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    SPTBN4 spectrin beta, non-erythrocytic 4 [ Homo sapiens (human) ]

    Gene ID: 57731, updated on 3-Dec-2024

    Summary

    Official Symbol
    SPTBN4provided by HGNC
    Official Full Name
    spectrin beta, non-erythrocytic 4provided by HGNC
    Primary source
    HGNC:HGNC:14896
    See related
    Ensembl:ENSG00000160460 MIM:606214; AllianceGenome:HGNC:14896
    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
    QV; CMND; SPNB4; NEDHND; SPTBN3
    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 localizes to the nuclear matrix, PML nuclear bodies, and cytoplasmic vesicles. A highly similar gene in the mouse is required for localization of specific membrane proteins in polarized regions of neurons. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
    Expression
    Biased expression in brain (RPKM 4.1), testis (RPKM 0.9) and 9 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See SPTBN4 in Genome Data Viewer
    Location:
    19q13.2
    Exon count:
    40
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (40467001..40576464)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (43287653..43397080)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (40972908..41082370)

    Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10628 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10629 Neighboring gene SERTAD3 antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14655 Neighboring gene biliverdin reductase B Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10630 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:41029231-41029526 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10631 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14656 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10632 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10633 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10634 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10635 Neighboring gene SH3KBP1 binding protein 1 Neighboring gene Sharpr-MPRA regulatory region 6117 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14657 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10636 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:41108540-41109063 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10637 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10638 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10639 Neighboring gene Sharpr-MPRA regulatory region 12022 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10640 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14658 Neighboring gene latent transforming growth factor beta binding protein 4 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:41119811-41120358 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14659 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:41128498-41129138 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14660

    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?

    HIV-1 interactions

    Protein interactions

    Protein Gene Interaction Pubs
    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

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • KIAA1642

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables actin binding ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    enables actin filament binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables ankyrin binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables cytoskeletal protein-membrane anchor activity TAS
    Traceable Author Statement
    more info
    PubMed 
    enables phosphatase binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables phospholipid binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables spectrin binding ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    enables structural constituent of cytoskeleton TAS
    Traceable Author Statement
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in actin cytoskeleton organization IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in actin filament capping IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in adult walking behavior ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in axonogenesis ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in cardiac conduction ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in central nervous system projection neuron axonogenesis IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in central nervous system projection neuron axonogenesis ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in clustering of voltage-gated sodium channels ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in fertilization IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in negative regulation of heart rate ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in neuromuscular junction development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in neuromuscular process IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of multicellular organism growth IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in protein localization to plasma membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in protein-containing complex assembly IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in regulation of sodium ion transport ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in sensory perception of sound ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in transmission of nerve impulse ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in vesicle-mediated transport TAS
    Traceable Author Statement
    more info
    PubMed 
    Component Evidence Code Pubs
    located_in PML body IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in actin filament ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    colocalizes_with adherens junction ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in axon hillock ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in axon initial segment ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in cell body fiber ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    is_active_in cell junction IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    is_active_in cell projection IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    is_active_in cortical actin cytoskeleton IBA
    Inferred from Biological aspect of Ancestor
    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 intercalated disc IEA
    Inferred from Electronic Annotation
    more info
     
    located_in juxtaparanode region of axon IEA
    Inferred from Electronic Annotation
    more info
     
    located_in membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in neuronal cell body ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in node of Ranvier ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in nuclear matrix IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in paranode region of axon IEA
    Inferred from Electronic Annotation
    more info
     
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in plasma membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    part_of spectrin IDA
    Inferred from Direct Assay
    more info
    PubMed 

    General protein information

    Preferred Names
    spectrin beta chain, non-erythrocytic 4
    Names
    beta-IV spectrin
    spectrin beta chain, brain 3
    spectrin, non-erythroid beta chain 3

    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_029905.2 RefSeqGene

      Range
      5002..114465
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_020971.3NP_066022.2  spectrin beta chain, non-erythrocytic 4 isoform sigma1

