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    SPATA13 spermatogenesis associated 13 [ Homo sapiens (human) ]

    Gene ID: 221178, updated on 10-Dec-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, Dec 2024]
    Expression
    Ubiquitous expression in spleen (RPKM 22.0), lymph node (RPKM 7.6) and 25 other tissues See more
    Orthologs
    mouse all
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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_2024_08 current GRCh38.p14 (GCF_000001405.40) 13 NC_000013.11 (23979802..24307069)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 13 NC_060937.1 (23186689..23514163)
    RS_2024_09 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. 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
    2. Mutations in SPATA13/ASEF2 cause primary angle closure glaucoma. Waseem NH, et al. PLoS Genet, 2020 Apr. PMID 32339198, Free PMC Article
    3. 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
    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 (34) 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)

    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 identical protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    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 anchoring junction IEA
    Inferred from Electronic Annotation
    more info
    		  
    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 podosome ISS
    Inferred from Sequence or Structural Similarity
    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_2024_08

    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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