Format

Send to:

Choose Destination
    • Showing Current items.

    SPTBN1 spectrin beta, non-erythrocytic 1 [ Homo sapiens (human) ]

    Gene ID: 6711, updated on 17-Oct-2021

    Summary

    Official Symbol
    SPTBN1provided by HGNC
    Official Full Name
    spectrin beta, non-erythrocytic 1provided by HGNC
    Primary source
    HGNC:HGNC:11275
    See related
    Ensembl:ENSG00000115306 MIM:182790
    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
    ELF; SPTB2; DDISBA; HEL102; betaSpII
    Summary
    Spectrin is an actin crosslinking and molecular scaffold protein that links the plasma membrane to the actin cytoskeleton, and functions in the determination of cell shape, arrangement of transmembrane proteins, and organization of organelles. It is composed of two antiparallel dimers of alpha- and beta- subunits. This gene is one member of a family of beta-spectrin genes. The encoded protein contains an N-terminal actin-binding domain, and 17 spectrin repeats which are involved in dimer formation. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
    Expression
    Ubiquitous expression in fat (RPKM 102.5), lung (RPKM 72.2) and 24 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See SPTBN1 in Genome Data Viewer
    Location:
    2p16.2
    Exon count:
    39
    Annotation release Status Assembly Chr Location
    109.20210514 current GRCh38.p13 (GCF_000001405.39) 2 NC_000002.12 (54456327..54671446)
    105.20201022 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (54683464..54898583)

    Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene chromosome 2 open reading frame 73 Neighboring gene uncharacterized LOC102724072 Neighboring gene SPTBN1 antisense RNA 1 Neighboring gene ribosomal protein L23a pseudogene 32 Neighboring gene Sharpr-MPRA regulatory region 11587 Neighboring gene uncharacterized LOC105374653

    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?

    Phenotypes

    Associated conditions

    Description Tests
    DEVELOPMENTAL DELAY, IMPAIRED SPEECH, AND BEHAVIORAL ABNORMALITIES
    MedGen: CN300333 OMIM: 619475 GeneReviews: Not available
    not available
    Genetic determinants of heel bone properties: genome-wide association meta-analysis and replication in the GEFOS/GENOMOS consortium.
    GeneReviews: Not available
    Genetic variants on chromosome 1q41 influence ocular axial length and high myopia.
    GeneReviews: Not available
    Genome-wide meta-analysis identifies 56 bone mineral density loci and reveals 14 loci associated with risk of fracture.
    GeneReviews: Not available
    Multiple genetic loci for bone mineral density and fractures.
    GeneReviews: Not available
    New sequence variants associated with bone mineral density.
    GeneReviews: Not available
    Twenty bone-mineral-density loci identified by large-scale meta-analysis of genome-wide association studies.
    GeneReviews: Not available

    HIV-1 interactions

    Replication interactions

    Interaction Pubs
    Knockdown of SPTBN1 by siRNA inhibits HIV-1 replication in primary macrophages PubMed
    Knockdown of spectrin, beta, non-erythrocytic 1 (SPTBN1) by siRNA inhibits HIV-1 replication in HeLa-derived TZM-bl cells PubMed

    Protein interactions

    Protein Gene Interaction Pubs
    Pr55(Gag) gag HIV-1 Gag co-localizes with SPTBN1 both at the plasma membrane and in cytoplasm PubMed
    Rev rev HIV-1 Rev interacting protein, spectrin, beta, non-erythrocytic 1 (SPTBN1), is identified by the in-vitro binding experiments involving cytosolic or nuclear extracts from HeLa cells PubMed
    Tat tat Spectrin, beta, non-erythrocytic 1 (SPTBN1) is identified to interact with HIV-1 Tat mutant Nullbasic in HeLa cells by LC MS/MS PubMed
    Vpr vpr Co-localization of Vpr-GFP-labeled virion and SPTBN1 is observed on plasma membrane (PM) and the intracellular side of PM PubMed
    capsid gag HIV-1 CA associates with SPTBN1 in cells PubMed
    matrix gag HIV-1 MA associates with SPTBN1 in cells PubMed
    retropepsin gag-pol A number of focal adhesion plaque proteins are specifically cleaved by HIV-1 protease, including fimbrin, focal adhesion plaque kinase (FAK), talin, and, to a lesser extent, filamin, spectrin and fibronectin PubMed

    Go to the HIV-1, Human Interaction Database

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables GTPase binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables RNA binding HDA PubMed 
    enables actin binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables actin filament binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    enables ankyrin binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables ankyrin binding NAS
    Non-traceable Author Statement
    more info
    PubMed 
    enables cadherin binding HDA PubMed 
    enables calmodulin binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables phospholipid binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables protein-containing complex binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables structural constituent of cytoskeleton IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    Component Evidence Code Pubs
    located_in M band IEA
    Inferred from Electronic Annotation
    more info
     
    located_in axolemma ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    is_active_in cell junction IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    is_active_in cell projection IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    is_active_in cortical actin cytoskeleton IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    located_in cuticular plate IEA
    Inferred from Electronic Annotation
    more info
     
