POLDIP3 DNA polymerase delta interacting protein 3 [Homo sapiens (human)] - Gene

Summary

Official Symbol: POLDIP3provided by HGNC
Official Full Name: DNA polymerase delta interacting protein 3provided by HGNC
Primary source: HGNC:HGNC:23782
See related: Ensembl:ENSG00000100227 MIM:611520; AllianceGenome:HGNC:23782
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: SKAR; PDIP3; PDIP46
Summary: This gene encodes an RRM (RNA recognition motif)-containing protein that participates in the regulation of translation by recruiting ribosomal protein S6 kinase beta-1 to mRNAs. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2013]
Expression: Ubiquitous expression in ovary (RPKM 49.2), bone marrow (RPKM 26.9) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 22q13.2

Exon count:: 9

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	22	NC_000022.11 (42583721..42614883, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	22	NC_060946.1 (43064586..43095749, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	22	NC_000022.10 (42979727..43010889, complement)

Chromosome 22 - NC_000022.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Tissue-specific circular RNA induction during human fetal development
Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
BioProject: PRJNA270632
Publication: PMID 26076956
Analysis date: Mon Apr 2 22:54:59 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Human RTEL1 associates with Poldip3 to facilitate responses to replication stress and R-loop resolution.
Title: Human RTEL1 associates with Poldip3 to facilitate responses to replication stress and R-loop resolution.
Altered expression of PDIP46 or its mutation may affect Pol delta functions in vivo, and thereby be a nexus for altered genomic stability.
Title: PDIP46 (DNA polymerase δ interacting protein 46) is an activating factor for human DNA polymerase δ.
hnRNP-U inhibits TDP-43-mediated alterations in splicing of POLDIP3 mRNA.
Title: Nuclear TDP-43 causes neuronal toxicity by escaping from the inhibitory regulation by hnRNPs.
PDIP3 and ZC11A associate with the human TREX complex in an ATP-dependent manner and function in mRNA export.
Title: The proteins PDIP3 and ZC11A associate with the human TREX complex in an ATP-dependent manner and function in mRNA export.
these findings establish critical and essential roles for SKAR in the regulation of mRNA translation of IFN-sensitive genes and induction of IFN-alpha biological responses.
Title: Regulatory effects of SKAR in interferon α signaling and its role in the generation of type I IFN responses.
Alteration of POLDIP3 splicing associated with loss of function of TDP-43 in tissues affected with amyotrophic lateral sclerosis (ALS) .
Title: Alteration of POLDIP3 splicing associated with loss of function of TDP-43 in tissues affected with ALS.
SKAR-mediated recruitment of activated S6K1 to newly processed mRNPs serves as a conduit between mTOR checkpoint signaling and the pioneer round of translation when cells exist in conditions supportive of protein synthesis.
Title: SKAR links pre-mRNA splicing to mTOR/S6K1-mediated enhanced translation efficiency of spliced mRNAs.
This study showed that PDIP46 aka SKAR, a protein possessing one RNA recognition motif (RRM) and being a protein partner of both the p50 subunit of DNA polymerase delta and p70 ribosomal protein S6 kinase 1 (S6K1).
Title: Human enhancer of rudimentary is a molecular partner of PDIP46/SKAR, a protein interacting with DNA polymerase delta and S6K1 and regulating cell growth.
SKAR is a specific target of S6K1 and regulates cell growth.
Title: SKAR is a specific target of S6 kinase 1 in cell growth control.

