proteins

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    56794154..56866397
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054354549.1 → XP_054210524.1  BEN domain-containing protein 6 isoform X1

    UniProtKB/Swiss-Prot
    Q4G0W8, Q5SZJ8, Q8N662, Q96NS6

  2. XM_054354552.1 → XP_054210527.1  BEN domain-containing protein 6 isoform X3

  3. XM_054354553.1 → XP_054210528.1  BEN domain-containing protein 6 isoform X4

  4. XM_054354550.1 → XP_054210525.1  BEN domain-containing protein 6 isoform X1

    UniProtKB/Swiss-Prot
    Q4G0W8, Q5SZJ8, Q8N662, Q96NS6

  5. XM_054354551.1 → XP_054210526.1  BEN domain-containing protein 6 isoform X2

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q5SZJ8.2 GenPept UniProtKB/Swiss-Prot:Q5SZJ8

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