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    PTCD2 pentatricopeptide repeat domain 2 [ Homo sapiens (human) ]

    Gene ID: 79810, updated on 27-Nov-2024

    Summary

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    Official Symbol
    PTCD2provided by HGNC
    Official Full Name
    pentatricopeptide repeat domain 2provided by HGNC
    Primary source
    HGNC:HGNC:25734
    See related
    Ensembl:ENSG00000049883 MIM:615484; AllianceGenome:HGNC:25734
    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
    Enables RNA binding activity. Predicted to be involved in mitochondrion organization and regulation of mRNA processing. Predicted to act upstream of or within several processes, including liver development; muscle cell development; and ventricular cardiac muscle tissue morphogenesis. Located in mitochondrion. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in thyroid (RPKM 1.9), brain (RPKM 1.5) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See PTCD2 in Genome Data Viewer
    Location:
    5q13.2
    Exon count:
    11
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (72320373..72368395)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (72801543..72849569)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (71616200..71664222)

    Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene mitochondrial ribosomal protein S27 Neighboring gene uncharacterized LOC107986422 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:71597159-71598114 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22646 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16079 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:71607834-71608334 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:71615118-71615659 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:71615660-71616200 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22648 Neighboring gene RNA, 7SL, cytoplasmic 153, pseudogene Neighboring gene ribosomal protein L10a pseudogene 8 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16080 Neighboring gene Y-box binding protein 1 pseudogene 5

    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. Pentatricopeptide Protein PTCD2 Regulates COIII Translation in Mitochondria of the HeLa Cell Line. Baleva MV, et al. Int J Mol Sci, 2022 Nov 17. PMID 36430722, Free PMC Article
    2. Human pentatricopeptide proteins: only a few and what do they do? Lightowlers RN, et al. RNA Biol, 2013. PMID 23635806, Free PMC Article
    3. Disruption of a mitochondrial RNA-binding protein gene results in decreased cytochrome b expression and a marked reduction in ubiquinol-cytochrome c reductase activity in mouse heart mitochondria. Xu F, et al. Biochem J, 2008 Nov 15. PMID 18729827
    4. A BioID-Derived Proximity Interactome for SARS-CoV-2 Proteins. May DG, et al. Viruses, 2022 Mar 15. PMID 35337019, Free PMC Article
    5. Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression. Hendrickson SL, et al. PLoS One, 2010 Sep 21. PMID 20877624, Free PMC Article

    See all (20) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Pentatricopeptide Protein PTCD2 Regulates COIII Translation in Mitochondria of the HeLa Cell Line.
      Title: Pentatricopeptide Protein PTCD2 Regulates COIII Translation in Mitochondria of the HeLa Cell Line.
    2. Observational study of gene-disease association. (HuGE Navigator)
      Title: Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression.
    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

    Clone Names

    • FLJ12598

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables RNA binding HDA PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in kidney development IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in liver development IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in mRNA processing IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in mitochondrion organization IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in muscle cell development IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in regulation of gene expression IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in regulation of mRNA processing IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in regulation of mRNA processing ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in ventricular cardiac muscle tissue morphogenesis IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in mitochondrion HTP PubMed 
    is_active_in mitochondrion IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in mitochondrion IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    pentatricopeptide repeat-containing protein 2, mitochondrial
    Names
    CTC-365E16.1

    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_001284403.2 → NP_001271332.1  pentatricopeptide repeat-containing protein 2, mitochondrial isoform 2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks 3 consecutive exons compared to variant 1, however, it maintains the reading frame and encodes a shorter isoform (2) missing an internal protein segment compared to isoform 1.
      Source sequence(s)
      AC026406, AC093278, AI798903, AK056761, AK298750, DC393817
      Consensus CDS
      CCDS68891.1
      UniProtKB/Swiss-Prot
      Q8WV60
      UniProtKB/TrEMBL
      B3KPU6
      Related
      ENSP00000427349.1, ENST00000503868.5

