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    IQSEC3 IQ motif and Sec7 domain ArfGEF 3 [ Homo sapiens (human) ]

    Gene ID: 440073, updated on 27-Nov-2024

    Summary

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    Official Symbol
    IQSEC3provided by HGNC
    Official Full Name
    IQ motif and Sec7 domain ArfGEF 3provided by HGNC
    Primary source
    HGNC:HGNC:29193
    See related
    Ensembl:ENSG00000120645 MIM:612118; AllianceGenome:HGNC:29193
    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
    Summary
    Predicted to enable guanyl-nucleotide exchange factor activity. Predicted to be involved in several processes, including activation of GTPase activity; postsynapse organization; and regulation of small GTPase mediated signal transduction. Located in cytosol and nucleoplasm. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Biased expression in brain (RPKM 5.8), fat (RPKM 2.6) and 12 other tissues See more
    Orthologs
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    Genomic context

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    See IQSEC3 in Genome Data Viewer
    Location:
    12p13.33
    Exon count:
    16
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (66767..178455)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (58888..174477)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (175933..287621)

    Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107987170 Neighboring gene OCT4-H3K4me1 hESC enhancer GRCh37_chr12:66685-67402 Neighboring gene family with sequence similarity 138 member D Neighboring gene IQSEC3 antisense RNA 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:254331-254832 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:254833-255332 Neighboring gene uncharacterized LOC574538 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:262202-263116 Neighboring gene ReSE screen-validated silencer GRCh37_chr12:277504-277977 Neighboring gene IQSEC3 antisense RNA 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:282005-282530 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:283058-283583 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:282531-283057 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:287986-288528 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:291153-291654 Neighboring gene ReSE screen-validated silencer GRCh37_chr12:294419-294609 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4100 Neighboring gene solute carrier family 6 member 12 Neighboring gene SLC6A12 antisense RNA 1 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr12:320888-321660 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5777 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:322433-323204 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:329915-330870 Neighboring gene solute carrier family 6 member 13 Neighboring gene uncharacterized LOC102723544

    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. IQSEC3 Deletion Impairs Fear Memory Through Upregulation of Ribosomal S6K1 Signaling in the Hippocampus. Kim D, et al. Biol Psychiatry, 2022 May 1. PMID 35219498
    2. Identification of a neuron-specific human gene, KIAA1110, that is a guanine nucleotide exchange factor for ARF1. Hattori Y, et al. Biochem Biophys Res Commun, 2007 Dec 28. PMID 17981261
    3. The genomic and clinical landscape of fetal akinesia. Pergande M, et al. Genet Med, 2020 Mar. PMID 31680123
    4. Loss of IQSEC3 Disrupts GABAergic Synapse Maintenance and Decreases Somatostatin Expression in the Hippocampus. Kim S, et al. Cell Rep, 2020 Feb 11. PMID 32049026
    5. IQ Motif and SEC7 Domain-containing Protein 3 (IQSEC3) Interacts with Gephyrin to Promote Inhibitory Synapse Formation. Um JW, et al. J Biol Chem, 2016 May 6. PMID 27002143, Free PMC Article

    See all (14) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. IQSEC3 Deletion Impairs Fear Memory Through Upregulation of Ribosomal S6K1 Signaling in the Hippocampus.
      Title: IQSEC3 Deletion Impairs Fear Memory Through Upregulation of Ribosomal S6K1 Signaling in the Hippocampus.
    2. Loss of IQSEC3 Disrupts GABAergic Synapse Maintenance and Decreases Somatostatin Expression in the Hippocampus.
      Title: Loss of IQSEC3 Disrupts GABAergic Synapse Maintenance and Decreases Somatostatin Expression in the Hippocampus.
    3. The genomic and clinical landscape of fetal akinesia.
      Title: The genomic and clinical landscape of fetal akinesia.
    4. these data reveal that IQSEC3 acts together with gephyrin to regulate inhibitory synapse development.
      Title: IQ Motif and SEC7 Domain-containing Protein 3 (IQSEC3) Interacts with Gephyrin to Promote Inhibitory Synapse Formation.
    5. These results suggest that KIAA1110 is expressed specifically in mature neurons and may play an important role in the secretion pathway as a GEF for ARF1.
      Title: Identification of a neuron-specific human gene, KIAA1110, that is a guanine nucleotide exchange factor for ARF1.
    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
    Genomic association analysis identifies multiple loci influencing antihypertensive response to an angiotensin II receptor blocker.
    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)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • KIAA1110, MGC30156

