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    PRRT1 proline rich transmembrane protein 1 [ Homo sapiens (human) ]

    Gene ID: 80863, updated on 2-Nov-2024

    Summary

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    Official Symbol
    PRRT1provided by HGNC
    Official Full Name
    proline rich transmembrane protein 1provided by HGNC
    Primary source
    HGNC:HGNC:13943
    See related
    Ensembl:ENSG00000204314 MIM:618297; AllianceGenome:HGNC:13943
    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
    NG5; DSPD1; C6orf31; IFITMD7; SynDIG4
    Summary
    Enables identical protein binding activity. Predicted to be involved in several processes, including long-term synaptic depression; protein localization to cell surface; and regulation of AMPA receptor activity. Predicted to act upstream of or within several processes, including learning or memory; long-term synaptic potentiation; and synapse organization. Predicted to be located in plasma membrane and synaptic vesicle membrane. Predicted to be active in glutamatergic synapse and postsynaptic density membrane. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Biased expression in brain (RPKM 24.0), ovary (RPKM 12.1) and 6 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See PRRT1 in Genome Data Viewer
    Location:
    6p21.32
    Exon count:
    6
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (32148363..32153083, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (32001551..32006271, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (32116140..32120860, complement)

    Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene Sharpr-MPRA regulatory region 2290 Neighboring gene activating transcription factor 6 beta Neighboring gene CRISPRi-validated cis-regulatory element chr6.1802 Neighboring gene FKBP prolyl isomerase like Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:32116858-32117395 Neighboring gene uncharacterized LOC100507547 Neighboring gene PPT2-EGFL8 readthrough (NMD candidate) Neighboring gene palmitoyl-protein thioesterase 2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:32134815-32135567 Neighboring gene EGF like domain multiple 8 Neighboring gene 1-acylglycerol-3-phosphate O-acyltransferase 1

    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 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. A genome-wide integrative genomic study localizes genetic factors influencing antibodies against Epstein-Barr virus nuclear antigen 1 (EBNA-1). Rubicz R, et al. PLoS Genet, 2013. PMID 23326239, Free PMC Article
    2. Association of MHC SNP genotype with susceptibility to type 1 diabetes: a modified survival approach. McKinnon E, et al. Diabetes Obes Metab, 2009 Feb. PMID 19143821, Free PMC Article
    3. Genetic association of the major histocompatibility complex with rheumatoid arthritis implicates two non-DRB1 loci. Vignal C, et al. Arthritis Rheum, 2009 Jan. PMID 19116923
    4. The dispanins: a novel gene family of ancient origin that contains 14 human members. Sällman Almén M, et al. PLoS One, 2012. PMID 22363774, Free PMC Article
    5. Analysis of the gene-dense major histocompatibility complex class III region and its comparison to mouse. Xie T, et al. Genome Res, 2003 Dec. PMID 14656967, Free PMC Article

    See all (14) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Observational study of gene-disease association and gene-gene interaction. (HuGE Navigator)
      Title: Association of MHC SNP genotype with susceptibility to type 1 diabetes: a modified survival approach.
    2. Observational study of gene-disease association. (HuGE Navigator)
      Title: High-density SNP screening of the major histocompatibility complex in systemic lupus erythematosus demonstrates strong evidence for independent susceptibility regions.
    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
    A genome-wide integrative genomic study localizes genetic factors influencing antibodies against Epstein-Barr virus nuclear antigen 1 (EBNA-1).
    EBI GWAS Catalog
    Loci associated with N-glycosylation of human immunoglobulin G show pleiotropy with autoimmune diseases and haematological cancers.
    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 identical protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables signaling receptor regulator activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in learning or memory IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in long-term synaptic depression ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in long-term synaptic potentiation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in protein localization to cell surface ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in protein phosphorylation ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in regulation of AMPA receptor activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in synapse organization IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in glutamatergic synapse IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in postsynaptic density membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in synaptic vesicle membrane IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    proline-rich transmembrane protein 1
    Names
    dispanin subfamily D member 1
    interferon induced transmembrane protein domain containing 7
    synapse differentiation-induced protein 4

    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_001363780.2 → NP_001350709.1  proline-rich transmembrane protein 1 isoform 2

      Status: VALIDATED

      Source sequence(s)
      AL662884, BC013201
      Conserved Domains (1) summary
      pfam04505
      Location:138 → 204
      CD225; Interferon-induced transmembrane protein

    2. NM_030651.4 → NP_085154.3  proline-rich transmembrane protein 1 isoform 1

      See identical proteins and their annotated locations for NP_085154.3

      Status: VALIDATED

      Source sequence(s)
      AK054885, BC063046
      Consensus CDS
      CCDS4739.1
      UniProtKB/Swiss-Prot
      A6ND08, A6ND40, B0S869, Q5SSW4, Q5SSX7, Q5STI1, Q96DW3, Q96NQ8, Q99946
      UniProtKB/TrEMBL
      A0A1U9X8D6, A0A1U9X8E5
      Related
      ENSP00000211413.5, ENST00000211413.10
      Conserved Domains (1) summary
      pfam04505
      Location:219 → 286
      CD225; Interferon-induced transmembrane protein

    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_000006.12 Reference GRCh38.p14 Primary Assembly

      Range
      32148363..32153083 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Reference GRCh38.p14 ALT_REF_LOCI_1

    Genomic

    1. NT_167244.2 Reference GRCh38.p14 ALT_REF_LOCI_1

      Range
      3480961..3485682 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Reference GRCh38.p14 ALT_REF_LOCI_2

    Genomic

    1. NT_113891.3 Reference GRCh38.p14 ALT_REF_LOCI_2

      Range
      3586700..3591422 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Reference GRCh38.p14 ALT_REF_LOCI_3

    Genomic

    1. NT_167245.2 Reference GRCh38.p14 ALT_REF_LOCI_3

      Range
      3389726..3394448 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Reference GRCh38.p14 ALT_REF_LOCI_4

    Genomic

    1. NT_167246.2 Reference GRCh38.p14 ALT_REF_LOCI_4

      Range
      3453364..3458084 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Reference GRCh38.p14 ALT_REF_LOCI_5

    Genomic

    1. NT_167247.2 Reference GRCh38.p14 ALT_REF_LOCI_5

      Range
      3490378..3495098 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Reference GRCh38.p14 ALT_REF_LOCI_6

    Genomic

    1. NT_167248.2 Reference GRCh38.p14 ALT_REF_LOCI_6

      Range
      3371560..3376277 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Reference GRCh38.p14 ALT_REF_LOCI_7

    Genomic

    1. NT_167249.2 Reference GRCh38.p14 ALT_REF_LOCI_7

      Range
      3464567..3469287 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060930.1 Alternate T2T-CHM13v2.0

      Range
      32001551..32006271 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q99946.2 GenPept UniProtKB/Swiss-Prot:Q99946

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