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    BEND3 BEN domain containing 3 [ Homo sapiens (human) ]

    Gene ID: 57673, updated on 17-Jun-2024

    Summary

    Official Symbol
    BEND3provided by HGNC
    Official Full Name
    BEN domain containing 3provided by HGNC
    Primary source
    HGNC:HGNC:23040
    See related
    Ensembl:ENSG00000178409 MIM:616374; AllianceGenome:HGNC:23040
    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
    KIAA1553
    Summary
    Enables rDNA binding activity. Involved in several processes, including histone modification; negative regulation of macromolecule metabolic process; and protein homooligomerization. Located in heterochromatin; nucleolus; and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Ubiquitous expression in stomach (RPKM 1.1), testis (RPKM 1.1) and 25 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See BEND3 in Genome Data Viewer
    Location:
    6q21
    Exon count:
    6
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (107065182..107115515, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (108244038..108294460, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (107386386..107436719, complement)

    Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17434 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17435 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:107312640-107312741 Neighboring gene CD24 molecule Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17436 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24898 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24899 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:107361561-107362452 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:107382561-107383456 Neighboring gene mitochondrial transcription rescue factor 1 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:107414410-107414593 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:107426683-107427338 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17437 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17438 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17439 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:107437205-107437968 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr6:107437969-107438734 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24900 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24901 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24902 Neighboring gene RNA, U6 small nuclear 1299, pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:107470292-107470792 Neighboring gene decaprenyl diphosphate synthase subunit 2 Neighboring gene ribosomal protein S24 pseudogene 12

    Genomic regions, transcripts, and products

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • KIAA1553

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables rDNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables rDNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Component Evidence Code Pubs
    part_of heterochromatin IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in nucleolus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
     

    General protein information

    Preferred Names
    BEN domain-containing protein 3
    Names
    BANP, E5R, and Nac1 (BEN) domain 3

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_001080450.3NP_001073919.1  BEN domain-containing protein 3

      See identical proteins and their annotated locations for NP_001073919.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript. Variants 1 and 2 both encode the same protein.
      Source sequence(s)
      AB046773, AL355586, BC131628
      Consensus CDS
      CCDS34507.1
      UniProtKB/Swiss-Prot
      A2RRH2, Q5T5X7, Q9HCL9
      Related
      ENSP00000411268.2, ENST00000429433.3
      Conserved Domains (1) summary
      smart01025
      Location:737816
      BEN; The BEN domain is found in diverse animal proteins
    2. NM_001367314.1NP_001354243.1  BEN domain-containing protein 3

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1 and 2 both encode the same protein.
      Source sequence(s)
      AL355586
      Consensus CDS
      CCDS34507.1
      UniProtKB/Swiss-Prot
      A2RRH2, Q5T5X7, Q9HCL9
      Related
      ENSP00000358038.1, ENST00000369042.6
      Conserved Domains (1) summary
      smart01025
      Location:737816
      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
      107065182..107115515 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011536005.4XP_011534307.1  BEN domain-containing protein 3 isoform X1

      See identical proteins and their annotated locations for XP_011534307.1

      UniProtKB/Swiss-Prot
      A2RRH2, Q5T5X7, Q9HCL9
      Conserved Domains (1) summary
      smart01025
      Location:737816
      BEN; The BEN domain is found in diverse animal proteins
    2. XM_005267080.5XP_005267137.1  BEN domain-containing protein 3 isoform X1

      See identical proteins and their annotated locations for XP_005267137.1

      UniProtKB/Swiss-Prot
      A2RRH2, Q5T5X7, Q9HCL9
      Conserved Domains (1) summary
      smart01025
      Location:737816
      BEN; The BEN domain is found in diverse animal proteins

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060930.1 Alternate T2T-CHM13v2.0

      Range
      108244038..108294460 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054356110.1XP_054212085.1  BEN domain-containing protein 3 isoform X1

      UniProtKB/Swiss-Prot
      A2RRH2, Q5T5X7, Q9HCL9
    2. XM_054356111.1XP_054212086.1  BEN domain-containing protein 3 isoform X1

      UniProtKB/Swiss-Prot
      A2RRH2, Q5T5X7, Q9HCL9