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

Summary

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 several functions, including 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, Apr 2022]
Expression: Low expression observed in reference dataset See more
Orthologs: mouse all
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Genomic context

Location:: 15q15.1

Exon count:: 69

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	15	NC_000015.10 (41848146..41894053, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	15	NC_060939.1 (39654101..39700011, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	15	NC_000015.9 (42140344..42186251, complement)

Chromosome 15 - NC_000015.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
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.
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.
Observational study of gene-disease association. (HuGE Navigator)
Title: Association of genetic variants with hemorrhagic stroke in Japanese individuals.
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.

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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

RH91785 (e-PCR)
- UniSTS:86288

D15S711E (e-PCR)
- UniSTS:151613

WI-13757 (e-PCR)
- UniSTS:20082

RH79820 (e-PCR)
- UniSTS:90003

SHGC-58472 (e-PCR)
- UniSTS:94355

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	IPI Inferred from Physical Interaction 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)

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_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000015.10 Reference GRCh38.p14 Primary Assembly

Range

41848146..41894053 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_017022299.2 → XP_016877788.1 spectrin beta chain, non-erythrocytic 5 isoform X1
XM_017022302.2 → XP_016877791.1 spectrin beta chain, non-erythrocytic 5 isoform X2

RNA

XR_001751302.2 RNA Sequence
XR_001751303.2 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

NC_060939.1 Alternate T2T-CHM13v2.0

Range

39654101..39700011 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054378164.1 → XP_054234139.1 spectrin beta chain, non-erythrocytic 5 isoform X1
XM_054378165.1 → XP_054234140.1 spectrin beta chain, non-erythrocytic 5 isoform X2