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

Gene ID: 79656, updated on 27-Nov-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 DNA-templated transcription. Predicted to be located in Golgi apparatus. [provided by Alliance of Genome Resources, Nov 2024]
Expression
Ubiquitous expression in ovary (RPKM 1.6), brain (RPKM 1.3) and 23 other tissues See more
Orthologs
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Genomic context

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See BEND5 in Genome Data Viewer
Location:
1p33
Exon count:
9
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (48727519..48776891, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (48606260..48655642, complement)
RS_2024_09 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 (23) 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)

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_2024_08

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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