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SPATA13 spermatogenesis associated 13 [ Homo sapiens (human) ]

Gene ID: 221178, updated on 5-Mar-2024

Summary

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Official Symbol
SPATA13provided by HGNC
Official Full Name
spermatogenesis associated 13provided by HGNC
Primary source
HGNC:HGNC:23222
See related
Ensembl:ENSG00000182957 MIM:613324; AllianceGenome:HGNC:23222
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
ASEF2; ARHGEF29
Summary
Enables guanyl-nucleotide exchange factor activity and identical protein binding activity. Involved in cell migration; plasma membrane bounded cell projection assembly; and regulation of cell migration. Located in several cellular components, including filopodium; lamellipodium; and ruffle membrane. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in spleen (RPKM 22.0), lymph node (RPKM 7.6) and 25 other tissues See more
Orthologs
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Genomic context

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See SPATA13 in Genome Data Viewer
Location:
13q12.12
Exon count:
20
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 13 NC_000013.11 (23979802..24307069)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 13 NC_060937.1 (23186689..23514163)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 13 NC_000013.10 (24553941..24881207)

Chromosome 13 - NC_000013.11Genomic Context describing neighboring genes Neighboring gene ankyrin repeat domain 20 family member A19, pseudogene Neighboring gene uncharacterized LOC105370115 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:24590503-24591404 Neighboring gene Sharpr-MPRA regulatory region 9740 Neighboring gene uncharacterized LOC124903136 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr13:24715254-24716122 Neighboring gene Sharpr-MPRA regulatory region 6352 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:24723586-24724262 Neighboring gene importin 7 pseudogene 2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5176 Neighboring gene microRNA 2276 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7470 Neighboring gene Sharpr-MPRA regulatory region 10151 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:24797397-24798253 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7472 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:24799112-24799968 Neighboring gene H3K27ac hESC enhancer GRCh37_chr13:24822035-24822534 Neighboring gene conserved acetylation island sequence 9 enhancer Neighboring gene SPATA13 antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7473 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7474 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7475 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7476 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7477 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5177 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:24855531-24856030 Neighboring gene cell cycle exit and neuronal differentiation protein 1-like Neighboring gene C1q and TNF related 9 Neighboring gene PCOTH pseudogene 1 Neighboring gene cell cycle exit and neuronal differentiation 1 pseudogene 2

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
  • 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. Mutations in SPATA13/ASEF2 cause primary angle closure glaucoma. Waseem NH, et al. PLoS Genet, 2020 Apr. PMID 32339198, Free PMC Article
  2. Phosphorylation of serine 106 in Asef2 regulates cell migration and adhesion turnover. Evans JC, et al. J Proteome Res, 2014 Jul 3. PMID 24874604, Free PMC Article
  3. Activation of Rac by Asef2 promotes myosin II-dependent contractility to inhibit cell migration on type I collagen. Jean L, et al. J Cell Sci, 2013 Dec 15. PMID 24144700, Free PMC Article
  4. Identification and characterization of Asef2, a guanine-nucleotide exchange factor specific for Rac1 and Cdc42. Kawasaki Y, et al. Oncogene, 2007 Dec 6. PMID 17599059
  5. Asef2 functions as a Cdc42 exchange factor and is stimulated by the release of an autoinhibitory module from a concealed C-terminal activation element. Hamann MJ, et al. Mol Cell Biol, 2007 Feb. PMID 17145773, Free PMC Article

See all (31) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Mutations in SPATA13 cause primary angle closure glaucoma.
    Title: Mutations in SPATA13/ASEF2 cause primary angle closure glaucoma.
  2. Phosphorylation of S106 modulates Asef2 guanine nucleotide exchange factor activity and Asef2-mediated cell migration and adhesion turnover.
    Title: Phosphorylation of serine 106 in Asef2 regulates cell migration and adhesion turnover.
  3. A new role for Rac activation, promoted by Asef2, in modulating actomyosin contractility.
    Title: Activation of Rac by Asef2 promotes myosin II-dependent contractility to inhibit cell migration on type I collagen.
  4. Asef2 activates Rac1 to modulate adhesion and actin dynamics and thereby regulate cell migration.
    Title: The Rho-family GEF Asef2 activates Rac to modulate adhesion and actin dynamics and thereby regulate cell migration.
  5. Observational study of gene-disease association. (HuGE Navigator)
    Title: Confirmation of genomewide association signals in Chinese Han population reveals risk loci for ischemic stroke.
  6. Asef2, Neurabin2 and APC cooperatively regulate actin cytoskeletal organization and are required for HGF-induced cell migration.
    Title: Asef2 and Neurabin2 cooperatively regulate actin cytoskeletal organization and are involved in HGF-induced cell migration.
  7. These results suggest that similar to Asef, Asef2 plays an important role in cell migration, and that Asef2 activated by truncated mutant APC is required for aberrant migration of colorectal tumor cells.
    Title: Identification and characterization of Asef2, a guanine-nucleotide exchange factor specific for Rac1 and Cdc42.
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

