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SPATA13 spermatogenesis associated 13 [ Homo sapiens (human) ]

Gene ID: 221178, updated on 24-Nov-2020

Summary

Official Symbol
SPATA13provided by HGNC
Official Full Name
spermatogenesis associated 13provided by HGNC
Primary source
HGNC:HGNC:23222
See related
Ensembl:ENSG00000182957 Ensembl:ENSG00000228741 Ensembl:ENSG00000273167 MIM:613324
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
Expression
Ubiquitous expression in spleen (RPKM 22.0), lymph node (RPKM 7.6) and 25 other tissues See more
Orthologs

Genomic context

See SPATA13 in Genome Data Viewer
Location:
13q12.12
Exon count:
20
Annotation release Status Assembly Chr Location
109.20201120 current GRCh38.p13 (GCF_000001405.39) 13 NC_000013.11 (23979802..24307069)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 13 NC_000013.10 (24553765..24881212)

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 importin 7 pseudogene 2 Neighboring gene microRNA 2276 Neighboring gene Sharpr-MPRA regulatory region 10151 Neighboring gene conserved acetylation island sequence 9 enhancer Neighboring gene SPATA13 antisense RNA 1 Neighboring gene cell cycle exit and neuronal differentiation protein 1-like Neighboring gene C1q and TNF related 9 Neighboring gene Pro-X-Gly collagen triple helix like repeat containing pseudogene 1 Neighboring gene cell cycle exit and neuronal differentiation 1 pseudogene 2

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
Genome wide study of maternal and parent-of-origin effects on the etiology of orofacial clefts.
GeneReviews: Not available
Genome-wide association scan of quantitative traits for attention deficit hyperactivity disorder identifies novel associations and confirms candidate gene associations.
GeneReviews: Not available
Genome-wide association studies identify CHRNA5/3 and HTR4 in the development of airflow obstruction.
GeneReviews: Not available
Genome-wide association study of comorbid depressive syndrome and alcohol dependence.
GeneReviews: Not available

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

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

Gene Ontology Provided by GOA

Function Evidence Code Pubs
guanyl-nucleotide exchange factor activity IDA
Inferred from Direct Assay
more info
PubMed 
guanyl-nucleotide exchange factor activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
cell migration IMP
Inferred from Mutant Phenotype
more info
PubMed 
filopodium assembly IMP
Inferred from Mutant Phenotype
more info
PubMed 
lamellipodium assembly IMP
Inferred from Mutant Phenotype
more info
PubMed 
regulation of cell migration IMP
Inferred from Mutant Phenotype
more info
PubMed 
Component Evidence Code Pubs
cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
cytosol IDA
Inferred from Direct Assay
more info
 
filopodium IDA
Inferred from Direct Assay
more info
PubMed 
lamellipodium IDA
Inferred from Direct Assay
more info
PubMed 
nucleoplasm IDA
Inferred from Direct Assay
more info
 
ruffle membrane IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

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)

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_001166271.3NP_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/Swiss-Prot
    Q96N96
    Related
    ENSP00000371542.3, ENST00000382108.8
    Conserved Domains (4) summary
    cd11973
    Location:759830
    SH3_ASEF; Src homology 3 domain of APC-Stimulated guanine nucleotide Exchange Factor
    cd01224
    Location:10531191
    PH_Collybistin_ASEF; Collybistin/APC-stimulated guanine nucleotide exchange factor pleckstrin homology (PH) domain
    pfam00169
    Location:10811180
    PH; PH domain
    pfam00621
    Location:8691048
    RhoGEF; RhoGEF domain
  2. NM_001286792.2NP_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/Swiss-Prot
    Q96N96
    Related
    ENSP00000371576.4, ENST00000382141.4
    Conserved Domains (4) summary
    cd11973
    Location:821892
    SH3_ASEF; Src homology 3 domain of APC-Stimulated guanine nucleotide Exchange Factor
    cd01224
    Location:11151253
    PH_Collybistin_ASEF; Collybistin/APC-stimulated guanine nucleotide exchange factor pleckstrin homology (PH) domain
    pfam00169
    Location:11431242
    PH; PH domain
    pfam00621
    Location:9311110
    RhoGEF; RhoGEF domain
  3. NM_001286793.2NP_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/Swiss-Prot
    Q96N96
    UniProtKB/TrEMBL
    B4DMC2, E9PFR9
    Related
    ENSP00000386471.1, ENST00000409126.5
    Conserved Domains (4) summary
    cd11973
    Location:56124
    SH3_ASEF; Src homology 3 domain of APC-Stimulated guanine nucleotide Exchange Factor
    cd01224
    Location:288426
    PH_Collybistin_ASEF; Collybistin/APC-stimulated guanine nucleotide exchange factor pleckstrin homology (PH) domain
    pfam00169
    Location:316415
    PH; PH domain
    pfam00621
    Location:123283
    RhoGEF; RhoGEF domain
  4. NM_001286794.2NP_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/Swiss-Prot
    Q96N96
    Related
    ENSP00000343631.6, ENST00000343003.10
    Conserved Domains (4) summary
    cd11973
    Location:78149
    SH3_ASEF; Src homology 3 domain of APC-Stimulated guanine nucleotide Exchange Factor
    cd01224
    Location:372510
    PH_Collybistin_ASEF; Collybistin/APC-stimulated guanine nucleotide exchange factor pleckstrin homology (PH) domain
    pfam00169
    Location:400499
    PH; PH domain
    pfam00621
    Location:188367
    RhoGEF; RhoGEF domain
  5. NM_001286795.2NP_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/Swiss-Prot
    Q96N96
    Related
    ENSP00000382830.2, ENST00000399949.6
    Conserved Domains (4) summary
    cd11973
    Location:56127
    SH3_ASEF; Src homology 3 domain of APC-Stimulated guanine nucleotide Exchange Factor
    cd01224
    Location:350488
    PH_Collybistin_ASEF; Collybistin/APC-stimulated guanine nucleotide exchange factor pleckstrin homology (PH) domain
    pfam00169
    Location:378477
    PH; PH domain
    pfam00621
    Location:166345
    RhoGEF; RhoGEF domain
  6. NM_153023.4NP_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
    Q96N96
    UniProtKB/TrEMBL
    A0A024RDM6
    Related
    ENSP00000371527.4, ENST00000382095.8
    Conserved Domains (3) summary
    cd11973
    Location:134205
    SH3_ASEF; Src homology 3 domain of APC-Stimulated guanine nucleotide Exchange Factor
    smart00325
    Location:244423
    RhoGEF; Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases
    cd01224
    Location:428566
    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
    Related
    ENST00000439928.2

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20201120

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000013.11 Reference GRCh38.p13 Primary Assembly

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