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

    Gene ID: 221336, updated on 10-Dec-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, Dec 2024]
    Expression
    Biased expression in brain (RPKM 5.4), gall bladder (RPKM 1.0) and 7 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See BEND6 in Genome Data Viewer
    Location:
    6p12.1
    Exon count:
    12
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (56955107..57027346)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (56794154..56866397)
    RS_2024_09 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: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 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. Protein interaction landscapes revealed by advanced in vivo cross-linking-mass spectrometry. Wheat A, et al. Proc Natl Acad Sci U S A, 2021 Aug 10. PMID 34349018, Free PMC Article
    5. Complete sequencing and characterization of 21,243 full-length human cDNAs. Ota T, et al. Nat Genet, 2004 Jan. PMID 14702039

    See all (8) 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)

    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_2024_08

    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
      UniProtKB/TrEMBL
      B7Z8N8

    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
      UniProtKB/TrEMBL
      B7Z8N8

    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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