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    BEND5 BEN domain containing 5 [ Homo sapiens (human) ]

    Gene ID: 79656, updated on 5-Mar-2024

    Summary

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    Official Symbol
    BEND5provided by HGNC
    Official Full Name
    BEN domain containing 5provided by HGNC
    Primary source
    HGNC:HGNC:25668
    See related
    Ensembl:ENSG00000162373 AllianceGenome:HGNC:25668
    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
    C1orf165
    Summary
    Predicted to enable DNA binding activity. Involved in negative regulation of transcription, DNA-templated. Predicted to be located in Golgi apparatus. [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Ubiquitous expression in ovary (RPKM 1.6), brain (RPKM 1.3) and 23 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    1p33
    Exon count:
    9
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (48727519..48776891, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (48606260..48655642, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (49193191..49242563, complement)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene spermatogenesis associated 6 Neighboring gene uncharacterized LOC124904175 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 861 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1010 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr1:48945175-48946016 Neighboring gene Sharpr-MPRA regulatory region 6906 Neighboring gene NANOG hESC enhancer GRCh37_chr1:48991897-48992398 Neighboring gene ribosomal protein L21 pseudogene 25 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr1:49110904-49111546 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr1:49111547-49112189 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:49152780-49153280 Neighboring gene AGBL carboxypeptidase 4 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:49174571-49174927 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1011 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr1:49357925-49358617 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:49471420-49472013 Neighboring gene uncharacterized LOC105378706 Neighboring gene uncharacterized LOC124904851

    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. Interaction between BEND5 and RBPJ suppresses breast cancer growth and metastasis via inhibiting Notch signaling. Shi Y, et al. Int J Biol Sci, 2022. PMID 35844785, Free PMC Article
    2. A method for global protein expression and antibody screening on high-density filters of an arrayed cDNA library. Büssow K, et al. Nucleic Acids Res, 1998 Nov 1. PMID 9776767, Free PMC Article
    3. The BEN domain is a novel sequence-specific DNA-binding domain conserved in neural transcriptional repressors. Dai Q, et al. Genes Dev, 2013 Mar 15. PMID 23468431, Free PMC Article
    4. Expressed sequence tag analysis of adult human iris for the NEIBank Project: steroid-response factors and similarities with retinal pigment epithelium. Wistow G, et al. Mol Vis, 2002 Jun 15. PMID 12107412
    5. Protein interaction network of alternatively spliced isoforms from brain links genetic risk factors for autism. Corominas R, et al. Nat Commun, 2014 Apr 11. PMID 24722188, Free PMC Article

    See all (22) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Interaction between BEND5 and RBPJ suppresses breast cancer growth and metastasis via inhibiting Notch signaling.
      Title: Interaction between BEND5 and RBPJ suppresses breast cancer growth and metastasis via inhibiting Notch signaling.
    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

    • FLJ11588, FLJ39254

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables DNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in negative regulation of DNA-templated transcription IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in negative regulation of DNA-templated transcription IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in Golgi apparatus IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    BEN domain-containing protein 5

    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.

    Genomic

    1. NG_053063.1 RefSeqGene

      Range
      6713..56085
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001302082.2 → NP_001289011.1  BEN domain-containing protein 5 isoform 2

      See identical proteins and their annotated locations for NP_001289011.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) uses an alternate splice site at an internal exon, and initiates translation at a downstream start codon, compared to variant 1. The encoded isoform (2) has a shorter N-terminus compared to isoform 1. Variants 2, 3, and 4 all encode the same isoform (2).
      Source sequence(s)
      AC097062, AK021650, BC007932, BX096297, CD579580
      UniProtKB/Swiss-Prot
      Q7L4P6
      Conserved Domains (1) summary
      pfam10523
      Location:154 → 228
      BEN; BEN domain

    2. NM_001349793.2 → NP_001336722.1  BEN domain-containing protein 5 isoform 2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3), as well as variants 2 and 4, encodes isoform 2.
      Source sequence(s)
      AC097062, BX096297, CD672851, KU178778
      Conserved Domains (1) summary
      pfam10523
      Location:154 → 228
      BEN; BEN domain

    3. NM_001349794.2 → NP_001336723.1  BEN domain-containing protein 5 isoform 2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4), as well as variants 2 and 3, encodes isoform 2.
      Source sequence(s)
      AC097062
      Conserved Domains (1) summary
      pfam10523
      Location:154 → 228
      BEN; BEN domain

    4. NM_001349795.2 → NP_001336724.1  BEN domain-containing protein 5 isoform 3

      Status: VALIDATED

      Description
      Transcript Variant: This variant (5) encodes isoform 3.
      Source sequence(s)
      AC097062
      Conserved Domains (1) summary
      pfam10523
      Location:238 → 312
      BEN; BEN domain

    5. NM_024603.4 → NP_078879.2  BEN domain-containing protein 5 isoform 1

      See identical proteins and their annotated locations for NP_078879.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (1).
      Source sequence(s)
      AC097062, BC007932, BX096297, CD579580
      Consensus CDS
      CCDS552.2
      UniProtKB/Swiss-Prot
      D3DQ27, Q7L4P6, Q96A62, Q9HAI3
      UniProtKB/TrEMBL
      A0A0S2Z5N0
      Related
      ENSP00000360899.3, ENST00000371833.4
      Conserved Domains (2) summary
      TIGR02168
      Location:70 → 277
      SMC_prok_B; chromosome segregation protein SMC, common bacterial type
      pfam10523
      Location:323 → 397
      BEN; BEN domain

    RNA

    1. NR_146232.2 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC097062

    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_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      48727519..48776891 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047430505.1 → XP_047286461.1  BEN domain-containing protein 5 isoform X2

    2. XM_047430497.1 → XP_047286453.1  BEN domain-containing protein 5 isoform X1

    3. XM_011542141.4 → XP_011540443.1  BEN domain-containing protein 5 isoform X2

      See identical proteins and their annotated locations for XP_011540443.1

      Conserved Domains (1) summary
      pfam10523
      Location:238 → 312
      BEN; BEN domain

    4. XM_047430520.1 → XP_047286476.1  BEN domain-containing protein 5 isoform X4

    5. XM_017002333.3 → XP_016857822.1  BEN domain-containing protein 5 isoform X3

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      48606260..48655642 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054338741.1 → XP_054194716.1  BEN domain-containing protein 5 isoform X5

    2. XM_054338739.1 → XP_054194714.1  BEN domain-containing protein 5 isoform X1

    3. XM_054338740.1 → XP_054194715.1  BEN domain-containing protein 5 isoform X5

    4. XM_054338743.1 → XP_054194718.1  BEN domain-containing protein 5 isoform X4

    5. XM_054338742.1 → XP_054194717.1  BEN domain-containing protein 5 isoform X3

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q7L4P6.1 GenPept UniProtKB/Swiss-Prot:Q7L4P6

    Gene LinkOut

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

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