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    BEST1 bestrophin 1 [ Homo sapiens (human) ]

    Gene ID: 7439, updated on 6-Jun-2017
    Official Symbol
    BEST1provided by HGNC
    Official Full Name
    bestrophin 1provided by HGNC
    Primary source
    HGNC:HGNC:12703
    See related
    Ensembl:ENSG00000167995 MIM:607854; Vega:OTTHUMG00000167469
    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
    ARB; BMD; BEST; RP50; VMD2; TU15B
    Summary
    This gene encodes a member of the bestrophin gene family. This small gene family is characterized by proteins with a highly conserved N-terminus with four to six transmembrane domains. Bestrophins may form chloride ion channels or may regulate voltage-gated L-type calcium-ion channels. Bestrophins are generally believed to form calcium-activated chloride-ion channels in epithelial cells but they have also been shown to be highly permeable to bicarbonate ion transport in retinal tissue. Mutations in this gene are responsible for juvenile-onset vitelliform macular dystrophy (VMD2), also known as Best macular dystrophy, in addition to adult-onset vitelliform macular dystrophy (AVMD) and other retinopathies. Alternative splicing results in multiple variants encoding distinct isoforms.[provided by RefSeq, Nov 2008]
    Orthologs
    Location:
    11q12.3
    Exon count:
    12
    Annotation release Status Assembly Chr Location
    108 current GRCh38.p7 (GCF_000001405.33) 11 NC_000011.10 (61946722..61964465)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (61717356..61731935)

    Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene fatty acid desaturase 3 Neighboring gene microRNA 6746 Neighboring gene RAB3A interacting protein like 1 Neighboring gene RNA, U6 small nuclear 1243, pseudogene Neighboring gene uncharacterized LOC107984334 Neighboring gene uncharacterized LOC399900 Neighboring gene ferritin heavy chain 1 Neighboring gene ribosomal protein S2 pseudogene 37

    • 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 Jun 15 11:32:44 2016

    Related articles in PubMed

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    Products Interactant Other Gene Complex Source Pubs Description

    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    bicarbonate transmembrane transporter activity TAS
    Traceable Author Statement
    more info
     
    chloride channel activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    contributes_to chloride channel activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    identical protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    intracellular calcium activated chloride channel activity TAS
    Traceable Author Statement
    more info
     
    Process Evidence Code Pubs
    bicarbonate transport IEA
    Inferred from Electronic Annotation
    more info
     
    chloride transmembrane transport IEA
    Inferred from Electronic Annotation
    more info
     
    chloride transport IDA
    Inferred from Direct Assay
    more info
    PubMed 
    detection of light stimulus involved in visual perception IEA
    Inferred from Electronic Annotation
    more info
     
    ion transmembrane transport TAS
    Traceable Author Statement
    more info
     
    regulation of calcium ion transport IEA
    Inferred from Electronic Annotation
    more info
     
    transepithelial chloride transport IDA
    Inferred from Direct Assay
    more info
    PubMed 
    visual perception TAS
    Traceable Author Statement
    more info
    PubMed 
    Component Evidence Code Pubs
    basolateral plasma membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    chloride channel complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    cytosol TAS
    Traceable Author Statement
    more info
    PubMed 
    integral component of membrane TAS
    Traceable Author Statement
    more info
    PubMed 
    membrane TAS
    Traceable Author Statement
    more info
    PubMed 
    plasma membrane TAS
    Traceable Author Statement
    more info
     
    Preferred Names
    bestrophin-1
    Names
    Best disease
    Best1V1Delta2
    vitelliform macular dystrophy protein 2

    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_009033.1 RefSeqGene

      Range
      5001..19580
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001139443.1NP_001132915.1  bestrophin-1 isoform 2

      See identical proteins and their annotated locations for NP_001132915.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) encodes the longest isoform (2).
      Source sequence(s)
      AF057169, BC015220, BC041664
      Consensus CDS
      CCDS44623.1
      UniProtKB/Swiss-Prot
      O76090
      Related
      ENSP00000399709.2, OTTHUMP00000235999, ENST00000449131.6, OTTHUMT00000394721
      Conserved Domains (1) summary
      pfam01062
      Location:16255
      Bestrophin; Bestrophin, RFP-TM, chloride channel
    2. NM_001300786.1NP_001287715.1  bestrophin-1 isoform 3

      See identical proteins and their annotated locations for NP_001287715.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) lacks an alternate in-frame exon and differs in the 3' UTR and coding sequence compared to variant 2. The resulting isoform (3) lacks an alternate internal segment and has a shorter and distinct C-terminus compared to isoform 2.
      Source sequence(s)
      AP003733, BC015220
      UniProtKB/Swiss-Prot
      O76090
      UniProtKB/TrEMBL
      A0A0S2Z4M4
      Conserved Domains (1) summary
      pfam01062
      Location:16231
      Bestrophin; Bestrophin, RFP-TM, chloride channel
    3. NM_001300787.1NP_001287716.1  bestrophin-1 isoform 4

