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PPWD1 peptidylprolyl isomerase domain and WD repeat containing 1 [ Homo sapiens (human) ]

Gene ID: 23398, updated on 14-Nov-2024

Summary

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Official Symbol
PPWD1provided by HGNC
Official Full Name
peptidylprolyl isomerase domain and WD repeat containing 1provided by HGNC
Primary source
HGNC:HGNC:28954
See related
Ensembl:ENSG00000113593 MIM:618274; AllianceGenome:HGNC:28954
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 peptidyl-prolyl cis-trans isomerase activity. Predicted to be involved in mRNA splicing, via spliceosome. Located in nuclear body. Part of catalytic step 2 spliceosome. [provided by Alliance of Genome Resources, Nov 2024]
Expression
Ubiquitous expression in lymph node (RPKM 13.9), appendix (RPKM 11.8) and 25 other tissues See more
Orthologs
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Genomic context

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See PPWD1 in Genome Data Viewer
Location:
5q12.3
Exon count:
13
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (65563296..65587549)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (66385056..66409311)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (64859123..64883376)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124900986 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:64780998-64781506 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:64781507-64782013 Neighboring gene centromere protein K Neighboring gene MPRA-validated peak5269 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:64855281-64855780 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:64858250-64858911 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:64858912-64859572 Neighboring gene tripartite motif containing 23 Neighboring gene RNA, U6 small nuclear 540, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22607 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22608 Neighboring gene trafficking protein particle complex subunit 13 Neighboring gene shieldin complex subunit 3

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 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. The crystal structure of human WD40 repeat-containing peptidylprolyl isomerase (PPWD1). Davis TL, et al. FEBS J, 2008 May. PMID 18397323
  2. Long non-coding RNA RP11-284F21.9 functions as a ceRNA regulating PPWD1 by competitively binding to miR-769-3p in cervical carcinoma. Han HF, et al. Biosci Rep, 2020 Sep 30. PMID 32936290, Free PMC Article
  3. Structural and biochemical characterization of the human cyclophilin family of peptidyl-prolyl isomerases. Davis TL, et al. PLoS Biol, 2010 Jul 27. PMID 20676357, Free PMC Article
  4. Prediction of the coding sequences of unidentified human genes. II. The coding sequences of 40 new genes (KIAA0041-KIAA0080) deduced by analysis of cDNA clones from human cell line KG-1. Nomura N, et al. DNA Res, 1994. PMID 7584044
  5. Binding of USP4 to cortactin enhances cell migration in HCT116 human colon cancer cells. Yun SI, et al. FASEB J, 2023 May. PMID 37039823

See all (44) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Long non-coding RNA RP11-284F21.9 functions as a ceRNA regulating PPWD1 by competitively binding to miR-769-3p in cervical carcinoma.
    Title: Long non-coding RNA RP11-284F21.9 functions as a ceRNA regulating PPWD1 by competitively binding to miR-769-3p in cervical carcinoma.
  2. The crystal structure of human PPWD1 was studied.
    Title: The crystal structure of human WD40 repeat-containing peptidylprolyl isomerase (PPWD1).
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)

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ33156, FLJ36356, KIAA0073

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables RNA polymerase II CTD heptapeptide repeat P3 isomerase activity IEA
Inferred from Electronic Annotation
more info
  
enables RNA polymerase II CTD heptapeptide repeat P6 isomerase activity IEA
Inferred from Electronic Annotation
more info
  
enables peptidyl-prolyl cis-trans isomerase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables peptidyl-prolyl cis-trans isomerase activity IDA
Inferred from Direct Assay
more info
 PubMed 
Process Evidence Code Pubs
involved_in mRNA splicing, via spliceosome IC
Inferred by Curator
more info
 PubMed 
involved_in protein folding IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in regulation of transcription by RNA polymerase II IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
part_of catalytic step 2 spliceosome IDA
Inferred from Direct Assay
more info
 PubMed 
located_in nuclear body IDA
Inferred from Direct Assay
more info
  
located_in nucleoplasm TAS
Traceable Author Statement
more info
  

General protein information

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Preferred Names
peptidylprolyl isomerase domain and WD repeat-containing protein 1
Names
epididymis secretory sperm binding protein
spliceosome-associated cyclophilin
NP_001265855.1
NP_001265856.1
NP_001265858.1
NP_056157.1
XP_047273004.1
XP_047273005.1
XP_054208223.1
XP_054208224.1

