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SPTBN2 spectrin beta, non-erythrocytic 2 [ Homo sapiens (human) ]

Gene ID: 6712, updated on 5-Feb-2024

Summary

Official Symbol
SPTBN2provided by HGNC
Official Full Name
spectrin beta, non-erythrocytic 2provided by HGNC
Primary source
HGNC:HGNC:11276
See related
Ensembl:ENSG00000173898 MIM:604985; AllianceGenome:HGNC:11276
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
SCA5; SCAR14; GTRAP41
Summary
Spectrins are principle components of a cell's membrane-cytoskeleton and are composed of two alpha and two beta spectrin subunits. The protein encoded by this gene (SPTBN2), is called spectrin beta non-erythrocytic 2 or beta-III spectrin. It is related to, but distinct from, the beta-II spectrin gene which is also known as spectrin beta non-erythrocytic 1 (SPTBN1). SPTBN2 regulates the glutamate signaling pathway by stabilizing the glutamate transporter EAAT4 at the surface of the plasma membrane. Mutations in this gene cause a form of spinocerebellar ataxia, SCA5, that is characterized by neurodegeneration, progressive locomotor incoordination, dysarthria, and uncoordinated eye movements. [provided by RefSeq, Dec 2009]
Expression
Biased expression in skin (RPKM 16.1), testis (RPKM 12.4) and 8 other tissues See more
Orthologs
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Genomic context

See SPTBN2 in Genome Data Viewer
Location:
11q13.2
Exon count:
46
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (66682497..66744682, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (66678745..66725466, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (66449968..66496687, complement)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:66384051-66384984 Neighboring gene RBM14-RBM4 readthrough Neighboring gene hESC enhancers GRCh37_chr11:66405625-66406338 and GRCh37_chr11:66406339-66407050 Neighboring gene RNA binding motif protein 14 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:66410755-66411278 Neighboring gene MPRA-validated peak1306 silencer Neighboring gene RNA binding motif protein 4 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3599 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3600 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:66453249-66453749 Neighboring gene RNA binding motif protein 4B Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:66462288-66462788 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:66487347-66488304 Neighboring gene RNA, 7SL, cytoplasmic 12, pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:66511467-66511967 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3601 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5056 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3602 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5057 Neighboring gene TOP6B like initiator of meiotic double strand breaks Neighboring gene fragile site, folic acid type, rare, fra(11)(q13.3) Neighboring gene complement C1q binding protein pseudogene 2 Neighboring gene ferritin light chain pseudogene 6

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
Autosomal recessive spinocerebellar ataxia 14
MedGen: C4706415 OMIM: 615386 GeneReviews: Not available
Compare labs
Spinocerebellar ataxia type 5
MedGen: C0752123 OMIM: 600224 GeneReviews: Hereditary Ataxia Overview
Compare labs

EBI GWAS Catalog

Description
Large-scale genome-wide association analysis of bipolar disorder identifies a new susceptibility locus near ODZ4.
EBI GWAS Catalog

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

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables actin binding TAS
Traceable Author Statement
more info
PubMed 
enables actin filament binding IBA
Inferred from Biological aspect of Ancestor
more info
 
enables cadherin binding HDA PubMed 
enables phospholipid binding IEA
Inferred from Electronic Annotation
more info
 
enables structural constituent of cytoskeleton TAS
Traceable Author Statement
more info
PubMed 
enables structural constituent of postsynapse IEA
Inferred from Electronic Annotation
more info
 
enables structural constituent of synapse IBA
Inferred from Biological aspect of Ancestor
more info
 
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 behavior IEA
Inferred from Electronic Annotation
more info
 
involved_in cerebellar Purkinje cell layer morphogenesis IEA
Inferred from Electronic Annotation
more info
 
involved_in multicellular organism growth IEA
Inferred from Electronic Annotation
more info
 
involved_in postsynapse organization IEA
Inferred from Electronic Annotation
more info
 
involved_in regulation of postsynaptic specialization assembly IEA
Inferred from Electronic Annotation
more info
 
involved_in synapse assembly IEA
Inferred from Electronic Annotation
more info
 
involved_in vesicle-mediated transport IDA
Inferred from Direct Assay
more info
PubMed 
Component Evidence Code Pubs
located_in apical plasma membrane 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 cytosol IDA
Inferred from Direct Assay
more info
 
located_in cytosol TAS
Traceable Author Statement
more info
 
located_in extracellular space HDA PubMed 
located_in glutamatergic synapse IEA
Inferred from Electronic Annotation
more info
 
