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    BEST4 bestrophin 4 [ Homo sapiens (human) ]

    Gene ID: 266675, updated on 13-Apr-2024

    Summary

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    Official Symbol
    BEST4provided by HGNC
    Official Full Name
    bestrophin 4provided by HGNC
    Primary source
    HGNC:HGNC:17106
    See related
    Ensembl:ENSG00000142959 MIM:607336; AllianceGenome:HGNC:17106
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    VMD2L2
    Summary
    This gene is a member of the bestrophin gene family of anion channels. Bestrophin genes share a similar gene structure with highly conserved exon-intron boundaries, but with distinct 3' ends. Bestrophins are transmembrane proteins that contain a homologous region rich in aromatic residues, including an invariant arg-phe-pro motif. Mutation in one of the family members (bestrophin 1) is associated with vitelliform macular dystrophy. The bestrophin 4 gene is predominantly expressed in the colon. [provided by RefSeq, Jul 2008]
    Expression
    Biased expression in colon (RPKM 7.6), duodenum (RPKM 2.6) and 2 other tissues See more
    Orthologs
    all
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    Genomic context

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    Location:
    1p34.1
    Exon count:
    12
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (44781840..44792828, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (44652829..44664929, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (45249257..45253842, complement)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:45245072-45245572 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:45245573-45246073 Neighboring gene ribosomal protein S8 Neighboring gene small nucleolar RNA, C/D box 38B Neighboring gene ribosomal protein S15a pseudogene 11 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 818 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:45251699-45252384 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:45252385-45253070 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:45257343-45258034 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:45258727-45259416 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:45265053-45265721 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 820 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 949 Neighboring gene polo like kinase 3 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:45271492-45272342 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr1:45272786-45273985 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:45274044-45274893 Neighboring gene dynein light chain Tctex-type 4 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 953 Neighboring gene BTB domain containing 19 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 821

    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. Ca2+-activated Cl- current from human bestrophin-4 in excised membrane patches. Tsunenari T, et al. J Gen Physiol, 2006 Jun. PMID 16702355, Free PMC Article
    2. Lineage-specific expression of bestrophin-2 and bestrophin-4 in human intestinal epithelial cells. Ito G, et al. PLoS One, 2013. PMID 24223998, Free PMC Article
    3. Bestrophin expression and function in the human pancreatic duct cell line, CFPAC-1. Marsey LL, et al. J Physiol, 2009 May 15. PMID 19237432, Free PMC Article
    4. Mutations in a novel gene, VMD2, encoding a protein of unknown properties cause juvenile-onset vitelliform macular dystrophy (Best's disease). Marquardt A, et al. Hum Mol Genet, 1998 Sep. PMID 9700209
    5. Structure-function analysis of the bestrophin family of anion channels. Tsunenari T, et al. J Biol Chem, 2003 Oct 17. PMID 12907679, Free PMC Article

    See all (11) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. BEST2 and BEST4 could be added to the lineage-specific genes of humans intestinal epithelial cells
      Title: Lineage-specific expression of bestrophin-2 and bestrophin-4 in human intestinal epithelial cells.
    2. Results provide evidence that the bestrophins are expressed in pancreatic duct cells and, more specifically, that hBest1 plays a role in the calcium activated chloride channels found in these cells.
      Title: Bestrophin expression and function in the human pancreatic duct cell line, CFPAC-1.
    3. identified three novel VMD2-related human genes demonstrating a high degree of conservation in their respective RFP-TM domains
      Title: Three novel human VMD2-like genes are members of the evolutionary highly conserved RFP-TM family.
    4. Human Best4 chloride channels on excised membrane patches can be activated by free calcium (Ca2+) on the cytoplasmic side.
      Title: Ca2+-activated Cl- current from human bestrophin-4 in excised membrane patches.
    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

    • MGC126872

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables bicarbonate channel activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables chloride channel activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables intracellularly calcium-gated chloride channel activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables molecular_function ND
    No biological Data available
    more info
    		  
    Process Evidence Code Pubs
    involved_in bicarbonate transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in biological_process ND
    No biological Data available
    more info
    		  
    involved_in chloride transmembrane transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    part_of chloride channel complex IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in plasma membrane IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    bestrophin-4
    Names
    vitelliform macular dystrophy 2-like 2
    vitelliform macular dystrophy 2-like protein 2

    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_153274.3 → NP_695006.1  bestrophin-4

      See identical proteins and their annotated locations for NP_695006.1

      Status: REVIEWED

      Source sequence(s)
      AF440757, AL592166, BC101823, BM142321
      Consensus CDS
      CCDS514.1
      UniProtKB/Swiss-Prot
      Q5JR93, Q8NFU0
      Related
      ENSP00000361281.3, ENST00000372207.4
      Conserved Domains (1) summary
      pfam01062
      Location:8 → 331
      Bestrophin; RFP-TM, chloride channel

    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
      44781840..44792828 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017001023.2 → XP_016856512.1  bestrophin-4 isoform X1

      UniProtKB/Swiss-Prot
      Q5JR93, Q8NFU0
      Conserved Domains (1) summary
      pfam01062
      Location:8 → 331
      Bestrophin; RFP-TM, chloride channel

    2. XM_024446367.1 → XP_024302135.1  bestrophin-4 isoform X1

      UniProtKB/Swiss-Prot
      Q5JR93, Q8NFU0
      Conserved Domains (1) summary
      pfam01062
      Location:8 → 331
      Bestrophin; RFP-TM, chloride channel

    3. XM_047417823.1 → XP_047273779.1  bestrophin-4 isoform X1

      UniProtKB/Swiss-Prot
      Q5JR93, Q8NFU0

    4. XM_047417821.1 → XP_047273777.1  bestrophin-4 isoform X1

      UniProtKB/Swiss-Prot
      Q5JR93, Q8NFU0

    5. XM_047417826.1 → XP_047273782.1  bestrophin-4 isoform X2

    RNA

    1. XR_007058647.1 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      44652829..44664929 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054335970.1 → XP_054191945.1  bestrophin-4 isoform X1

      UniProtKB/Swiss-Prot
      Q5JR93, Q8NFU0

    2. XM_054335971.1 → XP_054191946.1  bestrophin-4 isoform X1

      UniProtKB/Swiss-Prot
      Q5JR93, Q8NFU0
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8NFU0.1 GenPept UniProtKB/Swiss-Prot:Q8NFU0

    Gene LinkOut

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

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