SPTA1 spectrin alpha, erythrocytic 1 [Homo sapiens (human)] - Gene

Summary

Official Symbol: SPTA1provided by HGNC
Official Full Name: spectrin alpha, erythrocytic 1provided by HGNC
Primary source: HGNC:HGNC:11272
See related: Ensembl:ENSG00000163554 MIM:182860; AllianceGenome:HGNC:11272
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: EL2; HPP; HS3; SPH3; SPTA
Summary: This gene encodes a member of a family of molecular scaffold proteins that link the plasma membrane to the actin cytoskeleton and functions in the determination of cell shape, arrangement of transmembrane proteins, and organization of organelles. The encoded protein is primarily composed of 22 spectrin repeats which are involved in dimer formation. It forms a component of the erythrocyte plasma membrane. Mutations in this gene result in a variety of hereditary red blood cell disorders, including elliptocytosis-2, pyropoikilocytosis, and spherocytosis, type 3. [provided by RefSeq, Aug 2017]
Expression: Restricted expression toward bone marrow (RPKM 32.4) See more
Orthologs: mouse all
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Genomic context

Location:: 1q23.1

Exon count:: 52

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	1	NC_000001.11 (158610704..158686715, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	1	NC_060925.1 (157747803..157823815, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	1	NC_000001.10 (158580494..158656505, complement)

Chromosome 1 - NC_000001.11 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?

Hereditary elliptocytosis: A novel mutation in the SPTA1 gene and diagnosis after a stroke in paediatric patients. A two-case report.
Title: Hereditary elliptocytosis: A novel mutation in the SPTA1 gene and diagnosis after a stroke in paediatric patients. A two-case report.
Unravelling the genetic and phenotypic heterogeneity of SPTA1 gene variants in Hereditary Elliptocytosis and Hereditary Pyropoikilocytosis patients using next-generation sequencing.
Title: Unravelling the genetic and phenotypic heterogeneity of SPTA1 gene variants in Hereditary Elliptocytosis and Hereditary Pyropoikilocytosis patients using next-generation sequencing.
Effects of SPTA1 Gene Variants on the Hematological Phenotype of Mexican Patients with Hereditary Spherocytosis.
Title: Effects of SPTA1 Gene Variants on the Hematological Phenotype of Mexican Patients with Hereditary Spherocytosis.
Complex Modes of Inheritance in Hereditary Red Blood Cell Disorders: A Case Series Study of 155 Patients.
Title: Complex Modes of Inheritance in Hereditary Red Blood Cell Disorders: A Case Series Study of 155 Patients.
Clinical manifestation and phenotypic analysis of novel gene mutation in 28 Chinese children with hereditary spherocytosis.
Title: Clinical manifestation and phenotypic analysis of novel gene mutation in 28 Chinese children with hereditary spherocytosis.
Novel mechanism of hereditary pyropoikilocytosis phenotype due to co-inheritance of beta globin and alpha spectrin mutations.
Title: Novel mechanism of hereditary pyropoikilocytosis phenotype due to co-inheritance of β globin and α spectrin mutations.
A Novel alpha-Spectrin Pathogenic Variant in Trans to alpha-Spectrin LELY Causing Neonatal Jaundice With Hemolytic Anemia From Hereditary Pyropoikilocytosis Coexisting With Gilbert Syndrome.
Title: A Novel α-Spectrin Pathogenic Variant in Trans to α-Spectrin LELY Causing Neonatal Jaundice With Hemolytic Anemia From Hereditary Pyropoikilocytosis Coexisting With Gilbert Syndrome.
Hereditary spherocytosis overlooked for 7 years in a pediatric patient with beta-thalassemia trait and novel compound heterozygous mutations of SPTA1 gene.
Title: Hereditary spherocytosis overlooked for 7 years in a pediatric patient with β-thalassemia trait and novel compound heterozygous mutations of SPTA1 gene.
A family affair-Severe fetal and neonatal hemolytic anemia due to novel alpha-spectrin mutations in two siblings.
Title: A family affair-Severe fetal and neonatal hemolytic anemia due to novel alpha-spectrin mutations in two siblings.
the molecular origin of chaperone activity resides in the surface exposed hydrophobic patches of the spectrin domains.
Title: Localizing the chaperone activity of erythroid spectrin.

Submit: New GeneRIF Correction See all GeneRIFs (56)

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

Associated conditions

Description	Tests
Elliptocytosis 2 MedGen: C1851741 OMIM: 130600 GeneReviews: Not available	Compare labs
Hereditary spherocytosis type 3 MedGen: C2678338 OMIM: 270970 GeneReviews: Not available	Compare labs
Pyropoikilocytosis, hereditary MedGen: C0520739 OMIM: 266140 GeneReviews: Not available	Compare labs

EBI GWAS Catalog

Description
Common variants at 10 genomic loci influence hemoglobin A&#x000e2;&#x00082;&#x00081;(C) levels via glycemic and nonglycemic pathways. EBI GWAS Catalog EBI GWAS CatalogPubMed
Multiple loci influence erythrocyte phenotypes in the CHARGE Consortium. EBI GWAS Catalog EBI GWAS CatalogPubMed
Seventy-five genetic loci influencing the human red blood cell. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See Variation Viewer (GRCh37.p13)

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
	gag-pol	HIV-1 protease cleaves alpha-spectrin in vitro at amino acid positions 1352, 1376, and 1697	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