      See identical proteins and their annotated locations for NP_066022.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (sigma1) represents the longer transcript and encodes the longer isoform (sigma1), also known as the 289 kDa isoform.
      Source sequence(s)
      AB046862, AC020929, AF311855, AI962525
      Consensus CDS
      CCDS12559.1
      UniProtKB/Swiss-Prot
      E9PGQ5, Q9H1K7, Q9H1K8, Q9H1K9, Q9H253, Q9H254, Q9H3G8, Q9HCD0
      UniProtKB/TrEMBL
      C9JY79, E9PDB1, Q71S07
      Related
      ENSP00000469242.1, ENST00000598249.6
      Conserved Domains (7) summary
      smart00150
      Location:10911195
      SPEC; Spectrin repeats
      cd00014
      Location:181284
      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:15161727
      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:24212525
      PH_beta_spectrin; Beta-spectrin pleckstrin homology (PH) domain
      pfam00169
      Location:24192527
      PH; PH domain
      pfam00435
      Location:18341933
      Spectrin; Spectrin repeat
      cl02488
      Location:311419
      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; ...
    2. NM_025213.3NP_079489.2  spectrin beta chain, non-erythrocytic 4 isoform sigma5

      Status: REVIEWED

      Description
      Transcript Variant: This variant (sigma5) contains a distinct 5' and 3' UTR and lacks an in-frame portion of the 5' and 3' coding region, compared to variant sigma1. The resulting isoform (sigma5), also known as the 77 kDa isoform, has distinct and shorter N- and C-termini when compared to isoform sigma1.
      Source sequence(s)
      AC020929, AF311856, DA514440
      Consensus CDS
      CCDS42569.1
      UniProtKB/Swiss-Prot
      Q9H254
      Related
      ENSP00000375877.1, ENST00000392023.1
      Conserved Domains (1) summary
      cd00176
      Location:192403
      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; ...

    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_000019.10 Reference GRCh38.p14 Primary Assembly

      Range
      40467001..40576464
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017027051.2XP_016882540.1  spectrin beta chain, non-erythrocytic 4 isoform X3

      UniProtKB/TrEMBL
      M0QZQ3
      Related
      ENSP00000470693.1, ENST00000595535.5
    2. XM_017027052.2XP_016882541.1  spectrin beta chain, non-erythrocytic 4 isoform X4

    3. XM_017027049.2XP_016882538.1  spectrin beta chain, non-erythrocytic 4 isoform X1

      UniProtKB/Swiss-Prot
      E9PGQ5, Q9H1K7, Q9H1K8, Q9H1K9, Q9H253, Q9H254, Q9H3G8, Q9HCD0
      UniProtKB/TrEMBL
      C9JY79, E9PDB1, Q71S07
      Conserved Domains (7) summary
      smart00150
      Location:10911195
      SPEC; Spectrin repeats
      cd00014
      Location:181284
      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:15161727
      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:24212525
      PH_beta_spectrin; Beta-spectrin pleckstrin homology (PH) domain
      pfam00169
      Location:24192527
      PH; PH domain
      pfam00435
      Location:18341933
      Spectrin; Spectrin repeat
      cl02488
      Location:311419
      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; ...
    4. XM_017027050.2XP_016882539.1  spectrin beta chain, non-erythrocytic 4 isoform X2

      UniProtKB/TrEMBL
      C9JY79, E9PDB1, Q71S07

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060943.1 Alternate T2T-CHM13v2.0

      Range
      43287653..43397080
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054321577.1XP_054177552.1  spectrin beta chain, non-erythrocytic 4 isoform X3

      UniProtKB/TrEMBL
      M0QZQ3
    2. XM_054321578.1XP_054177553.1  spectrin beta chain, non-erythrocytic 4 isoform X4

    3. XM_054321575.1XP_054177550.1  spectrin beta chain, non-erythrocytic 4 isoform X1

      UniProtKB/Swiss-Prot
      E9PGQ5, Q9H1K7, Q9H1K8, Q9H1K9, Q9H253, Q9H254, Q9H3G8, Q9HCD0
      UniProtKB/TrEMBL
      C9JY79, E9PDB1, Q71S07
    4. XM_054321576.1XP_054177551.1  spectrin beta chain, non-erythrocytic 4 isoform X2

      UniProtKB/TrEMBL
      C9JY79, E9PDB1, Q71S07