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

Gene ID: 79810, updated on 3-Apr-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 animal organ development; muscle cell development; and regulation of gene expression. Located in mitochondrion. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in thyroid (RPKM 1.9), brain (RPKM 1.5) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
5q13.2
Exon count:
11
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (72320373..72368395)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (72801543..72849569)
105.20220307 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 (19) 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)

Genotypes

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 multicellular organism development 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
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_2023_10

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

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