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

Gene ID: 6711, updated on 5-Sep-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
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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)

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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_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

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