located_in intracellular membrane-bounded organelle IDA
Inferred from Direct Assay
more info
 
located_in neuronal cell body IEA
Inferred from Electronic Annotation
more info
 
located_in parallel fiber to Purkinje cell synapse IEA
Inferred from Electronic Annotation
more info
 
located_in paranodal junction 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 IDA
Inferred from Direct Assay
more info
 
located_in postsynaptic spectrin-associated cytoskeleton IEA
Inferred from Electronic Annotation
more info
 
located_in presynapse IEA
Inferred from Electronic Annotation
more info
 
part_of spectrin IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
spectrin beta chain, non-erythrocytic 2
Names
beta-III spectrin
glutamate transporter EAAT4-associated protein 41
spectrin beta III sigma 2
spectrin beta chain, brain 2
spectrin, non-erythroid beta chain 2
spinocerebellar ataxia 5 protein

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_016150.3 RefSeqGene

    Range
    20466..67185
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001411025.1NP_001397954.1  spectrin beta chain, non-erythrocytic 2 isoform 2

    Status: REVIEWED

    Source sequence(s)
    AP001157
    Consensus CDS
    CCDS91511.1
    UniProtKB/TrEMBL
    A0A087WYQ1
    Related
    ENSP00000482000.2, ENST00000617502.5
  2. NM_006946.4NP_008877.2  spectrin beta chain, non-erythrocytic 2 isoform 1

    Status: REVIEWED

    Source sequence(s)
    AB008567, AP001157
    Consensus CDS
    CCDS8150.1
    UniProtKB/Swiss-Prot
    O14872, O14873, O15020
    Related
    ENSP00000432568.1, ENST00000533211.6
    Conserved Domains (7) summary
    smart00150
    Location:20182075
    SPEC; Spectrin repeats
    PRK14086
    Location:20972241
    dnaA; chromosomal replication initiator protein DnaA
    cd00176
    Location:13841588
    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:22212324
    PH_beta_spectrin; Beta-spectrin pleckstrin homology (PH) domain
    pfam00435
    Location:429522
    Spectrin; Spectrin repeat
    cd21246
    Location:43159
    CH_SPTB-like_rpt1; first calponin homology (CH) domain found in the beta-I spectrin-like subfamily
    cd21321
    Location:173291
    CH_SPTBN2_rpt2; second calponin homology (CH) domain found in spectrin beta chain, non-erythrocytic 2 (SPTBN2) and similar proteins

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

  1. NC_000011.10 Reference GRCh38.p14 Primary Assembly

    Range
    66682497..66744682 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047427495.1XP_047283451.1  spectrin beta chain, non-erythrocytic 2 isoform X1

    UniProtKB/Swiss-Prot
    O14872, O14873, O15020
  2. XM_005274193.4XP_005274250.1  spectrin beta chain, non-erythrocytic 2 isoform X1

    See identical proteins and their annotated locations for XP_005274250.1

    UniProtKB/Swiss-Prot
    O14872, O14873, O15020
    Related
    ENSP00000311489.2, ENST00000309996.7
    Conserved Domains (7) summary
    smart00150
    Location:20182075
    SPEC; Spectrin repeats
    PRK14086
    Location:20972241
    dnaA; chromosomal replication initiator protein DnaA
    cd00176
    Location:13841588
    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:22212324
    PH_beta_spectrin; Beta-spectrin pleckstrin homology (PH) domain
    pfam00435
    Location:429522
    Spectrin; Spectrin repeat
    cd21246
    Location:43159
    CH_SPTB-like_rpt1; first calponin homology (CH) domain found in the beta-I spectrin-like subfamily
    cd21321
    Location:173291
    CH_SPTBN2_rpt2; second calponin homology (CH) domain found in spectrin beta chain, non-erythrocytic 2 (SPTBN2) and similar proteins
  3. XM_017018174.2XP_016873663.1  spectrin beta chain, non-erythrocytic 2 isoform X1

    UniProtKB/Swiss-Prot
    O14872, O14873, O15020
    Related
    ENSP00000508362.1, ENST00000647510.2
    Conserved Domains (7) summary
    smart00150
    Location:20182075
    SPEC; Spectrin repeats
    PRK14086
    Location:20972241
    dnaA; chromosomal replication initiator protein DnaA
    cd00176
    Location:13841588
    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:22212324
    PH_beta_spectrin; Beta-spectrin pleckstrin homology (PH) domain
    pfam00435
    Location:429522
    Spectrin; Spectrin repeat
    cd21246
    Location:43159
    CH_SPTB-like_rpt1; first calponin homology (CH) domain found in the beta-I spectrin-like subfamily
    cd21321
    Location:173291
    CH_SPTBN2_rpt2; second calponin homology (CH) domain found in spectrin beta chain, non-erythrocytic 2 (SPTBN2) and similar proteins
  4. XM_017018178.2XP_016873667.1  spectrin beta chain, non-erythrocytic 2 isoform X1

