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    PITPNM3 PITPNM family member 3 [ Homo sapiens (human) ]

    Gene ID: 83394, updated on 6-Jun-2024

    Summary

    Official Symbol
    PITPNM3provided by HGNC
    Official Full Name
    PITPNM family member 3provided by HGNC
    Primary source
    HGNC:HGNC:21043
    See related
    Ensembl:ENSG00000091622 MIM:608921; AllianceGenome:HGNC:21043
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    NIR1; ACKR6; CORD5; RDGBA3
    Summary
    This gene encodes a member of a family of membrane-associated phosphatidylinositol transfer domain-containing proteins. The calcium-binding protein has phosphatidylinositol (PI) transfer activity and interacts with the protein tyrosine kinase PTK2B (also known as PYK2). The protein is homologous to a Drosophila protein that is implicated in the visual transduction pathway in flies. Mutations in this gene result in autosomal dominant cone dystrophy. Multiple transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Sep 2009]
    Expression
    Biased expression in spleen (RPKM 27.1), ovary (RPKM 12.0) and 6 other tissues See more
    Orthologs
    NEW
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    Genomic context

    See PITPNM3 in Genome Data Viewer
    Location:
    17p13.2-p13.1
    Exon count:
    22
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (6451263..6556555, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (6350993..6456410, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (6354583..6459875, complement)

    Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107985017 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:6347155-6347733 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:6347797-6348024 Neighboring gene aryl hydrocarbon receptor interacting protein like 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:6350771-6351437 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:6357121-6357839 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8075 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8076 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:6360909-6361690 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:6361691-6362472 Neighboring gene PICALM interacting mitotic regulator Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:6367015-6367566 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:6367567-6368118 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:6373134-6373634 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:6374667-6375190 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:6377377-6377969 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:6377970-6378561 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:6396251-6396752 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:6400873-6401763 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:6404362-6404908 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:6447205-6447705 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:6452242-6452960 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:6458140-6458786 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:6471007-6471507 Neighboring gene KIAA0753 Neighboring gene RNA, 5S ribosomal pseudogene 435 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:6540081-6540863 Neighboring gene uncharacterized LOC122526780 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:6540864-6541645 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11584 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:6543558-6544439

    Genomic regions, transcripts, and products

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • MGC157740, MGC157741

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables calcium ion binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables lipid binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables phosphatidylinositol transfer activity TAS
    Traceable Author Statement
    more info
     
    enables phospholipase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables receptor tyrosine kinase binding IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in intermembrane lipid transfer IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in phosphatidylinositol biosynthetic process TAS
    Traceable Author Statement
    more info
     
    involved_in phospholipid transport IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    located_in cell body IEA
    Inferred from Electronic Annotation
    more info
     
    located_in cell projection IEA
    Inferred from Electronic Annotation
    more info
     
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in cytosol TAS
    Traceable Author Statement
    more info
     
    located_in endomembrane system IEA
    Inferred from Electronic Annotation
    more info
     
    located_in membrane IEA
    Inferred from Electronic Annotation
    more info
     

    General protein information

    Preferred Names
    membrane-associated phosphatidylinositol transfer protein 3
    Names
    NIR-1
    PITPnm 3
    PYK2 N-terminal domain-interacting receptor 1
    atypical chemokine receptor 6
    cone rod dystrophy 5
    phosphatidylinositol transfer protein, membrane-associated 3
    retinal degeneration B alpha 3

    NCBI Reference Sequences (RefSeq)

    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.

    Genomic

    1. NG_016020.1 RefSeqGene

      Range
      5003..110295
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001165966.2NP_001159438.1  membrane-associated phosphatidylinositol transfer protein 3 isoform 2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an alternate in-frame exon in the 5' coding region, compared to variant 1. The resulting isoform (2) lacks an internal segment, compared to isoform 1.
      Source sequence(s)
      AC055872, AI333030, BC035799, BC128583
      Consensus CDS
      CCDS54080.1
      UniProtKB/TrEMBL
      A1A5C9
      Related
      ENSP00000407882.3, ENST00000421306.7
      Conserved Domains (2) summary
      smart00775
      Location:703833
      LNS2; This domain is found in Saccharomyces cerevisiae protein SMP2, proteins with an N-terminal lipin domain and phosphatidylinositol transfer proteins
      pfam02862
      Location:357557
      DDHD; DDHD domain
    2. NM_031220.4NP_112497.2  membrane-associated phosphatidylinositol transfer protein 3 isoform 1

      See identical proteins and their annotated locations for NP_112497.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AC055872, AF334586, AI333030, BC035799
      Consensus CDS
      CCDS11076.1
      UniProtKB/Swiss-Prot
      A1A5D0, F8WEW5, Q59GH9, Q9BZ71, Q9NPQ4
      UniProtKB/TrEMBL
      A1A5C9
      Related
      ENSP00000262483.8, ENST00000262483.13
      Conserved Domains (2) summary
      smart00775
      Location:739869
      LNS2; This domain is found in Saccharomyces cerevisiae protein SMP2, proteins with an N-terminal lipin domain and phosphatidylinositol transfer proteins
      pfam02862
      Location:393593
      DDHD; DDHD 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_000017.11 Reference GRCh38.p14 Primary Assembly

      Range
      6451263..6556555 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011524015.4XP_011522317.1  membrane-associated phosphatidylinositol transfer protein 3 isoform X1

      UniProtKB/TrEMBL
      A1A5C9
      Conserved Domains (2) summary
      pfam02862
      Location:393593
      DDHD; DDHD domain
      cl21460
      Location:739830
      HAD_like; Haloacid Dehalogenase-like Hydrolases
    2. XM_011524016.4XP_011522318.1  membrane-associated phosphatidylinositol transfer protein 3 isoform X2

      Conserved Domains (2) summary
      pfam02862
      Location:393593
      DDHD; DDHD domain
      cl21460
      Location:739770
      HAD_like; Haloacid Dehalogenase-like Hydrolases
    3. XM_011524017.4XP_011522319.1  membrane-associated phosphatidylinositol transfer protein 3 isoform X3

      Conserved Domains (1) summary
      pfam02862
      Location:393495
      DDHD; DDHD domain

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060941.1 Alternate T2T-CHM13v2.0

      Range
      6350993..6456410 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054317461.1XP_054173436.1  membrane-associated phosphatidylinositol transfer protein 3 isoform X1

      UniProtKB/TrEMBL
      A1A5C9
    2. XM_054317462.1XP_054173437.1  membrane-associated phosphatidylinositol transfer protein 3 isoform X2

    3. XM_054317463.1XP_054173438.1  membrane-associated phosphatidylinositol transfer protein 3 isoform X3