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    ITFG2 integrin alpha FG-GAP repeat containing 2 [ Homo sapiens (human) ]

    Gene ID: 55846, updated on 5-Mar-2024

    Summary

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    Official Symbol
    ITFG2provided by HGNC
    Official Full Name
    integrin alpha FG-GAP repeat containing 2provided by HGNC
    Primary source
    HGNC:HGNC:30879
    See related
    Ensembl:ENSG00000111203 MIM:617421; AllianceGenome:HGNC:30879
    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
    KICS3; FGGAP1; MDS028
    Summary
    Involved in cellular response to amino acid starvation; cellular response to glucose starvation; and negative regulation of TORC1 signaling. Located in lysosomal membrane. Part of KICSTOR complex. [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Ubiquitous expression in thyroid (RPKM 9.5), ovary (RPKM 9.0) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See ITFG2 in Genome Data Viewer
    Location:
    12p13.33
    Exon count:
    17
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (2812668..2859791)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (2818668..2865802)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (2921834..2968957)

    Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene ITFG2 antisense RNA 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:2903015-2903560 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:2903561-2904105 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4131 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4132 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr12:2905599-2906798 Neighboring gene CBX3 pseudogene 4 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr12:2921381-2922130 Neighboring gene FKBP prolyl isomerase 4 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:2928702-2929202 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:2929203-2929703 Neighboring gene Sharpr-MPRA regulatory region 8339 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:2943338-2943882 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:2943883-2944427 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:2944428-2944971 Neighboring gene nuclear receptor interacting protein 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:2953993-2954980 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:2954981-2955966 Neighboring gene testis expressed 52 Neighboring gene forkhead box M1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4134 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4135 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:2988229-2989182 Neighboring gene uncharacterized LOC124902860 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5816 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4136 Neighboring gene RAD9-HUS1-RAD1 interacting nuclear orphan 1 Neighboring gene TUB like protein 3 Neighboring gene Sharpr-MPRA regulatory region 7040 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:3032139-3032645 Neighboring gene U7 small nuclear RNA

    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. KICSTOR recruits GATOR1 to the lysosome and is necessary for nutrients to regulate mTORC1. Wolfson RL, et al. Nature, 2017 Mar 16. PMID 28199306, Free PMC Article
    2. Viral protein engagement of GBF1 induces host cell vulnerability through synthetic lethality. Navare AT, et al. J Cell Biol, 2022 Nov 7. PMID 36305789, Free PMC Article
    3. A "double adaptor" method for improved shotgun library construction. Andersson B, et al. Anal Biochem, 1996 Apr 5. PMID 8619474
    4. Widespread Expansion of Protein Interaction Capabilities by Alternative Splicing. Yang X, et al. Cell, 2016 Feb 11. PMID 26871637, Free PMC Article
    5. Large-scale mapping of human protein-protein interactions by mass spectrometry. Ewing RM, et al. Mol Syst Biol, 2007. PMID 17353931, Free PMC Article

    See all (13) citations in PubMed

    GeneRIFs: Gene References Into Functions

    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

    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

    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

    Gene Ontology Provided by GOA

    Process Evidence Code Pubs
    involved_in cellular response to amino acid starvation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in cellular response to glucose starvation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in germinal center B cell differentiation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in negative regulation of TORC1 signaling IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in regulation of TOR signaling IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    located_in Golgi apparatus IDA
    Inferred from Direct Assay
    more info
    		  
    part_of KICSTOR complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of KICSTOR complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of KICSTOR complex NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    located_in cytosol IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in intracellular membrane-bounded organelle IDA
    Inferred from Direct Assay
    more info
    		  
    located_in lysosomal membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in lysosomal membrane NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    located_in lysosomal membrane TAS
    Traceable Author Statement
    more info
    		  
    located_in nucleoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    KICSTOR complex protein ITFG2
    Names
    FG-GAP repeat containing 1
    integrin-alpha FG-GAP repeat-containing 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_018463.4 → NP_060933.3  KICSTOR complex protein ITFG2

      See identical proteins and their annotated locations for NP_060933.3

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes a functional protein.
      Source sequence(s)
      AC005841, BC013399, BQ003916, BQ058412
      Consensus CDS
      CCDS8513.1
      UniProtKB/Swiss-Prot
      A8K4Z5, D3DUQ2, Q6PKU5, Q969R8, Q96SX6
      UniProtKB/TrEMBL
      A0A0S2Z5G6, A0A0S2Z5P1
      Related
      ENSP00000228799.2, ENST00000228799.7
      Conserved Domains (2) summary
      pfam15907
      Location:49 → 386
      Itfg2; Integrin-alpha FG-GAP repeat-containing protein 2
      cl24051
      Location:22 → 53
      BBS2_Mid; Ciliary BBSome complex subunit 2, middle region

    RNA

    1. NR_130744.3 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) has an alternate splice site in an internal exon and an alternate 3' terminal sequence, compared to variant 1. This variant is represented as non-coding because the transcript is a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AC005841, AK027483, AK300905, BQ058412

    2. NR_147202.2 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) uses an alternate 3' exon structure compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AC005841, AW151238
      Related
      ENST00000645513.1

    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
      2812668..2859791
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060936.1 Alternate T2T-CHM13v2.0

      Range
      2818668..2865802
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NR_038933.1: Suppressed sequence

      Description
      NR_038933.1: This RefSeq was removed because it is now thought that this transcript is partial.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q969R8.1 GenPept UniProtKB/Swiss-Prot:Q969R8

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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