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables guanyl-nucleotide exchange factor activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in actin cytoskeleton organization IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in regulation of ARF protein signal transduction IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in GABA-ergic synapse IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		  
    located_in glycinergic synapse IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in inhibitory synapse IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		  
    located_in postsynaptic density ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in postsynaptic membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in postsynaptic specialization of symmetric synapse IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    IQ motif and SEC7 domain-containing protein 3
    Names
    IQ motif and Sec7 domain 3

    NCBI Reference Sequences (RefSeq)

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    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.

    mRNA and Protein(s)

    1. NM_001170738.2 → NP_001164209.1  IQ motif and SEC7 domain-containing protein 3 isoform 1

      See identical proteins and their annotated locations for NP_001164209.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AC007406, AC026369
      Consensus CDS
      CCDS53728.1
      UniProtKB/Swiss-Prot
      A6NIF2, A6NKV9, Q8TB43, Q9UPP2
      UniProtKB/TrEMBL
      A0A0G2JLG2
      Related
      ENSP00000437554.1, ENST00000538872.6
      Conserved Domains (3) summary
      cd14686
      Location:32 → 63
      bZIP; Basic leucine zipper (bZIP) domain of bZIP transcription factors: a DNA-binding and dimerization domain
      cd13318
      Location:866 → 996
      PH_IQSEC; IQ motif and SEC7 domain-containing protein family Pleckstrin homology domain
      pfam01369
      Location:651 → 839
      Sec7; Sec7 domain

    2. NM_015232.2 → NP_056047.1  IQ motif and SEC7 domain-containing protein 3 isoform 2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) represents use of an alternate promoter, lacks an alternate exon, uses a downstream start codon, and uses a distinct exon in the 3' coding region and 3' UTR, compared to variant 1. The resulting isoform (2) has a shorter N-terminus and a shorter and distinct C-terminus, compared to isoform 1.
      Source sequence(s)
      AC026369, AK091953
      Consensus CDS
      CCDS31725.1
      UniProtKB/Swiss-Prot
      Q9UPP2
      Related
      ENSP00000372292.2, ENST00000382841.2
      Conserved Domains (2) summary
      cd13318
      Location:563 → 693
      PH_IQSEC; IQ motif and SEC7 domain-containing protein family Pleckstrin homology domain
      pfam01369
      Location:348 → 536
      Sec7; Sec7 domain

    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_000012.12 Reference GRCh38.p14 Primary Assembly

      Range
      66767..178455
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011520958.3 → XP_011519260.1  IQ motif and SEC7 domain-containing protein 3 isoform X1

      UniProtKB/TrEMBL
      A0A0G2JLG2
      Conserved Domains (3) summary
      cd14686
      Location:32 → 63
      bZIP; Basic leucine zipper (bZIP) domain of bZIP transcription factors: a DNA-binding and dimerization domain
      cd13318
      Location:866 → 996
      PH_IQSEC; IQ motif and SEC7 domain-containing protein family Pleckstrin homology domain
      pfam01369
      Location:651 → 839
      Sec7; Sec7 domain

    2. XM_011520960.2 → XP_011519262.1  IQ motif and SEC7 domain-containing protein 3 isoform X2

      See identical proteins and their annotated locations for XP_011519262.1

      UniProtKB/TrEMBL
      A0A0G2JLG2
      Conserved Domains (3) summary
      cd14686
      Location:32 → 63
      bZIP; Basic leucine zipper (bZIP) domain of bZIP transcription factors: a DNA-binding and dimerization domain
      cd13318
      Location:866 → 996
      PH_IQSEC; IQ motif and SEC7 domain-containing protein family Pleckstrin homology domain
      pfam01369
      Location:651 → 839
      Sec7; Sec7 domain

    3. XM_017019311.2 → XP_016874800.1  IQ motif and SEC7 domain-containing protein 3 isoform X3

      UniProtKB/TrEMBL
      A0A0G2JLG2

    4. XM_047428865.1 → XP_047284821.1  IQ motif and SEC7 domain-containing protein 3 isoform X3

    5. XM_011520961.2 → XP_011519263.1  IQ motif and SEC7 domain-containing protein 3 isoform X4

      See identical proteins and their annotated locations for XP_011519263.1

      Conserved Domains (2) summary
      cd13318
      Location:563 → 693
      PH_IQSEC; IQ motif and SEC7 domain-containing protein family Pleckstrin homology domain
      pfam01369
      Location:348 → 536
      Sec7; Sec7 domain

    Reference GRCh38.p14 ALT_REF_LOCI_1

    Genomic

    1. NW_003571049.1 Reference GRCh38.p14 ALT_REF_LOCI_1

      Range
      60782..165345
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060936.1 Alternate T2T-CHM13v2.0

      Range
      58888..174477
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9UPP2.3 GenPept UniProtKB/Swiss-Prot:Q9UPP2

    Gene LinkOut

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