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SPTBN5 spectrin beta, non-erythrocytic 5 [ Homo sapiens (human) ]

Gene ID: 51332, updated on 3-Nov-2024

Summary

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Official Symbol
SPTBN5provided by HGNC
Official Full Name
spectrin beta, non-erythrocytic 5provided by HGNC
Primary source
HGNC:HGNC:15680
See related
Ensembl:ENSG00000137877 MIM:605916; AllianceGenome:HGNC:15680
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
BSPECV; HUSPECV; HUBSPECV
Summary
Enables cytoskeletal protein binding activity; dynein intermediate chain binding activity; and identical protein binding activity. Acts upstream of or within Golgi organization and lysosomal transport. Located in cytoplasm; photoreceptor connecting cilium; and photoreceptor disc membrane. [provided by Alliance of Genome Resources, Nov 2024]
Expression
Low expression observed in reference dataset See more
Orthologs
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Genomic context

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See SPTBN5 in Genome Data Viewer
Location:
15q15.1
Exon count:
69
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (41848146..41894053, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (39654101..39700011, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (42140344..42186251, complement)

Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene JMJD7-PLA2G4B readthrough Neighboring gene Sharpr-MPRA regulatory region 5929 Neighboring gene jumonji domain containing 7 Neighboring gene phospholipase A2 group IVB Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:42144871-42145480 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:42145481-42146091 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:42147073-42147589 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:42147590-42148105 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:42148623-42149137 Neighboring gene RNA, 5S ribosomal pseudogene 393 Neighboring gene ReSE screen-validated silencer GRCh37_chr15:42161952-42162212 Neighboring gene microRNA 4310 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:42170147-42170648 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:42182967-42183842 Neighboring gene uncharacterized LOC105370792 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9287 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:42195822-42196326 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:42196327-42196830 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9288 Neighboring gene EH domain containing 4 Neighboring gene Sharpr-MPRA regulatory region 4481 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:42211607-42212106 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:42218089-42218606 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9289 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:42221112-42221615 Neighboring gene EHD4 antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9291 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9292 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:42234574-42235431 Neighboring gene uncharacterized LOC124903477

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 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. Identification and characterization of beta V spectrin, a mammalian ortholog of Drosophila beta H spectrin. Stabach PR, et al. J Biol Chem, 2000 Jul 14. PMID 10764729
  2. The spectrin cytoskeleton influences the surface expression and activation of human transient receptor potential channel 4 channels. Odell AF, et al. J Biol Chem, 2008 Feb 15. PMID 18048348
  3. Association of genetic variants with ischemic stroke in Japanese individuals with or without metabolic syndrome. Yoshida T, et al. Int J Mol Med, 2010 Feb. PMID 20043139
  4. Spectrin βV adaptive mutations and changes in subcellular location correlate with emergence of hair cell electromotility in mammalians. Cortese M, et al. Proc Natl Acad Sci U S A, 2017 Feb 21. PMID 28179572, Free PMC Article
  5. Organization of focal adhesion plaques is disrupted by action of the HIV-1 protease. Shoeman RL, et al. Cell Biol Int, 2002. PMID 12119179

See all (26) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Adaptive mutations of spectrin-betaV occurred in the mammalian lineage and were accompanied with substantial changes in the protein distribution within inner ear hair cells.
    Title: Spectrin βV adaptive mutations and changes in subcellular location correlate with emergence of hair cell electromotility in mammalians.
  2. study identified spectrin betaV as a myosin VIIa- and rhodopsin-interacting partner in photoreceptor cells; suggest that spectrin betaV homomers couple some USH1 proteins, opsin and other phototransduction proteins to both actin- and microtubule-based motors, thereby contributing to their transport towards the photoreceptor outer disks
    Title: The giant spectrin βV couples the molecular motors to phototransduction and Usher syndrome type I proteins along their trafficking route.
  3. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
    Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
  4. The initial chi-square test revealed that the Cright curved arrow T polymorphism of CLEC16A and the Aright curved arrow G polymorphism of SPTBN5 were significantly ssociated with ischemic stroke among individuals with metabolic syndrome.
    Title: Association of genetic variants with ischemic stroke in Japanese individuals with or without metabolic syndrome.
  5. Observational study of gene-disease association. (HuGE Navigator)
    Title: Association of genetic variants with hemorrhagic stroke in Japanese individuals.
  6. interaction of hTRPC4 with alphaII-spectrin and betaV-spectrin was confirmed by glutathione S-transferase pulldown and co-immunoprecipitation experiments
    Title: The spectrin cytoskeleton influences the surface expression and activation of human transient receptor potential channel 4 channels.
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)