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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

D22S965E (e-PCR)
- UniSTS:98901

AL008665 (e-PCR)
- UniSTS:51302

G19963 (e-PCR)
- UniSTS:73096

RH10763 (e-PCR)
- UniSTS:91791

D22S1560 (e-PCR)
- UniSTS:33947

WI-18150 (e-PCR)
- UniSTS:51377

WIAF-2172 (e-PCR)
- UniSTS:87986

RH28567 (e-PCR)
- UniSTS:86459

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables RNA binding	HDA more info	PubMed
enables mRNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein-containing complex binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in poly(A)+ mRNA export from nucleus	IBA Inferred from Biological aspect of Ancestor more info
involved_in poly(A)+ mRNA export from nucleus	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of translation	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in cytoplasm	TAS Traceable Author Statement more info	PubMed
located_in cytoplasmic ribonucleoprotein granule	IDA Inferred from Direct Assay more info
located_in cytosol	TAS Traceable Author Statement more info
is_active_in nuclear speck	IBA Inferred from Biological aspect of Ancestor more info
located_in nuclear speck	IDA Inferred from Direct Assay more info	PubMed
located_in nucleoplasm	TAS Traceable Author Statement more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: polymerase delta-interacting protein 3

Names: 46 kDa DNA polymerase delta interaction protein; RNA-binding protein P46; S6K1 Aly/REF-like target; polymerase (DNA) delta interacting protein 3; polymerase (DNA-directed), delta interacting protein 3

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)

NM_001278657.2 → NP_001265586.1 polymerase delta-interacting protein 3 isoform 3

Status: REVIEWED

Description

Transcript Variant: This variant (3) uses an alternate in-frame splice site, compared to variant 1. The encoded isoform (3) is longer than isoform 1.

Source sequence(s)

AK303419, AL137743, DC368557

Consensus CDS

CCDS74873.1

UniProtKB/TrEMBL

B4E0L0, F6VRR5

Related

ENSP00000397927.3, ENST00000451060.6

Conserved Domains (2) summary

COG0724
Location:301 → 424

RRM; RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis]

cd12681
Location:297 → 365

RRM_SKAR; RNA recognition motif in S6K1 Aly/REF-like target (SKAR) and similar proteins
NM_001363052.2 → NP_001349981.1 polymerase delta-interacting protein 3 isoform 4

Status: REVIEWED

Description

Transcript Variant: This variant (5) lacks an alternate exon in the 3' coding region, compared to variant 1. The encoded isoform (4) has a shorter and distinct C-terminus, compared to isoform 1.

Source sequence(s)

AL137743, Z93241

UniProtKB/TrEMBL

Q96DI9

Conserved Domains (1) summary

cd12681
Location:280 → 341

RRM_SKAR; RNA recognition motif in S6K1 Aly/REF-like target (SKAR) and similar proteins
NM_032311.5 → NP_115687.2 polymerase delta-interacting protein 3 isoform 1

See identical proteins and their annotated locations for NP_115687.2

Status: REVIEWED

Description

Transcript Variant: This variant (1) encodes isoform 1.

Source sequence(s)

AL160111, DC368557

Consensus CDS

CCDS14038.1

UniProtKB/Swiss-Prot

A8K6F8, A8K6V9, Q009A7, Q5H972, Q6PGN6, Q7Z6Z0, Q9BY77, Q9NSP5, Q9NSP6

UniProtKB/TrEMBL

Q96DI9

Related

ENSP00000252115.5, ENST00000252115.10

Conserved Domains (2) summary

COG0724
Location:284 → 407

RRM; RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis]

cd12681
Location:280 → 348

RRM_SKAR; RNA recognition motif in S6K1 Aly/REF-like target (SKAR) and similar proteins
NM_178136.3 → NP_835237.1 polymerase delta-interacting protein 3 isoform 2

See identical proteins and their annotated locations for NP_835237.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) lacks an alternate in-frame exon, compared to variant 1. The encoded isoform (2) is shorter than isoform 1.

Source sequence(s)

AL160112, DC368557

Consensus CDS

CCDS14039.1

UniProtKB/TrEMBL

Q96DI9

Related

ENSP00000252116.5, ENST00000348657.6

Conserved Domains (2) summary

COG0724
Location:255 → 378

RRM; RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis]

cd12681
Location:251 → 319

RRM_SKAR; RNA recognition motif in S6K1 Aly/REF-like target (SKAR) and similar proteins

RNA

NR_103820.2 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (4) uses an alternate splice site at an internal exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AL137743, DC368557

Related

ENST00000445215.5