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in cytosol TAS
    Traceable Author Statement
    more info
     
    located_in extracellular exosome HDA PubMed 
    located_in glutamatergic synapse IEA
    Inferred from Electronic Annotation
    more info
     
    located_in nucleolus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    located_in postsynaptic density IEA
    Inferred from Electronic Annotation
    more info
     
    part_of spectrin IEA
    Inferred from Electronic Annotation
    more info
     
    located_in spectrin-associated cytoskeleton NAS
    Non-traceable Author Statement
    more info
    PubMed 

    General protein information

    Preferred Names
    spectrin beta chain, non-erythrocytic 1
    Names
    beta-G spectrin
    beta-II spectrin
    beta-fodrin
    beta-spectrin 2
    beta-spectrin II
    beta-spectrin non-erythrocytic 1
    embryonic liver beta-fodrin
    epididymis luminal protein 102
    fodrin beta chain
    spectrin beta chain, brain 1
    spectrin, non-erythroid beta chain 1

    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.

    Genomic

    1. NG_029817.1 RefSeqGene

      Range
      5011..220130
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_003128.3NP_003119.2  spectrin beta chain, non-erythrocytic 1 isoform 1

      See identical proteins and their annotated locations for NP_003119.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1), also known as long or sigma-1, represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AB209748, AC093110, BM679686, BP218428, BP312037
      Consensus CDS
      CCDS33198.1
      UniProtKB/Swiss-Prot
      Q01082
      UniProtKB/TrEMBL
      B2ZZ89
      Related
      ENSP00000349259.4, ENST00000356805.9
      Conserved Domains (6) summary
      COG5069
      Location:48530
      SAC6; Ca2+-binding actin-bundling protein fimbrin/plastin (EF-Hand superfamily) [Cytoskeleton]
      cd00176
      Location:530743
      SPEC; Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; ...
      cd10571
      Location:22002305
      PH_beta_spectrin; Beta-spectrin pleckstrin homology (PH) domain
      pfam00435
      Location:20172075
      Spectrin; Spectrin repeat
      cd21248
      Location:173277
      CH_SPTB_like_rpt2; second calponin homology (CH) domain found in the beta-I spectrin-like subfamily
      cd21316
      Location:3156
      CH_SPTBN1_rpt1; first calponin homology (CH) domain found in spectrin beta chain, non-erythrocytic 1 (SPTBN1) and similar proteins
    2. NM_178313.3NP_842565.2  spectrin beta chain, non-erythrocytic 1 isoform 2

      See identical proteins and their annotated locations for NP_842565.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2), also known as short or sigma-2, differs in the 5' UTR, 3' UTR, and coding region (compared to variant 1). The resulting protein (isoform 2) maintains the reading frame but has shorter and distinct sequences at both the N- and C-termini, compared to isoform 1.
      Source sequence(s)
      AC092839, AC093110, AF327441, AK025071, CR980403
      Consensus CDS
      CCDS33199.1
      UniProtKB/Swiss-Prot
      Q01082
      Related
      ENSP00000334156.5, ENST00000333896.5
      Conserved Domains (3) summary
      COG5069
      Location:34517
      SAC6; Ca2+-binding actin-bundling protein fimbrin/plastin (EF-Hand superfamily) [Cytoskeleton]
      cd00176
      Location:517730
      SPEC; Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; ...
      pfam00435
      Location:20042062
      Spectrin; Spectrin repeat

    RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20210514

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

    Reference GRCh38.p13 Primary Assembly

    Genomic

    1. NC_000002.12 Reference GRCh38.p13 Primary Assembly

      Range
      54456327..54671446
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017004779.1XP_016860268.1  spectrin beta chain, non-erythrocytic 1 isoform X1

      UniProtKB/Swiss-Prot
      Q01082
      UniProtKB/TrEMBL
      B2ZZ89
      Conserved Domains (6) summary
      COG5069
      Location:48530
      SAC6; Ca2+-binding actin-bundling protein fimbrin/plastin (EF-Hand superfamily) [Cytoskeleton]
      cd00176
      Location:530743
      SPEC; Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; ...
      cd10571
      Location:22002305
      PH_beta_spectrin; Beta-spectrin pleckstrin homology (PH) domain
      pfam00435
      Location:20172075
      Spectrin; Spectrin repeat
      cd21248
      Location:173277
      CH_SPTB_like_rpt2; second calponin homology (CH) domain found in the beta-I spectrin-like subfamily
      cd21316
      Location:3156
      CH_SPTBN1_rpt1; first calponin homology (CH) domain found in spectrin beta chain, non-erythrocytic 1 (SPTBN1) and similar proteins
    2. XM_017004781.1XP_016860270.1  spectrin beta chain, non-erythrocytic 1 isoform X1