    2. NM_001284404.2 → NP_001271333.1  pentatricopeptide repeat-containing protein 2, mitochondrial isoform 3

      See identical proteins and their annotated locations for NP_001271333.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) lacks 2 consecutive exons, which results in a frame-shift and translation initiation from an alternative start codon compared to variant 1. The resulting shorter isoform (3) has a distinct N-terminus compared to isoform 1.
      Source sequence(s)
      AC026406, AC093278, AI798903, AK056761, AK303639, DC393817
      Consensus CDS
      CCDS68892.1
      UniProtKB/TrEMBL
      D6RGK0
      Related
      ENSP00000444772.1, ENST00000536805.5

    3. NM_001284405.2 → NP_001271334.1  pentatricopeptide repeat-containing protein 2, mitochondrial isoform 4

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) lacks an exon in the mid-coding region and initiates translation from an in-frame downstream start codon compared to variant 1. The resulting isoform (4) has a shorter N-terminus compared to isoform 1.
      Source sequence(s)
      AC026406, AC093278, AI798903, AK056761, AK303776
      Consensus CDS
      CCDS75258.1
      UniProtKB/TrEMBL
      D6RGK0, F6S289
      Related
      ENSP00000438810.2, ENST00000543322.5

    4. NM_024754.5 → NP_079030.3  pentatricopeptide repeat-containing protein 2, mitochondrial isoform 1

      See identical proteins and their annotated locations for NP_079030.3

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      AC026406, AC093278, AI798903, AK056761, DC393817
      Consensus CDS
      CCDS4014.2
      UniProtKB/Swiss-Prot
      B7Z5D0, B7Z8L7, E9PFV7, Q6IA65, Q8WV60, Q9H9R0
      Related
      ENSP00000370013.4, ENST00000380639.10
      Conserved Domains (2) summary
      sd00004
      Location:165 → 194
      PPR; PPR repeat [structural motif]
      pfam10037
      Location:103 → 354
      MRP-S27; Mitochondrial 28S ribosomal protein S27

    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_000005.10 Reference GRCh38.p14 Primary Assembly

      Range
      72320373..72368395
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005248601.3 → XP_005248658.1  pentatricopeptide repeat-containing protein 2, mitochondrial isoform X1

      Conserved Domains (2) summary
      sd00004
      Location:165 → 194
      PPR; PPR repeat [structural motif]
      pfam10037
      Location:103 → 212
      MRP-S27; Mitochondrial 28S ribosomal protein S27

    2. XM_047417743.1 → XP_047273699.1  pentatricopeptide repeat-containing protein 2, mitochondrial isoform X2

      UniProtKB/TrEMBL
      B3KPU6

    3. XM_047417745.1 → XP_047273701.1  pentatricopeptide repeat-containing protein 2, mitochondrial isoform X4

      UniProtKB/TrEMBL
      F6S289

    4. XM_047417744.1 → XP_047273700.1  pentatricopeptide repeat-containing protein 2, mitochondrial isoform X3

      Related
      ENSP00000426295.2, ENST00000510676.6

    RNA

    1. XR_948298.3 RNA Sequence

    2. XR_241790.6 RNA Sequence

    3. XR_007058635.1 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060929.1 Alternate T2T-CHM13v2.0

      Range
      72801543..72849569
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054353496.1 → XP_054209471.1  pentatricopeptide repeat-containing protein 2, mitochondrial isoform X1

    2. XM_054353497.1 → XP_054209472.1  pentatricopeptide repeat-containing protein 2, mitochondrial isoform X2

      UniProtKB/TrEMBL
      B3KPU6

    3. XM_054353499.1 → XP_054209474.1  pentatricopeptide repeat-containing protein 2, mitochondrial isoform X4

      UniProtKB/TrEMBL
      F6S289

    4. XM_054353498.1 → XP_054209473.1  pentatricopeptide repeat-containing protein 2, mitochondrial isoform X3

    RNA

    1. XR_008487162.1 RNA Sequence

    2. XR_008487161.1 RNA Sequence

    3. XR_008487163.1 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8WV60.3 GenPept UniProtKB/Swiss-Prot:Q8WV60

    Gene LinkOut

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

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