    UniProtKB/Swiss-Prot
    O14872, O14873, O15020
    Conserved Domains (7) summary
    smart00150
    Location:20182075
    SPEC; Spectrin repeats
    PRK14086
    Location:20972241
    dnaA; chromosomal replication initiator protein DnaA
    cd00176
    Location:13841588
    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:22212324
    PH_beta_spectrin; Beta-spectrin pleckstrin homology (PH) domain
    pfam00435
    Location:429522
    Spectrin; Spectrin repeat
    cd21246
    Location:43159
    CH_SPTB-like_rpt1; first calponin homology (CH) domain found in the beta-I spectrin-like subfamily
    cd21321
    Location:173291
    CH_SPTBN2_rpt2; second calponin homology (CH) domain found in spectrin beta chain, non-erythrocytic 2 (SPTBN2) and similar proteins
  5. XM_006718671.5XP_006718734.1  spectrin beta chain, non-erythrocytic 2 isoform X1

    See identical proteins and their annotated locations for XP_006718734.1

    UniProtKB/Swiss-Prot
    O14872, O14873, O15020
    Conserved Domains (7) summary
    smart00150
    Location:20182075
    SPEC; Spectrin repeats
    PRK14086
    Location:20972241
    dnaA; chromosomal replication initiator protein DnaA
    cd00176
    Location:13841588
    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:22212324
    PH_beta_spectrin; Beta-spectrin pleckstrin homology (PH) domain
    pfam00435
    Location:429522
    Spectrin; Spectrin repeat
    cd21246
    Location:43159
    CH_SPTB-like_rpt1; first calponin homology (CH) domain found in the beta-I spectrin-like subfamily
    cd21321
    Location:173291
    CH_SPTBN2_rpt2; second calponin homology (CH) domain found in spectrin beta chain, non-erythrocytic 2 (SPTBN2) and similar proteins
  6. XM_047427489.1XP_047283445.1  spectrin beta chain, non-erythrocytic 2 isoform X1

    UniProtKB/Swiss-Prot
    O14872, O14873, O15020
  7. XM_017018176.2XP_016873665.1  spectrin beta chain, non-erythrocytic 2 isoform X1

    UniProtKB/Swiss-Prot
    O14872, O14873, O15020
    Conserved Domains (7) summary
    smart00150
    Location:20182075
    SPEC; Spectrin repeats
    PRK14086
    Location:20972241
    dnaA; chromosomal replication initiator protein DnaA
    cd00176
    Location:13841588
    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:22212324
    PH_beta_spectrin; Beta-spectrin pleckstrin homology (PH) domain
    pfam00435
    Location:429522
    Spectrin; Spectrin repeat
    cd21246
    Location:43159
    CH_SPTB-like_rpt1; first calponin homology (CH) domain found in the beta-I spectrin-like subfamily
    cd21321
    Location:173291
    CH_SPTBN2_rpt2; second calponin homology (CH) domain found in spectrin beta chain, non-erythrocytic 2 (SPTBN2) and similar proteins
  8. XM_047427488.1XP_047283444.1  spectrin beta chain, non-erythrocytic 2 isoform X1

    UniProtKB/Swiss-Prot
    O14872, O14873, O15020
  9. XM_047427494.1XP_047283450.1  spectrin beta chain, non-erythrocytic 2 isoform X1

    UniProtKB/Swiss-Prot
    O14872, O14873, O15020
  10. XM_047427493.1XP_047283449.1  spectrin beta chain, non-erythrocytic 2 isoform X1

    UniProtKB/Swiss-Prot
    O14872, O14873, O15020
  11. XM_017018177.3XP_016873666.1  spectrin beta chain, non-erythrocytic 2 isoform X1