      UniProtKB/Swiss-Prot
      Q01082
      UniProtKB/TrEMBL
      B2ZZ89
      Conserved Domains (6) summary
      COG5069
      Location:48530
      SAC6; Ca2+-binding actin-bundling protein fimbrin/plastin (EF-Hand superfamily) [Cytoskeleton]
      cd00176
      Location:530743
      SPEC; Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; ...
      cd10571
      Location:22002305
      PH_beta_spectrin; Beta-spectrin pleckstrin homology (PH) domain
      pfam00435
      Location:20172075
      Spectrin; Spectrin repeat
      cd21248
      Location:173277
      CH_SPTB_like_rpt2; second calponin homology (CH) domain found in the beta-I spectrin-like subfamily
      cd21316
      Location:3156
      CH_SPTBN1_rpt1; first calponin homology (CH) domain found in spectrin beta chain, non-erythrocytic 1 (SPTBN1) and similar proteins
    3. XM_006712087.3XP_006712150.1  spectrin beta chain, non-erythrocytic 1 isoform X1

      See identical proteins and their annotated locations for XP_006712150.1

      UniProtKB/Swiss-Prot
      Q01082
      UniProtKB/TrEMBL
      B2ZZ89
      Conserved Domains (6) summary
      COG5069
      Location:48530
      SAC6; Ca2+-binding actin-bundling protein fimbrin/plastin (EF-Hand superfamily) [Cytoskeleton]
      cd00176
      Location:530743
      SPEC; Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; ...
      cd10571
      Location:22002305
      PH_beta_spectrin; Beta-spectrin pleckstrin homology (PH) domain
      pfam00435
      Location:20172075
      Spectrin; Spectrin repeat
      cd21248
      Location:173277
      CH_SPTB_like_rpt2; second calponin homology (CH) domain found in the beta-I spectrin-like subfamily
      cd21316
      Location:3156
      CH_SPTBN1_rpt1; first calponin homology (CH) domain found in spectrin beta chain, non-erythrocytic 1 (SPTBN1) and similar proteins
    4. XM_005264517.2XP_005264574.1  spectrin beta chain, non-erythrocytic 1 isoform X1

      See identical proteins and their annotated locations for XP_005264574.1

      UniProtKB/Swiss-Prot
      Q01082
      UniProtKB/TrEMBL
      B2ZZ89
      Conserved Domains (6) summary
      COG5069
      Location:48530
      SAC6; Ca2+-binding actin-bundling protein fimbrin/plastin (EF-Hand superfamily) [Cytoskeleton]
      cd00176
      Location:530743
      SPEC; Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; ...
      cd10571
      Location:22002305
      PH_beta_spectrin; Beta-spectrin pleckstrin homology (PH) domain
      pfam00435
      Location:20172075
      Spectrin; Spectrin repeat
      cd21248
      Location:173277
      CH_SPTB_like_rpt2; second calponin homology (CH) domain found in the beta-I spectrin-like subfamily
      cd21316
      Location:3156
      CH_SPTBN1_rpt1; first calponin homology (CH) domain found in spectrin beta chain, non-erythrocytic 1 (SPTBN1) and similar proteins
    5. XM_017004780.1XP_016860269.1  spectrin beta chain, non-erythrocytic 1 isoform X1

      UniProtKB/Swiss-Prot
      Q01082
      UniProtKB/TrEMBL
      B2ZZ89
      Conserved Domains (6) summary
      COG5069
      Location:48530
      SAC6; Ca2+-binding actin-bundling protein fimbrin/plastin (EF-Hand superfamily) [Cytoskeleton]
      cd00176
      Location:530743
      SPEC; Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; ...
      cd10571
      Location:22002305
      PH_beta_spectrin; Beta-spectrin pleckstrin homology (PH) domain
      pfam00435
      Location:20172075
      Spectrin; Spectrin repeat
      cd21248
      Location:173277
      CH_SPTB_like_rpt2; second calponin homology (CH) domain found in the beta-I spectrin-like subfamily
      cd21316
      Location:3156
      CH_SPTBN1_rpt1; first calponin homology (CH) domain found in spectrin beta chain, non-erythrocytic 1 (SPTBN1) and similar proteins
    6. XM_005264518.2XP_005264575.1  spectrin beta chain, non-erythrocytic 1 isoform X2

      See identical proteins and their annotated locations for XP_005264575.1

      Conserved Domains (5) summary
      cd00014
      Location:161264
      CH; Calponin homology domain; actin-binding domain which may be present as a single copy or in tandem repeats (which increases binding affinity). The CH domain is found in cytoskeletal and signal transduction proteins, including actin-binding proteins like ...
      cd00176
      Location:517730
      SPEC; Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; ...
      cd10571
      Location:21872292
      PH_beta_spectrin; Beta-spectrin pleckstrin homology (PH) domain
      pfam00169
      Location:21872294
      PH; PH domain
      pfam00435
      Location:409512
      Spectrin; Spectrin repeat

    RNA

    1. XR_002959325.1 RNA Sequence

    Support Center