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PNLDC1 PARN like ribonuclease domain containing exonuclease 1 [ Homo sapiens (human) ]

Gene ID: 154197, updated on 5-Mar-2024

Summary

Official Symbol
PNLDC1provided by HGNC
Official Full Name
PARN like ribonuclease domain containing exonuclease 1provided by HGNC
Primary source
HGNC:HGNC:21185
See related
Ensembl:ENSG00000146453 MIM:619529; AllianceGenome:HGNC:21185
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
SPGF57; Trimmer; HsPNLDC1
Summary
Enables poly(A)-specific ribonuclease activity. Involved in nuclear-transcribed mRNA poly(A) tail shortening. Located in endoplasmic reticulum. Implicated in spermatogenic failure. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Restricted expression toward testis (RPKM 4.8) See more
Orthologs
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Genomic context

See PNLDC1 in Genome Data Viewer
Location:
6q25.3
Exon count:
20
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (159799455..159820704)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (161045047..161066381)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (160221308..160241736)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:160209832-160210496 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:160210497-160211160 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25392 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25393 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:160215999-160216870 Neighboring gene small nucleolar RNA, H/ACA box 29 Neighboring gene t-complex 1 Neighboring gene mitochondrial ribosomal protein L18 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:160240240-160240966 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:160242614-160243420 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:160251537-160252270 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr6:160296296-160296948 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr6:160339473-160340672 Neighboring gene MAS1 proto-oncogene, G protein-coupled receptor Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25394 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25395 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25396 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17756 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17757 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17758 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:160399030-160400020 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:160401011-160402001 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25397 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25398 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25399 Neighboring gene Sharpr-MPRA regulatory region 15614 Neighboring gene Sharpr-MPRA regulatory region 12427 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr6:160408528-160409102 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:160417106-160417992 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:160417993-160418878 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr6:160419578-160420777 Neighboring gene insulin like growth factor 2 receptor Neighboring gene antisense of IGF2R non-protein coding RNA

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

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Clone Names

  • FLJ40240, MGC138451

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables RNA binding IBA
Inferred from Biological aspect of Ancestor
more info
 
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
 
enables poly(A)-specific ribonuclease activity IBA
Inferred from Biological aspect of Ancestor
more info
 
enables poly(A)-specific ribonuclease activity IDA
Inferred from Direct Assay
more info
PubMed 
Process Evidence Code Pubs
involved_in blastocyst formation IEA
Inferred from Electronic Annotation
more info
 
involved_in nuclear-transcribed mRNA catabolic process, nonsense-mediated decay IEA
Inferred from Electronic Annotation
more info
 
involved_in nuclear-transcribed mRNA poly(A) tail shortening IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in nuclear-transcribed mRNA poly(A) tail shortening IDA
Inferred from Direct Assay
more info
PubMed 
involved_in piRNA processing IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in spermatogenesis IMP
Inferred from Mutant Phenotype
more info
PubMed 
Component Evidence Code Pubs
is_active_in cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
 
is_active_in endoplasmic reticulum IBA
Inferred from Biological aspect of Ancestor
more info
 
located_in endoplasmic reticulum IDA
Inferred from Direct Assay
more info
PubMed 
located_in endoplasmic reticulum membrane IEA
Inferred from Electronic Annotation
more info
 

General protein information

Preferred Names
poly(A)-specific ribonuclease PNLDC1
Names
PARN like, ribonuclease domain containing 1
PARN-like domain-containing protein 1
poly(A)-specific ribonuclease (PARN)-like domain containing 1
poly(A)-specific ribonuclease PARN-like domain-containing protein 1
poly(A)-specific ribonuclease domain-containing protein 1
NP_001258791.1
NP_775787.1
XP_011533793.1
XP_011533795.1
XP_016865801.1
XP_016865802.1
XP_016865803.1
XP_016865804.1
XP_016865805.1
XP_024302107.1
XP_054210331.1
XP_054210332.1
XP_054210333.1
XP_054210334.1
XP_054210335.1
XP_054210336.1
XP_054210337.1
XP_054210338.1

