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SMAP2 small ArfGAP2 [ Homo sapiens (human) ]

Gene ID: 64744, updated on 7-Sep-2023

Summary

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Official Symbol
SMAP2provided by HGNC
Official Full Name
small ArfGAP2provided by HGNC
Primary source
HGNC:HGNC:25082
See related
Ensembl:ENSG00000084070 MIM:616916; AllianceGenome:HGNC:25082
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
SMAP1L
Summary
Predicted to enable GTPase activator activity. Predicted to be involved in regulation of catalytic activity. Predicted to be located in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Broad expression in lymph node (RPKM 80.3), spleen (RPKM 58.9) and 23 other tissues See more
Orthologs
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Genomic context

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See SMAP2 in Genome Data Viewer
Location:
1p34.2
Exon count:
19
Annotation release Status Assembly Chr Location
RS_2023_03 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (40344834..40423326)
RS_2023_03 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (40214315..40292887)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (40839399..40888998)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancers GRCh37_chr1:40781816-40782452 and GRCh37_chr1:40782453-40783089 Neighboring gene H3K4me1 hESC enhancers GRCh37_chr1:40781816-40782452 and GRCh37_chr1:40782453-40783089 Neighboring gene collagen type IX alpha 2 chain Neighboring gene ribosomal protein L21 pseudogene 20 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:40839657-40840156 Neighboring gene Sharpr-MPRA regulatory region 11139 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr1:40916242-40917441 Neighboring gene ZFP69 zinc finger protein B Neighboring gene ZFP69 zinc finger protein Neighboring gene EXO5 divergent transcript

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. The carboxy-terminal region of SMAP2 directs subcellular localization as well as Arf protein specificity. Sakakura I, et al. Biochem Biophys Res Commun, 2011 Jan 14. PMID 21147065
  2. Putative association of SMAPIL polymorphisms with risk of aspirin intolerance in asthmatics. Kim JY, et al. J Asthma, 2010 Nov. PMID 20831471
  3. The Arf GTPase-activating protein SMAP1 promotes transferrin receptor endocytosis and interacts with SMAP2. Kobayashi N, et al. Biochem Biophys Res Commun, 2014 Oct 24. PMID 25281535
  4. Transport of the cholera toxin B-subunit from recycling endosomes to the Golgi requires clathrin and AP-1. Matsudaira T, et al. J Cell Sci, 2015 Aug 15. PMID 26136365
  5. SMAP2, a novel ARF GTPase-activating protein, interacts with clathrin and clathrin assembly protein and functions on the AP-1-positive early endosome/trans-Golgi network. Natsume W, et al. Mol Biol Cell, 2006 Jun. PMID 16571680, Free PMC Article

See all (45) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. SMAP2 immunoprecipitated clathrin and AP-1 through a putative clathrin-binding domain and a CALM-binding domain, and SMAP2 mutants that did not interact with clathrin or AP-1 could not localize to recycling endosomes
    Title: Transport of the cholera toxin B-subunit from recycling endosomes to the Golgi requires clathrin and AP-1.
  2. Results also demonstrated a physical association between SMAP1 and SMAP2, which might serve as a basis for a functional interaction, and identified the intramolecular domains responsible for this association
    Title: The Arf GTPase-activating protein SMAP1 promotes transferrin receptor endocytosis and interacts with SMAP2.
  3. In the current study, there were identified sequences in the carboxy-terminal region of SMAP2 that are critical for its specific subcellular localization and its specificity for Arf proteins.
    Title: The carboxy-terminal region of SMAP2 directs subcellular localization as well as Arf protein specificity.
  4. analyses revealed that three common polymorphisms, rs2982510, rs2294752, and rs446738, were putatively associated with the increased susceptibility to AIA
    Title: Putative association of SMAPIL polymorphisms with risk of aspirin intolerance in asthmatics.
  5. Observational study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
    Title: Putative association of SMAPIL polymorphisms with risk of aspirin intolerance in asthmatics.
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 association study (GWAS) of Chagas cardiomyopathy in Trypanosoma cruzi seropositive subjects.
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

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables GTPase activator activity IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Component Evidence Code Pubs
is_active_in cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
located_in cytosol IDA
Inferred from Direct Assay
more info
  
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
  

General protein information

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Preferred Names
stromal membrane-associated protein 2
Names
stromal membrane-associated GTPase-activating protein 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_001198978.2 → NP_001185907.1  stromal membrane-associated protein 2 isoform 3

    See identical proteins and their annotated locations for NP_001185907.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) has an alternate 5' exon compared to variant 1. The resulting isoform (3) has a shorter and distinct N-terminus, as compared to isoform 1.
    Source sequence(s)
    AL133206, DC411665
    Consensus CDS
    CCDS55592.1
    UniProtKB/Swiss-Prot
    Q8WU79
    Related
    ENSP00000361793.1, ENST00000372708.5
    Conserved Domains (2) summary
    pfam01412
    Location:4 → 96
    ArfGap; Putative GTPase activating protein for Arf
    pfam09606
    Location:247 → 391
    Med15; ARC105 or Med15 subunit of Mediator complex non-fungal

