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

Gene ID: 440073, updated on 3-Apr-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 actin cytoskeleton organization; activation of GTPase activity; and regulation of small GTPase mediated signal transduction. Located in cytosol and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]
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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Location:
12p13.33
Exon count:
16
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (66767..178455)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (58888..174477)
105.20220307 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)

Genotypes

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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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_2023_10

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

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