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_001278926.2 → NP_001265855.1  peptidylprolyl isomerase domain and WD repeat-containing protein 1 isoform 2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) includes an alternate exon in the 5' region and uses a downstream start codon, compared to variant 1. It encodes isoform 2 which is shorter and has a distinct N-terminus, compared to isoform 1.
    Source sequence(s)
    AC008560, AK300022, BC015385
    Consensus CDS
    CCDS64161.1
    UniProtKB/TrEMBL
    B4DT22, F5H7P7
    Related
    ENSP00000442371.1, ENST00000535264.5
    Conserved Domains (4) summary
    COG2319
    Location:59 → 276
    WD40; WD40 repeat [General function prediction only]
    cd01927
    Location:465 → 613
    cyclophilin_WD40; cyclophilin_WD40: cyclophilin-type peptidylprolyl cis- trans isomerases (cyclophilins) having a WD40 domain. This group consists of several hypothetical and putative eukaryotic and bacterial proteins which have a cyclophilin domain and a WD40 domain. ...
    sd00039
    Location:106 → 147
    7WD40; WD40 repeat [structural motif]
    cl02567
    Location:59 → 288
    WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...

  2. NM_001278927.2 → NP_001265856.1  peptidylprolyl isomerase domain and WD repeat-containing protein 1 isoform 3

    See identical proteins and their annotated locations for NP_001265856.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) uses an alternate splice site and uses a downstream start codon compared to variant 1. It encodes isoform 3 which is shorter and has a distinct N-terminus compared to isoform 1. Translation is predicted to
    Source sequence(s)
    AC008560, AK298175, BC015385, DB454273
    UniProtKB/TrEMBL
    B4DP34
    Conserved Domains (4) summary
    COG2319
    Location:51 → 189
    WD40; WD40 repeat [General function prediction only]
    cd01927
    Location:355 → 503
    cyclophilin_WD40; cyclophilin_WD40: cyclophilin-type peptidylprolyl cis- trans isomerases (cyclophilins) having a WD40 domain. This group consists of several hypothetical and putative eukaryotic and bacterial proteins which have a cyclophilin domain and a WD40 domain. ...
    sd00039
    Location:39 → 81
    7WD40; WD40 repeat [structural motif]
    cl02567
    Location:53 → 178
    WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...

  3. NM_001278929.2 → NP_001265858.1  peptidylprolyl isomerase domain and WD repeat-containing protein 1 isoform 4

    See identical proteins and their annotated locations for NP_001265858.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) lacks an exon in the 5' region and uses a downstream start codon, compared to variant 1. It encodes isoform 4 which has a shorter N-terminus compared to isoform 1.
    Source sequence(s)
    AC008560, AK301654, BC015385, D38552, DB454273
    Consensus CDS
    CCDS64162.1
    UniProtKB/Swiss-Prot
    Q96BP3
    Related
    ENSP00000444496.1, ENST00000538977.5
    Conserved Domains (4) summary
    COG2319
    Location:35 → 173
    WD40; WD40 repeat [General function prediction only]
    cd01927
    Location:339 → 487
    cyclophilin_WD40; cyclophilin_WD40: cyclophilin-type peptidylprolyl cis- trans isomerases (cyclophilins) having a WD40 domain. This group consists of several hypothetical and putative eukaryotic and bacterial proteins which have a cyclophilin domain and a WD40 domain. ...
    sd00039
    Location:23 → 65
    7WD40; WD40 repeat [structural motif]
    cl02567
    Location:37 → 162
    WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...

  4. NM_015342.4 → NP_056157.1  peptidylprolyl isomerase domain and WD repeat-containing protein 1 isoform 1

    See identical proteins and their annotated locations for NP_056157.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (1).
    Source sequence(s)
    BM669378, D38552, DB454273
    Consensus CDS
    CCDS3985.1
    UniProtKB/Swiss-Prot
    B4DWR9, Q15002, Q7KZ89, Q96BP3
    UniProtKB/TrEMBL
    A0A384MTS1, B4DT22
    Related
    ENSP00000261308.4, ENST00000261308.10
    Conserved Domains (3) summary
    cd01927
    Location:495 → 643
    cyclophilin_WD40; cyclophilin-type peptidylprolyl cis- trans isomerases (cyclophilins) having a WD40 domain. This group consists of several hypothetical and putative eukaryotic and bacterial proteins which have a cyclophilin domain and a WD40 domain. Function of the ...
    sd00039
    Location:136 → 177
    7WD40; WD40 repeat [structural motif]
    cl29593
    Location:89 → 318
    WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...

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
    65563296..65587549
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047417048.1 → XP_047273004.1  peptidylprolyl isomerase domain and WD repeat-containing protein 1 isoform X1

  2. XM_047417049.1 → XP_047273005.1  peptidylprolyl isomerase domain and WD repeat-containing protein 1 isoform X2

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    66385056..66409311
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054352248.1 → XP_054208223.1  peptidylprolyl isomerase domain and WD repeat-containing protein 1 isoform X1

  2. XM_054352249.1 → XP_054208224.1  peptidylprolyl isomerase domain and WD repeat-containing protein 1 isoform X2

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q96BP3.1 GenPept UniProtKB/Swiss-Prot:Q96BP3

Gene LinkOut

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