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    ITM2C integral membrane protein 2C [ Homo sapiens (human) ]

    Gene ID: 81618, updated on 10-Dec-2024

    Summary

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    Official Symbol
    ITM2Cprovided by HGNC
    Official Full Name
    integral membrane protein 2Cprovided by HGNC
    Primary source
    HGNC:HGNC:6175
    See related
    Ensembl:ENSG00000135916 MIM:609554; AllianceGenome:HGNC:6175
    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
    E25; BRI3; E25C; ITM3; BRICD2C
    Summary
    Enables amyloid-beta binding activity. Involved in negative regulation of neuron projection development and neuron differentiation. Located in several cellular components, including Golgi apparatus; lysosome; and perinuclear region of cytoplasm. [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Broad expression in colon (RPKM 478.6), brain (RPKM 266.8) and 17 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See ITM2C in Genome Data Viewer
    Location:
    2q37.1
    Exon count:
    7
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (230864185..230879254)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (231347355..231362416)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (231728900..231743969)

    Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene calcium binding protein 39 Neighboring gene BANF1 pseudogene 3 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17248 Neighboring gene RNA, U6 small nuclear 268, pseudogene Neighboring gene Sharpr-MPRA regulatory region 14077 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:231654665-231655164 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr2:231657991-231659190 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17249 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12413 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr2:231708391-231709016 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:231726605-231727215 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:231728341-231728999 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:231729658-231730316 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:231730317-231730973 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:231734265-231734922 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:231734923-231735580 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17250 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17251 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12417 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:231742513-231743287 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17253 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:231757691-231758270 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:231758271-231758850 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12418 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12419 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr2:231773167-231774366 Neighboring gene GPR55 cis regulatory suppressor of immune response RNA Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:231789302-231790090 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17259 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12420 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12421 Neighboring gene G protein-coupled receptor 55 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:231804174-231804714 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:231804715-231805254 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17260 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17261 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17262 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17263 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17264 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17265 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17266 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17267 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12422 Neighboring gene COX20 pseudogene 2

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 2018

    Bibliography

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    Related articles in PubMed

    1. A catalogue of genes in the cardiovascular system as identified by expressed sequence tags. Liew CC, et al. Proc Natl Acad Sci U S A, 1994 Oct 25. PMID 7938007, Free PMC Article
    2. Sequence, genomic structure and tissue expression of Human BRI3, a member of the BRI gene family. Vidal R, et al. Gene, 2001 Mar 21. PMID 11290423
    3. Unlocking the Potential of the CA2, CA7, and ITM2C Gene Signatures for the Early Detection of Colorectal Cancer: A Comprehensive Analysis of RNA-Seq Data by Utilizing Machine Learning Algorithms. Maurya NS, et al. Genes (Basel), 2023 Sep 22. PMID 37895185, Free PMC Article
    4. Isolation of markers for chondro-osteogenic differentiation using cDNA library subtraction. Molecular cloning and characterization of a gene belonging to a novel multigene family of integral membrane proteins. Deleersnijder W, et al. J Biol Chem, 1996 Aug 9. PMID 8702637
    5. BRI3 inhibits amyloid precursor protein processing in a mechanistically distinct manner from its homologue dementia gene BRI2. Matsuda S, et al. J Biol Chem, 2009 Jun 5. PMID 19366692, Free PMC Article

    See all (69) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Unlocking the Potential of the CA2, CA7, and ITM2C Gene Signatures for the Early Detection of Colorectal Cancer: A Comprehensive Analysis of RNA-Seq Data by Utilizing Machine Learning Algorithms.
      Title: Unlocking the Potential of the CA2, CA7, and ITM2C Gene Signatures for the Early Detection of Colorectal Cancer: A Comprehensive Analysis of RNA-Seq Data by Utilizing Machine Learning Algorithms.
    2. Observational study of gene-disease association. (HuGE Navigator)
      Title: Association of genetic variants with hemorrhagic stroke in Japanese individuals.
    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

    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

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables ATP binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables amyloid-beta binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables amyloid-beta binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in negative regulation of amyloid precursor protein biosynthetic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in negative regulation of neuron projection development IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in neuron differentiation IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in positive regulation of extrinsic apoptotic signaling pathway IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    is_active_in Golgi apparatus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in Golgi apparatus IDA
    Inferred from Direct Assay
    more info
    		  
    located_in extracellular exosome HDA PubMed 
    located_in lysosomal membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in lysosome IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in perinuclear region of cytoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in plasma membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    integral membrane protein 2C
    Names
    BRICHOS domain containing 2C
    cerebral protein 14
    integral membrane protein 3
    transmembrane protein BRI3