EBI GWAS Catalog

Description
Genome wide study of maternal and parent-of-origin effects on the etiology of orofacial clefts.
EBI GWAS Catalog
Genome-wide association scan of quantitative traits for attention deficit hyperactivity disorder identifies novel associations and confirms candidate gene associations.
EBI GWAS Catalog
Genome-wide association studies identify CHRNA5/3 and HTR4 in the development of airflow obstruction.
EBI GWAS Catalog
Genome-wide association study of comorbid depressive syndrome and alcohol dependence.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ31208, FLJ35435, FLJ35440, FLJ41231, MGC129988, MGC129989

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables guanyl-nucleotide exchange factor activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables guanyl-nucleotide exchange factor activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables guanyl-nucleotide exchange factor activity IMP
Inferred from Mutant Phenotype
more info
 PubMed 
enables guanyl-nucleotide exchange factor activity TAS
Traceable Author Statement
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in cell migration IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in filopodium assembly IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in filopodium assembly IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in lamellipodium assembly IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in lamellipodium assembly IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in regulation of cell migration IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in regulation of small GTPase mediated signal transduction TAS
Traceable Author Statement
more info
  
Component Evidence Code Pubs
located_in cytoplasm IDA
Inferred from Direct Assay
more info
 PubMed 
is_active_in cytosol 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 filopodium IDA
Inferred from Direct Assay
more info
 PubMed 
located_in lamellipodium IDA
Inferred from Direct Assay
more info
 PubMed 
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
  
located_in ruffle membrane IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
spermatogenesis-associated protein 13
Names
APC-stimulated guanine nucleotide exchange factor 2
adenomatous polyposis coli stimulated exchange factor 2

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_001166271.3 → NP_001159743.1  spermatogenesis-associated protein 13 isoform 1

    See identical proteins and their annotated locations for NP_001159743.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) encodes isoform (1).
    Source sequence(s)
    AK055770, AK092754, AL359736, BP201334, DB221004
    Consensus CDS
    CCDS53857.1
    UniProtKB/TrEMBL
    A0A0A0MRY4
    Related
    ENSP00000371542.3, ENST00000382108.8
    Conserved Domains (4) summary
    cd11973
    Location:759 → 830
    SH3_ASEF; Src homology 3 domain of APC-Stimulated guanine nucleotide Exchange Factor
    cd01224
    Location:1053 → 1191
    PH_Collybistin_ASEF; Collybistin/APC-stimulated guanine nucleotide exchange factor pleckstrin homology (PH) domain
    pfam00169
    Location:1081 → 1180
    PH; PH domain
    pfam00621
    Location:869 → 1048
    RhoGEF; RhoGEF domain

  2. NM_001286792.2 → NP_001273721.1  spermatogenesis-associated protein 13 isoform 3

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR and contains multiple additional 5' coding exons, compared to variant 1. It represents use of an alternate promoter and initiates translation at an alternate start codon. The encoded isoform (3) has a longer N-terminus than isoform 1.
    Source sequence(s)
    AK055770, AL359736, BX648244, HY002340
    UniProtKB/TrEMBL
    A0A0A0MRY4
    Conserved Domains (4) summary
    cd11973
    Location:821 → 892
    SH3_ASEF; Src homology 3 domain of APC-Stimulated guanine nucleotide Exchange Factor
    cd01224
    Location:1115 → 1253
    PH_Collybistin_ASEF; Collybistin/APC-stimulated guanine nucleotide exchange factor pleckstrin homology (PH) domain
    pfam00169
    Location:1143 → 1242
    PH; PH domain
    pfam00621
    Location:931 → 1110
    RhoGEF; RhoGEF domain

  3. NM_001286793.2 → NP_001273722.1  spermatogenesis-associated protein 13 isoform 4

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) differs in the 5' UTR and contains multiple differences in the coding region, compared to variant 1, including the lack of multiple 5' coding exons. It represents use of an alternate promoter and initiates translation at an alternate start codon. The encoded isoform (4) has a distinct N-terminus and is shorter than isoform 1.
    Source sequence(s)
    AK055770, AK297394, AL359736
    Consensus CDS
    CCDS73553.1
    UniProtKB/TrEMBL
    B4DMC2, E9PFR9
    Related
    ENSP00000386471.1, ENST00000409126.5
    Conserved Domains (4) summary
    cd11973
    Location:56 → 124
    SH3_ASEF; Src homology 3 domain of APC-Stimulated guanine nucleotide Exchange Factor
    cd01224
    Location:288 → 426
    PH_Collybistin_ASEF; Collybistin/APC-stimulated guanine nucleotide exchange factor pleckstrin homology (PH) domain
    pfam00169
    Location:316 → 415
    PH; PH domain
    pfam00621
    Location:123 → 283
    RhoGEF; RhoGEF domain