RH65132 (e-PCR)
- UniSTS:57112

D1S3249 (e-PCR)
- UniSTS:46677

G15944 (e-PCR)
- UniSTS:75377

GDB:181583 (e-PCR)
- UniSTS:155294

RH102597 (e-PCR)
- UniSTS:96931

RH68459 (e-PCR)
- UniSTS:17603

GDB:196442 (e-PCR)
- UniSTS:155850

RH69635 (e-PCR)
- UniSTS:40405

GDB:191077 (e-PCR)
- UniSTS:155640

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables actin filament binding	IBA Inferred from Biological aspect of Ancestor more info
enables calcium ion binding	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
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 actin filament organization	TAS Traceable Author Statement more info	PubMed
involved_in hemopoiesis	IEA Inferred from Electronic Annotation more info
involved_in lymphocyte homeostasis	IEA Inferred from Electronic Annotation more info
involved_in plasma membrane organization	IEA Inferred from Electronic Annotation more info
involved_in porphyrin-containing compound biosynthetic process	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of T cell proliferation	IEA Inferred from Electronic Annotation more info
involved_in regulation of cell shape	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in actin cytoskeleton	TAS Traceable Author Statement more info	PubMed
located_in axon	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 cuticular plate	IEA Inferred from Electronic Annotation more info
located_in cytoplasmic side of plasma membrane	TAS Traceable Author Statement more info	PubMed
located_in cytosol	TAS Traceable Author Statement more info
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
part_of spectrin	IEA Inferred from Electronic Annotation more info
located_in spectrin-associated cytoskeleton	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: spectrin alpha chain, erythrocytic 1

Names: alpha-I spectrin; elliptocytosis 2; erythroid alpha-spectrin; spectrin alpha chain, erythrocyte

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

NG_011474.1 RefSeqGene

Range

5002..81011

Download

GenBank, FASTA, Sequence Viewer (Graphics), LRG_1131

mRNA and Protein(s)

NM_003126.4 → NP_003117.2 spectrin alpha chain, erythrocytic 1

See identical proteins and their annotated locations for NP_003117.2

Status: REVIEWED

Source sequence(s)

AL353894, BU665064, CD616351, M61877

Consensus CDS

CCDS41423.1

UniProtKB/Swiss-Prot

P02549, Q15514, Q5VYL1, Q5VYL2, Q6LDY5

Related

ENSP00000495214.1, ENST00000643759.2

Conserved Domains (7) summary

smart00150
Location:902 → 958

SPEC; Spectrin repeats

cd00176
Location:1608 → 1819

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:1082 → 1179

Spectrin; Spectrin repeat

pfam08726
Location:2350 → 2418

EFhand_Ca_insen; Ca2+ insensitive EF hand

pfam13499
Location:2278 → 2343

EF-hand_7; EF-hand domain pair

cl08302
Location:2275 → 2343

EFh; EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to ...

cl17036
Location:982 → 1033

SH3; Src Homology 3 domain superfamily

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

NC_000001.11 Reference GRCh38.p14 Primary Assembly

Range

158610704..158686715 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_011509916.3 → XP_011508218.1 spectrin alpha chain, erythrocytic 1 isoform X1

See identical proteins and their annotated locations for XP_011508218.1

UniProtKB/Swiss-Prot

P02549, Q15514, Q5VYL1, Q5VYL2, Q6LDY5

Conserved Domains (7) summary

smart00150
Location:902 → 958

SPEC; Spectrin repeats

cd00176
Location:1608 → 1819

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:1082 → 1179

Spectrin; Spectrin repeat

pfam08726
Location:2350 → 2418

EFhand_Ca_insen; Ca2+ insensitive EF hand

pfam13499
Location:2278 → 2343

EF-hand_7; EF-hand domain pair

cl08302
Location:2275 → 2343

EFh; EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to ...

cl17036
Location:982 → 1033

SH3; Src Homology 3 domain superfamily
XM_047428883.1 → XP_047284839.1 spectrin alpha chain, erythrocytic 1 isoform X3
XM_011509917.4 → XP_011508219.1 spectrin alpha chain, erythrocytic 1 isoform X2

Conserved Domains (7) summary

smart00150
Location:902 → 958

SPEC; Spectrin repeats

cd00176
Location:1608 → 1819

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:1082 → 1179

Spectrin; Spectrin repeat

pfam08726
Location:2344 → 2412

EFhand_Ca_insen; Ca2+ insensitive EF hand

pfam13499
Location:2272 → 2337

EF-hand_7; EF-hand domain pair

cl08302
Location:2269 → 2337

EFh; EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to ...

cl17036
Location:982 → 1033

SH3; Src Homology 3 domain superfamily
XM_011509918.4 → XP_011508220.1 spectrin alpha chain, erythrocytic 1 isoform X4

Conserved Domains (4) summary

smart00150
Location:902 → 958

SPEC; Spectrin repeats

cd00176
Location:1608 → 1819

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:1928 → 2033

Spectrin; Spectrin repeat

cl17036
Location:982 → 1033

SH3; Src Homology 3 domain superfamily
XM_011509919.4 → XP_011508221.1 spectrin alpha chain, erythrocytic 1 isoform X5

Conserved Domains (4) summary

smart00150
Location:902 → 958

SPEC; Spectrin repeats

cd00176
Location:266 → 476

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:1082 → 1179

Spectrin; Spectrin repeat

cl17036
Location:982 → 1033

SH3; Src Homology 3 domain superfamily
XM_047428888.1 → XP_047284844.1 spectrin alpha chain, erythrocytic 1 isoform X6