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Ptcd3 pentatricopeptide repeat domain 3 [ Mus musculus (house mouse) ]

Gene ID: 69956, updated on 1-Mar-2024

Summary

Official Symbol
Ptcd3provided by MGI
Official Full Name
pentatricopeptide repeat domain 3provided by MGI
Primary source
MGI:MGI:1917206
See related
Ensembl:ENSMUSG00000063884 AllianceGenome:MGI:1917206
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Mus musculus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as
MRP-S39; 2610034F17Rik; 2810422B04Rik
Summary
Predicted to enable rRNA binding activity and ribosomal small subunit binding activity. Predicted to be involved in mitochondrial translation. Predicted to act upstream of or within regulation of translation. Located in mitochondrion. Is expressed in several structures, including alimentary system; brain; cardiovascular system; genitourinary system; and immune system. Human ortholog(s) of this gene implicated in combined oxidative phosphorylation deficiency 51. Orthologous to human PTCD3 (pentatricopeptide repeat domain 3). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in CNS E11.5 (RPKM 15.2), liver E14 (RPKM 12.3) and 24 other tissues See more
Orthologs
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Genomic context

See Ptcd3 in Genome Data Viewer
Location:
6 C1; 6 32.21 cM
Exon count:
25
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 6 NC_000072.7 (71857622..71886080, complement)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 6 NC_000072.6 (71880638..71908773, complement)

Chromosome 6 - NC_000072.7Genomic Context describing neighboring genes Neighboring gene STARR-seq mESC enhancer starr_16268 Neighboring gene mitochondrial ribosomal protein L35 Neighboring gene inner membrane protein, mitochondrial Neighboring gene ribosomal protein L7A pseudogene Neighboring gene small nucleolar RNA, C/D box 94 Neighboring gene STARR-positive B cell enhancer ABC_E9096 Neighboring gene polymerase (RNA) I polypeptide A Neighboring gene STARR-positive B cell enhancer ABC_E6439 Neighboring gene STARR-seq mESC enhancer starr_16273 Neighboring gene eukaryotic translation initiation factor 3, subunit H pseudogene Neighboring gene STARR-seq mESC enhancer starr_16274 Neighboring gene STARR-seq mESC enhancer starr_16275 Neighboring gene CapStarr-seq enhancer MGSCv37_chr6:71912891-71913074 Neighboring gene predicted gene, 26628

Genomic regions, transcripts, and products

Expression

  • Project title: Mouse ENCODE transcriptome data
  • Description: RNA profiling data sets generated by the Mouse ENCODE project.
  • BioProject: PRJNA66167
  • Publication: PMID 25409824
  • Analysis date: n/a

Variation

Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)
  • Targeted (2) 
  • Endonuclease-mediated (1) 

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables RNA binding IEA
Inferred from Electronic Annotation
more info
 
enables rRNA binding IBA
Inferred from Biological aspect of Ancestor
more info
 
enables rRNA binding ISO
Inferred from Sequence Orthology
more info
 
enables ribosomal small subunit binding IBA
Inferred from Biological aspect of Ancestor
more info
 
enables ribosomal small subunit binding ISO
Inferred from Sequence Orthology
more info
 
Process Evidence Code Pubs
involved_in mitochondrial translation IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in mitochondrial translation ISO
Inferred from Sequence Orthology
more info
 
involved_in mitochondrial translation NAS
Non-traceable Author Statement
more info
PubMed 
acts_upstream_of_or_within regulation of translation IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
located_in cytosol ISO
Inferred from Sequence Orthology
more info
 
located_in mitochondrial inner membrane NAS
Non-traceable Author Statement
more info
PubMed 
part_of mitochondrial small ribosomal subunit NAS
Non-traceable Author Statement
more info
PubMed 
located_in mitochondrion HDA PubMed 
is_active_in mitochondrion IBA
Inferred from Biological aspect of Ancestor
more info
 
located_in mitochondrion ISO
Inferred from Sequence Orthology
more info
 
located_in nucleoplasm ISO
Inferred from Sequence Orthology
more info
 
located_in plasma membrane ISO
Inferred from Sequence Orthology
more info
 
part_of ribonucleoprotein complex IEA
Inferred from Electronic Annotation
more info
 
located_in ribosome IEA
Inferred from Electronic Annotation
more info
 

General protein information

Preferred Names
small ribosomal subunit protein mS39
Names
28S ribosomal protein S39, mitochondrial
pentatricopeptide repeat domain-containing protein 3, mitochondrial
pentatricopeptide repeat-containing protein 3, mitochondrial

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_001362068.1NP_001348997.1  small ribosomal subunit protein mS39 isoform 2 precursor

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks an alternate in-frame exon compared to variant 1. The resulting isoform (2) has the same N- and C-termini but is shorter compared to isoform 1.
    Source sequence(s)
    AC122200
    UniProtKB/TrEMBL
    Q3UK51
    Conserved Domains (3) summary
    sd00004
    Location:257284
    PPR; PPR repeat [structural motif]
    pfam13041
    Location:289343
    PPR_2; PPR repeat family
    cl25449
    Location:253299
    PPR_2; PPR repeat family
  2. NM_001362069.1NP_001348998.1  small ribosomal subunit protein mS39 isoform 3 precursor

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) lacks two alternate in-frame exons compared to variant 1. The resulting isoform (3) has the same N- and C-termini but is shorter compared to isoform 1.
    Source sequence(s)
    AC122200
    UniProtKB/TrEMBL
    Q3UK51
    Conserved Domains (3) summary
    sd00004
    Location:257284
    PPR; PPR repeat [structural motif]
    pfam13041
    Location:289343
    PPR_2; PPR repeat family
    cl25449
    Location:253299
    PPR_2; PPR repeat family
  3. NM_027275.3NP_081551.2  small ribosomal subunit protein mS39 isoform 1 precursor

    See identical proteins and their annotated locations for NP_081551.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (1).
    Source sequence(s)
    AK013131, AK146005, BB844000, BF020753
    Consensus CDS
    CCDS20235.1
    UniProtKB/Swiss-Prot
    Q14C51, Q3UKH5, Q5XG65, Q6P9N5, Q9CZ12
    UniProtKB/TrEMBL
    Q3UK51
    Related
    ENSMUSP00000080743.3, ENSMUST00000082094.5
    Conserved Domains (2) summary
    sd00004
    Location:257284
    PPR; PPR repeat [structural motif]
    pfam13041
    Location:289343
    PPR_2; PPR repeat family

RNA

  1. NR_155284.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) uses an alternate splice junction compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AC122200
  2. NR_155285.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (5) contains an alternate exon and uses an alternate splice junction compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AC122200
    Related
    ENSMUST00000206879.2

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCm39 C57BL/6J

Genomic

  1. NC_000072.7 Reference GRCm39 C57BL/6J

    Range
    71857622..71886080 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006506574.3XP_006506637.1  small ribosomal subunit protein mS39 isoform X1

    Conserved Domains (3) summary
    sd00004
    Location:116143
    PPR; PPR repeat [structural motif]
    pfam13812
    Location:177240
    PPR_3; Pentatricopeptide repeat domain
    pfam13041
    Location:148202
    PPR_2; PPR repeat family
  2. XM_011241461.3XP_011239763.1  small ribosomal subunit protein mS39 isoform X2

RNA

  1. XR_001785166.3 RNA Sequence

  2. XR_001785167.3 RNA Sequence

  3. XR_001785164.3 RNA Sequence

  4. XR_868886.4 RNA Sequence

  5. XR_868888.4 RNA Sequence