    UniProtKB/Swiss-Prot
    O14872, O14873, O15020
    Conserved Domains (7) summary
    smart00150
    Location:20182075
    SPEC; Spectrin repeats
    PRK14086
    Location:20972241
    dnaA; chromosomal replication initiator protein DnaA
    cd00176
    Location:13841588
    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:22212324
    PH_beta_spectrin; Beta-spectrin pleckstrin homology (PH) domain
    pfam00435
    Location:429522
    Spectrin; Spectrin repeat
    cd21246
    Location:43159
    CH_SPTB-like_rpt1; first calponin homology (CH) domain found in the beta-I spectrin-like subfamily
    cd21321
    Location:173291
    CH_SPTBN2_rpt2; second calponin homology (CH) domain found in spectrin beta chain, non-erythrocytic 2 (SPTBN2) and similar proteins
  12. XM_017018175.3XP_016873664.1  spectrin beta chain, non-erythrocytic 2 isoform X1

    UniProtKB/Swiss-Prot
    O14872, O14873, O15020
    Conserved Domains (7) summary
    smart00150
    Location:20182075
    SPEC; Spectrin repeats
    PRK14086
    Location:20972241
    dnaA; chromosomal replication initiator protein DnaA
    cd00176
    Location:13841588
    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:22212324
    PH_beta_spectrin; Beta-spectrin pleckstrin homology (PH) domain
    pfam00435
    Location:429522
    Spectrin; Spectrin repeat
    cd21246
    Location:43159
    CH_SPTB-like_rpt1; first calponin homology (CH) domain found in the beta-I spectrin-like subfamily
    cd21321
    Location:173291
    CH_SPTBN2_rpt2; second calponin homology (CH) domain found in spectrin beta chain, non-erythrocytic 2 (SPTBN2) and similar proteins
  13. XM_047427491.1XP_047283447.1  spectrin beta chain, non-erythrocytic 2 isoform X1

    UniProtKB/Swiss-Prot
    O14872, O14873, O15020
  14. XM_047427492.1XP_047283448.1  spectrin beta chain, non-erythrocytic 2 isoform X1

    UniProtKB/Swiss-Prot
    O14872, O14873, O15020
  15. XM_047427490.1XP_047283446.1  spectrin beta chain, non-erythrocytic 2 isoform X1

    UniProtKB/Swiss-Prot
    O14872, O14873, O15020
  16. XM_047427496.1XP_047283452.1  spectrin beta chain, non-erythrocytic 2 isoform X2

    Related
    ENSP00000433593.1, ENST00000529997.5
  17. XM_011545216.4XP_011543518.1  spectrin beta chain, non-erythrocytic 2 isoform X3

    Conserved Domains (4) summary
    smart00033
    Location:68166
    CH; Calponin homology domain
    cd00014
    Location:184287
    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:541753
    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:436529
    Spectrin; Spectrin repeat
  18. XM_011545217.3XP_011543519.1  spectrin beta chain, non-erythrocytic 2 isoform X4

    Conserved Domains (4) summary
    smart00033
    Location:68166
    CH; Calponin homology domain
    cd00014
    Location:184287
    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:541753
    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:436529
    Spectrin; Spectrin repeat

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    66678745..66725466 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054369743.1XP_054225718.1  spectrin beta chain, non-erythrocytic 2 isoform X1

  2. XM_054369745.1XP_054225720.1  spectrin beta chain, non-erythrocytic 2 isoform X1

  3. XM_054369747.1XP_054225722.1  spectrin beta chain, non-erythrocytic 2 isoform X1

  4. XM_054369750.1XP_054225725.1  spectrin beta chain, non-erythrocytic 2 isoform X1

  5. XM_054369748.1XP_054225723.1  spectrin beta chain, non-erythrocytic 2 isoform X1

  6. XM_054369749.1XP_054225724.1  spectrin beta chain, non-erythrocytic 2 isoform X1

  7. XM_054369741.1XP_054225716.1  spectrin beta chain, non-erythrocytic 2 isoform X1

  8. XM_054369746.1XP_054225721.1  spectrin beta chain, non-erythrocytic 2 isoform X1

  9. XM_054369740.1XP_054225715.1  spectrin beta chain, non-erythrocytic 2 isoform X1

  10. XM_054369744.1XP_054225719.1  spectrin beta chain, non-erythrocytic 2 isoform X1

  11. XM_054369742.1XP_054225717.1  spectrin beta chain, non-erythrocytic 2 isoform X1

  12. XM_054369751.1XP_054225726.1  spectrin beta chain, non-erythrocytic 2 isoform X2

  13. XM_054369752.1XP_054225727.1  spectrin beta chain, non-erythrocytic 2 isoform X3

  14. XM_054369753.1XP_054225728.1  spectrin beta chain, non-erythrocytic 2 isoform X4