      See identical proteins and their annotated locations for NP_001287716.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) differs in the 3' UTR and coding sequence compared to variant 2. The resulting isoform (4) has a shorter and distinct C-terminus compared to isoform 2.
      Source sequence(s)
      AK295998, AP003733, BC015220
      UniProtKB/Swiss-Prot
      O76090
      UniProtKB/TrEMBL
      A0A0S2Z579
      Conserved Domains (1) summary
      pfam01062
      Location:16255
      Bestrophin; Bestrophin, RFP-TM, chloride channel
    4. NM_004183.3NP_004174.1  bestrophin-1 isoform 1

      See identical proteins and their annotated locations for NP_004174.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) differs in the 5' UTR and coding sequence and in the 3' UTR and coding sequence compared to variant 2. The resulting isoform (1) is longer at the N-terminus and has a shorter and distinct C-terminus compared to isoform 2.
      Source sequence(s)
      AF057169, BC015220
      Consensus CDS
      CCDS31580.1
      UniProtKB/Swiss-Prot
      O76090
      Related
      ENSP00000367282.4, OTTHUMP00000235994, ENST00000378043.8, OTTHUMT00000394715
      Conserved Domains (1) summary
      pfam01062
      Location:9315
      Bestrophin; Bestrophin, RFP-TM, chloride channel

    RNA

    1. NR_134580.1 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) contains an alternate exon, uses an alternate internal splice junction, and differs in the 3' end compared to variant 2. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AF057170, AP003733, BC015220

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 108 details...Open this link in a new tab

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p7 Primary Assembly

    Genomic

    1. NC_000011.10 Reference GRCh38.p7 Primary Assembly

      Range
      61946722..61964465
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011545229.2XP_011543531.1  bestrophin-1 isoform X1

      See identical proteins and their annotated locations for XP_011543531.1

      Conserved Domains (1) summary
      pfam01062
      Location:9315
      Bestrophin; Bestrophin, RFP-TM, chloride channel
    2. XM_011545230.2XP_011543532.1  bestrophin-1 isoform X2

      Conserved Domains (1) summary
      pfam01062
      Location:20284
      Bestrophin; Bestrophin, RFP-TM, chloride channel
    3. XM_017018229.1XP_016873718.1  bestrophin-1 isoform X5

      UniProtKB/Swiss-Prot
      O76090
      UniProtKB/TrEMBL
      A0A0C4DGE9
      Related
      ENSP00000432681.1, OTTHUMP00000235998, ENST00000524926.5, OTTHUMT00000394720
      Conserved Domains (1) summary
      pfam01062
      Location:9291
      Bestrophin; Bestrophin, RFP-TM, chloride channel
    4. XM_005274210.3XP_005274267.1  bestrophin-1 isoform X1

      See identical proteins and their annotated locations for XP_005274267.1

      Conserved Domains (1) summary
      pfam01062
      Location:9315
      Bestrophin; Bestrophin, RFP-TM, chloride channel
    5. XM_005274219.3XP_005274276.1  bestrophin-1 isoform X9

      Conserved Domains (1) summary
      pfam01062
      Location:9289
      Bestrophin; Bestrophin, RFP-TM, chloride channel
    6. XM_005274221.3XP_005274278.1  bestrophin-1 isoform X10

      See identical proteins and their annotated locations for XP_005274278.1

      UniProtKB/TrEMBL
      B7Z375
      Conserved Domains (1) summary
      pfam01062
      Location:9238
      Bestrophin; Bestrophin, RFP-TM, chloride channel
    7. XM_005274216.3XP_005274273.1  bestrophin-1 isoform X7

      Conserved Domains (1) summary
      pfam01062
      Location:16231
      Bestrophin; Bestrophin, RFP-TM, chloride channel
    8. XM_017018230.1XP_016873719.1  bestrophin-1 isoform X8

      UniProtKB/TrEMBL
      B7Z1N8
      Related
      ENSP00000433195.1, OTTHUMP00000236000, ENST00000526988.1, OTTHUMT00000394722
      Conserved Domains (1) summary
      pfam01062
      Location:3185
      Bestrophin; Bestrophin, RFP-TM, chloride channel
    9. XM_017018228.1XP_016873717.1  bestrophin-1 isoform X3

      Conserved Domains (1) summary
      pfam01062
      Location:3209
      Bestrophin; Bestrophin, RFP-TM, chloride channel
    10. XM_005274215.3XP_005274272.1  bestrophin-1 isoform X4

      See identical proteins and their annotated locations for XP_005274272.1

      UniProtKB/Swiss-Prot
      O76090
      Conserved Domains (1) summary
      pfam01062
      Location:3209
      Bestrophin; Bestrophin, RFP-TM, chloride channel
    11. XM_011545233.2XP_011543535.1  bestrophin-1 isoform X6

      Conserved Domains (1) summary
      cl01544
      Location:734
      Bestrophin; Bestrophin, RFP-TM, chloride channel

    RNA

    1. XR_001747953.1 RNA Sequence

    2. XR_001747954.1 RNA Sequence

    3. XR_001747952.1 RNA Sequence

    Alternate CHM1_1.1

    Genomic

    1. NC_018922.2 Alternate CHM1_1.1

      Range
      61600555..61615131
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
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