    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_001012514.3 → NP_001012532.1  integral membrane protein 2C isoform 3

      See identical proteins and their annotated locations for NP_001012532.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) lacks an in-frame exon in the central coding region, compared to variant 1. The encoded isoform (3) is shorter, compared to isoform 1.
      Source sequence(s)
      AK056321, BC098563, DA182471
      Consensus CDS
      CCDS33396.1
      UniProtKB/Swiss-Prot
      Q9NQX7
      Related
      ENSP00000335121.6, ENST00000335005.10
      Conserved Domains (1) summary
      smart01039
      Location:89 → 181
      BRICHOS; The BRICHOS domain is found in a variety of proteins implicated in dementia, respiratory distress and cancer

    2. NM_001012516.2 → NP_001012534.1  integral membrane protein 2C isoform 2

      See identical proteins and their annotated locations for NP_001012534.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks an in-frame exon in the central coding region, compared to variant 1. The encoded isoform (2) is shorter, compared to isoform 1.
      Source sequence(s)
      AK056321, BC098563, DA138409
      Consensus CDS
      CCDS33395.1
      UniProtKB/TrEMBL
      B4DIB1
      Related
      ENSP00000322100.6, ENST00000326407.10
      Conserved Domains (1) summary
      cl04394
      Location:136 → 191
      BRICHOS; BRICHOS domain

    3. NM_001287240.2 → NP_001274169.1  integral membrane protein 2C isoform 4

      See identical proteins and their annotated locations for NP_001274169.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) differs in its 5' UTR and initiates translation from a downstream start codon, compared to variant 1. The encoded isoform (4) has a shorter N-terminus, compared to isoform 1.
      Source sequence(s)
      AC012507, AF272043, BC098563, BX444331
      Consensus CDS
      CCDS74665.1
      UniProtKB/TrEMBL
      B8ZZM6
      Related
      ENSP00000387242.2, ENST00000409704.6
      Conserved Domains (1) summary
      smart01039
      Location:74 → 166
      BRICHOS; The BRICHOS domain is found in a variety of proteins implicated in dementia, respiratory distress and cancer

    4. NM_001287241.2 → NP_001274170.1  integral membrane protein 2C isoform 1

      See identical proteins and their annotated locations for NP_001274170.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (5) differs in the 5' UTR, compared to variant 1. Both variants 1 and 5 encode the same isoform (1).
      Source sequence(s)
      AC012507, AF272043, BC098563, BX444331
      Consensus CDS
      CCDS2479.1
      UniProtKB/Swiss-Prot
      B3KPG4, Q4G0A8, Q53H84, Q6IAE7, Q86VK5, Q8N288, Q8TAW0, Q9BUP8, Q9NQX7
      UniProtKB/TrEMBL
      B4DIB1
      Conserved Domains (1) summary
      smart01039
      Location:136 → 228
      BRICHOS; The BRICHOS domain is found in a variety of proteins implicated in dementia, respiratory distress and cancer

    5. NM_030926.6 → NP_112188.1  integral membrane protein 2C isoform 1

      See identical proteins and their annotated locations for NP_112188.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (1). Both variants 1 and 5 encode the same isoform.
      Source sequence(s)
      AF272043, BC098563
      Consensus CDS
      CCDS2479.1
      UniProtKB/Swiss-Prot
      B3KPG4, Q4G0A8, Q53H84, Q6IAE7, Q86VK5, Q8N288, Q8TAW0, Q9BUP8, Q9NQX7
      UniProtKB/TrEMBL
      B4DIB1
      Related
      ENSP00000322730.6, ENST00000326427.11
      Conserved Domains (1) summary
      smart01039
      Location:136 → 228
      BRICHOS; The BRICHOS domain is found in a variety of proteins implicated in dementia, respiratory distress and cancer

    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_000002.12 Reference GRCh38.p14 Primary Assembly

      Range
      230864185..230879254
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060926.1 Alternate T2T-CHM13v2.0

      Range
      231347355..231362416
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9NQX7.1 GenPept UniProtKB/Swiss-Prot:Q9NQX7

    Gene LinkOut

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

    Chemical Information
    Molecular Biology Databases
    Research Materials
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