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

    Gene ID: 23398, updated on 27-Dec-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 protein folding. Located in nuclear body. Part of catalytic step 2 spliceosome. [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Ubiquitous expression in lymph node (RPKM 13.9), appendix (RPKM 11.8) and 25 other tissues See more
    Orthologs
    mouse all
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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: 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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    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

      UniProtKB/TrEMBL
      B4DT22

    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

      UniProtKB/TrEMBL
      B4DT22

    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

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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