HIV-1 interactions

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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

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables actin binding NAS
Non-traceable Author Statement
more info
 PubMed 
enables actin filament binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables dynactin binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables dynein intermediate chain binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables identical protein binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables kinesin binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables myosin tail binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables opsin binding IEA
Inferred from Electronic Annotation
more info
  
enables spectrin binding IDA
Inferred from Direct Assay
more info
 PubMed 
Process Evidence Code Pubs
acts_upstream_of_or_within Golgi organization IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in actin cytoskeleton organization IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in actin cytoskeleton organization NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in actin filament capping IEA
Inferred from Electronic Annotation
more info
  
acts_upstream_of_or_within lysosomal transport IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
located_in apical cortex IEA
Inferred from Electronic Annotation
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 membrane NAS
Non-traceable Author Statement
more info
 PubMed 
part_of microtubule associated complex IEA
Inferred from Electronic Annotation
more info
  
located_in photoreceptor connecting cilium IDA
Inferred from Direct Assay
more info
 PubMed 
located_in photoreceptor disc membrane IDA
Inferred from Direct Assay
more info
 PubMed 
is_active_in plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of spectrin NAS
Non-traceable Author Statement
more info
 PubMed 

General protein information

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Preferred Names
spectrin beta chain, non-erythrocytic 5
Names
beta V spectrin
spectrin beta chain, brain 4
spectrin, non-erythroid beta chain 4

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_016642.4 → NP_057726.4  spectrin beta chain, non-erythrocytic 5

    See identical proteins and their annotated locations for NP_057726.4

    Status: VALIDATED

    Source sequence(s)
    AA599654, AC020659, AF233523
    Consensus CDS
    CCDS61599.1
    UniProtKB/Swiss-Prot
    Q9NRC6
    Related
    ENSP00000317790.6, ENST00000320955.8
    Conserved Domains (7) summary
    smart00150
    Location:3423 → 3482
    SPEC; Spectrin repeats
    cd00014
    Location:178 → 280
    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:1521 → 1727
    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; ...
    pfam00169
    Location:3534 → 3636
    PH; PH domain
    pfam00307
    Location:56 → 152
    CH; Calponin homology (CH) domain
    cl02488
    Location:311 → 532
    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; ...
    cl17171
    Location:3536 → 3636
    PH-like; Pleckstrin homology-like domain

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_000015.10 Reference GRCh38.p14 Primary Assembly

    Range
    41848146..41894053 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017022299.2 → XP_016877788.1  spectrin beta chain, non-erythrocytic 5 isoform X1

  2. XM_017022302.2 → XP_016877791.1  spectrin beta chain, non-erythrocytic 5 isoform X2

RNA

  1. XR_001751302.2 RNA Sequence

  2. XR_001751303.2 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060939.1 Alternate T2T-CHM13v2.0

    Range
    39654101..39700011 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054378164.1 → XP_054234139.1  spectrin beta chain, non-erythrocytic 5 isoform X1

  2. XM_054378165.1 → XP_054234140.1  spectrin beta chain, non-erythrocytic 5 isoform X2

RNA

  1. XR_008488958.1 RNA Sequence

  2. XR_008488959.1 RNA Sequence

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9NRC6.2 GenPept UniProtKB/Swiss-Prot:Q9NRC6

Gene LinkOut

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

Chemical Information
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