  4. NM_001286794.2 → NP_001273723.1  spermatogenesis-associated protein 13 isoform 5

    See identical proteins and their annotated locations for NP_001273723.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (5) differs in the 5' UTR and lacks multiple 5' coding exons, compared to variant 1. It represents use of an alternate promoter and initiates translation at an alternate start codon. The encoded isoform (5) has a distinct N-terminus and is shorter than isoform 1.
    Source sequence(s)
    AK055770, AK298717, AL359736
    Consensus CDS
    CCDS66518.1
    UniProtKB/TrEMBL
    B4DMC2
    Related
    ENSP00000343631.6, ENST00000343003.10
    Conserved Domains (4) summary
    cd11973
    Location:78 → 149
    SH3_ASEF; Src homology 3 domain of APC-Stimulated guanine nucleotide Exchange Factor
    cd01224
    Location:372 → 510
    PH_Collybistin_ASEF; Collybistin/APC-stimulated guanine nucleotide exchange factor pleckstrin homology (PH) domain
    pfam00169
    Location:400 → 499
    PH; PH domain
    pfam00621
    Location:188 → 367
    RhoGEF; RhoGEF domain

  5. NM_001286795.2 → NP_001273724.1  spermatogenesis-associated protein 13 isoform 6

    See identical proteins and their annotated locations for NP_001273724.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (6) differs in the 5' UTR and lacks multiple 5' coding exons, compared to variant 1. It represents use of an alternate promoter and initiates translation at an alternate start codon. The encoded isoform (6) has a distinct N-terminus and is shorter than isoform 1.
    Source sequence(s)
    AK123031, AL359736
    Consensus CDS
    CCDS66517.1
    UniProtKB/TrEMBL
    B4DMC2
    Related
    ENSP00000382830.2, ENST00000399949.6
    Conserved Domains (4) summary
    cd11973
    Location:56 → 127
    SH3_ASEF; Src homology 3 domain of APC-Stimulated guanine nucleotide Exchange Factor
    cd01224
    Location:350 → 488
    PH_Collybistin_ASEF; Collybistin/APC-stimulated guanine nucleotide exchange factor pleckstrin homology (PH) domain
    pfam00169
    Location:378 → 477
    PH; PH domain
    pfam00621
    Location:166 → 345
    RhoGEF; RhoGEF domain

  6. NM_153023.4 → NP_694568.1  spermatogenesis-associated protein 13 isoform 2

    See identical proteins and their annotated locations for NP_694568.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR, lacks a portion of the 5' reading frame, and initiates translation at a downstream in-frame start codon, compared to variant 1. The encoded isoform (2) has a shorter N-terminus than isoform 1.
    Source sequence(s)
    AK055770, AK092754, AL359736, BP201334
    Consensus CDS
    CCDS9305.1
    UniProtKB/Swiss-Prot
    A2VEA9, A6NF85, B4DQB1, B4DSZ0, B4DVM8, J3KPJ7, J3KQH2, Q5VX68, Q6ZML1, Q8N873, Q8TEK6, Q96N96
    UniProtKB/TrEMBL
    A0A024RDM6, J3KQJ8
    Related
    ENSP00000371527.4, ENST00000382095.8
    Conserved Domains (3) summary
    cd11973
    Location:134 → 205
    SH3_ASEF; Src homology 3 domain of APC-Stimulated guanine nucleotide Exchange Factor
    smart00325
    Location:244 → 423
    RhoGEF; Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases
    cd01224
    Location:428 → 566
    PH_Collybistin_ASEF; Collybistin/APC-stimulated guanine nucleotide exchange factor pleckstrin homology (PH) domain

RNA

  1. NR_104595.2 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (7) contains a distinct set of exons, compared to variant 1, but shares multiple splice junctions with variant 3. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 3, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AL139324, BC043582, HY002340

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_000013.11 Reference GRCh38.p14 Primary Assembly

    Range
    23979802..24307069
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060937.1 Alternate T2T-CHM13v2.0

    Range
    23186689..23514163
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q96N96.1 GenPept UniProtKB/Swiss-Prot:Q96N96

Gene LinkOut

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

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