  2. NM_001198979.2 → NP_001185908.1  stromal membrane-associated protein 2 isoform 2

    See identical proteins and their annotated locations for NP_001185908.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) has an alternate 5' exon compared to variant 1. The resulting isoform (2) has a shorter and distinct N-terminus, as compared to isoform 1.
    Source sequence(s)
    AK308280, BC014512, BC021133
    Consensus CDS
    CCDS72763.1
    UniProtKB/Swiss-Prot
    Q8WU79
    UniProtKB/TrEMBL
    A0A087WV97
    Related
    ENSP00000479285.1, ENST00000614549.4
    Conserved Domains (1) summary
    cl28907
    Location:31 → 117
    ArfGap; GTPase-activating protein (GAP) for the ADP ribosylation factors (ARFs)

  3. NM_001198980.1 → NP_001185909.1  stromal membrane-associated protein 2 isoform 4

    See identical proteins and their annotated locations for NP_001185909.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) has an alternate 5' exon, resulting in a downstream AUG start codon, compared to variant 1. The resulting isoform (4) is shorter at the N-terminus, as compared to isoform 1.
    Source sequence(s)
    AK316218, BC014512, BC021133, BU617889
    Consensus CDS
    CCDS55593.1
    UniProtKB/Swiss-Prot
    Q8WU79
    Related
    ENSP00000442835.1, ENST00000539317.2
    Conserved Domains (2) summary
    pfam09606
    Location:197 → 341
    Med15; ARC105 or Med15 subunit of Mediator complex non-fungal
    cl28907
    Location:1 → 42
    ArfGap; GTPase-activating protein (GAP) for the ADP ribosylation factors (ARFs)

  4. NM_022733.3 → NP_073570.1  stromal membrane-associated protein 2 isoform 1

    See identical proteins and their annotated locations for NP_073570.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (1).
    Source sequence(s)
    AL133206, BC021133, DA082592
    Consensus CDS
    CCDS451.1
    UniProtKB/Swiss-Prot
    B2R7T1, B7Z5B5, B7Z8V2, D3DPV2, Q5QPL2, Q8WU79, Q96C93, Q9NST2, Q9UJL8
    Related
    ENSP00000361803.3, ENST00000372718.8
    Conserved Domains (1) summary
    cd08859
    Location:16 → 122
    ArfGap_SMAP2; Stromal membrane-associated protein 2; a subfamily of the ArfGAP family

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_03

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    40344834..40423326
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047428009.1 → XP_047283965.1  stromal membrane-associated protein 2 isoform X1

  2. XM_047428011.1 → XP_047283967.1  stromal membrane-associated protein 2 isoform X2

  3. XM_047428017.1 → XP_047283973.1  stromal membrane-associated protein 2 isoform X3

  4. XM_047428014.1 → XP_047283970.1  stromal membrane-associated protein 2 isoform X2

  5. XM_011541960.3 → XP_011540262.1  stromal membrane-associated protein 2 isoform X2

    Conserved Domains (1) summary
    pfam01412
    Location:8 → 101
    ArfGap; Putative GTPase activating protein for Arf

  6. XM_047428015.1 → XP_047283971.1  stromal membrane-associated protein 2 isoform X3

  7. XM_047428013.1 → XP_047283969.1  stromal membrane-associated protein 2 isoform X2

  8. XM_047428012.1 → XP_047283968.1  stromal membrane-associated protein 2 isoform X2

  9. XM_047428016.1 → XP_047283972.1  stromal membrane-associated protein 2 isoform X3

  10. XM_047428010.1 → XP_047283966.1  stromal membrane-associated protein 2 isoform X2

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    40214315..40292887
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054338264.1 → XP_054194239.1  stromal membrane-associated protein 2 isoform X1

  2. XM_054338265.1 → XP_054194240.1  stromal membrane-associated protein 2 isoform X2

  3. XM_054338271.1 → XP_054194246.1  stromal membrane-associated protein 2 isoform X3

  4. XM_054338268.1 → XP_054194243.1  stromal membrane-associated protein 2 isoform X2

  5. XM_054338267.1 → XP_054194242.1  stromal membrane-associated protein 2 isoform X2

  6. XM_054338269.1 → XP_054194244.1  stromal membrane-associated protein 2 isoform X3

  7. XM_054338266.1 → XP_054194241.1  stromal membrane-associated protein 2 isoform X2

  8. XM_054338270.1 → XP_054194245.1  stromal membrane-associated protein 2 isoform X3

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8WU79.1 GenPept UniProtKB/Swiss-Prot:Q8WU79

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