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_001271862.2NP_001258791.1  poly(A)-specific ribonuclease PNLDC1 isoform 1

    See identical proteins and their annotated locations for NP_001258791.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the shorter transcript and encodes the longer isoform (1).
    Source sequence(s)
    AK093139, AK097559, BM666663
    Consensus CDS
    CCDS5271.2
    UniProtKB/Swiss-Prot
    Q8NA58
    Related
    ENSP00000376007.3, ENST00000392167.4
    Conserved Domains (1) summary
    pfam04857
    Location:3373
    CAF1; CAF1 family ribonuclease
  2. NM_173516.3NP_775787.1  poly(A)-specific ribonuclease PNLDC1 isoform 2

    See identical proteins and their annotated locations for NP_775787.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR and initiates translation at an alternate downstream start codon, compared to variant 1. The encoded isoform (2) is shorter and has a distinct N-terminus, compared to isoform 1.
    Source sequence(s)
    AK097559, BM666663
    Consensus CDS
    CCDS64561.1
    UniProtKB/Swiss-Prot
    Q5TAP7, Q8N7X5, Q8NA58
    Related
    ENSP00000476448.1, ENST00000610273.5
    Conserved Domains (1) summary
    pfam04857
    Location:11362
    CAF1; CAF1 family ribonuclease

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_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    159799455..159820704
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_024446339.2XP_024302107.1  poly(A)-specific ribonuclease PNLDC1 isoform X8

    Conserved Domains (1) summary
    pfam04857
    Location:59293
    CAF1; CAF1 family ribonuclease
  2. XM_017010312.3XP_016865801.1  poly(A)-specific ribonuclease PNLDC1 isoform X1

  3. XM_017010314.3XP_016865803.1  poly(A)-specific ribonuclease PNLDC1 isoform X4

  4. XM_017010313.3XP_016865802.1  poly(A)-specific ribonuclease PNLDC1 isoform X2

  5. XM_017010316.2XP_016865805.1  poly(A)-specific ribonuclease PNLDC1 isoform X6

  6. XM_011535491.3XP_011533793.1  poly(A)-specific ribonuclease PNLDC1 isoform X3

    See identical proteins and their annotated locations for XP_011533793.1

    UniProtKB/Swiss-Prot
    Q5TAP7, Q8N7X5, Q8NA58
    Conserved Domains (1) summary
    pfam04857
    Location:11362
    CAF1; CAF1 family ribonuclease
  7. XM_017010315.3XP_016865804.1  poly(A)-specific ribonuclease PNLDC1 isoform X5

  8. XM_011535493.3XP_011533795.1  poly(A)-specific ribonuclease PNLDC1 isoform X7

    Conserved Domains (1) summary
    pfam04857
    Location:30246
    CAF1; CAF1 family ribonuclease

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    161045047..161066381
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054354363.1XP_054210338.1  poly(A)-specific ribonuclease PNLDC1 isoform X8

  2. XM_054354359.1XP_054210334.1  poly(A)-specific ribonuclease PNLDC1 isoform X4

  3. XM_054354356.1XP_054210331.1  poly(A)-specific ribonuclease PNLDC1 isoform X1

  4. XM_054354357.1XP_054210332.1  poly(A)-specific ribonuclease PNLDC1 isoform X2

  5. XM_054354361.1XP_054210336.1  poly(A)-specific ribonuclease PNLDC1 isoform X6

  6. XM_054354358.1XP_054210333.1  poly(A)-specific ribonuclease PNLDC1 isoform X3

    UniProtKB/Swiss-Prot
    Q5TAP7, Q8N7X5, Q8NA58
  7. XM_054354360.1XP_054210335.1  poly(A)-specific ribonuclease PNLDC1 isoform X5

  8. XM_054354362.1XP_054210337.1  poly(A)-specific ribonuclease PNLDC1 isoform X7