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PHACTR1 phosphatase and actin regulator 1 [ Homo sapiens (human) ]

Gene ID: 221692, updated on 28-Aug-2018

Summary

Official Symbol
PHACTR1provided by HGNC
Official Full Name
phosphatase and actin regulator 1provided by HGNC
Primary source
HGNC:HGNC:20990
See related
Ensembl:ENSG00000112137 MIM:608723; Vega:OTTHUMG00000014270
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
RPEL; RPEL1; dJ257A7.2
Summary
The protein encoded by this gene is a member of the phosphatase and actin regulator family of proteins. This family member can bind actin and regulate the reorganization of the actin cytoskeleton. It plays a role in tubule formation and in endothelial cell survival. Polymorphisms in this gene are associated with susceptibility to myocardial infarction, coronary artery disease and cervical artery dissection. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Apr 2016]
Expression
Biased expression in brain (RPKM 12.6), bone marrow (RPKM 5.8) and 12 other tissues See more
Orthologs

Genomic context

See PHACTR1 in Genome Data Viewer
Location:
6p24.1
Exon count:
20
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 6 NC_000006.12 (12716635..13290462)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (12716888..13290476)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene ribosomal protein L15 pseudogene 3 Neighboring gene long intergenic non-protein coding RNA 2530 Neighboring gene uncharacterized LOC107984015 Neighboring gene uncharacterized LOC105374935 Neighboring gene uncharacterized LOC105374934 Neighboring gene TBC1D7-LOC100130357 readthrough Neighboring gene uncharacterized LOC105374933 Neighboring gene RNA, U1 small nuclear 11, pseudogene Neighboring gene uncharacterized LOC100130357 Neighboring gene uncharacterized LOC105374936 Neighboring gene TBC1 domain family member 7

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 Jun 15 11:32:44 2016

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Phenotypes

NHGRI GWAS Catalog

Description
A genome-wide association study in europeans and South asians identifies 5 new Loci for coronary artery disease.
NHGRI GWA Catalog
A genome-wide association study in Europeans and South Asians identifies five new loci for coronary artery disease.
NHGRI GWA Catalog
Genome wide association study (GWAS) of Chagas cardiomyopathy in Trypanosoma cruzi seropositive subjects.
NHGRI GWA Catalog
Genome-wide association analysis identifies susceptibility loci for migraine without aura.
NHGRI GWA Catalog
Genome-wide association of early-onset myocardial infarction with single nucleotide polymorphisms and copy number variants.
NHGRI GWA Catalog
Genome-wide association study for coronary artery calcification with follow-up in myocardial infarction.
NHGRI GWA Catalog
Genome-wide association study in a Lebanese cohort confirms PHACTR1 as a major determinant of coronary artery stenosis.
NHGRI GWA Catalog
Genome-wide association study in Han Chinese identifies four new susceptibility loci for coronary artery disease.
NHGRI GWA Catalog
Genome-wide association with bone mass and geometry in the Framingham Heart Study.
NHGRI GWA Catalog
Genome-wide linkage and association scans for pulse pressure in Chinese twins.
NHGRI GWA Catalog
Genome-wide meta-analysis identifies new susceptibility loci for migraine.
NHGRI GWA Catalog
Large-scale association analysis identifies 13 new susceptibility loci for coronary artery disease.
NHGRI GWA Catalog
Shared genetic susceptibility to ischemic stroke and coronary artery disease: a genome-wide analysis of common variants.
NHGRI GWA Catalog

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • KIAA1733, MGC126575, MGC126577

Gene Ontology Provided by GOA

Function Evidence Code Pubs
actin binding ISS
Inferred from Sequence or Structural Similarity
more info
 
protein phosphatase 1 binding IEA
Inferred from Electronic Annotation
more info
 
protein phosphatase inhibitor activity IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
actin cytoskeleton reorganization ISS
Inferred from Sequence or Structural Similarity
more info
 
actomyosin structure organization IMP
Inferred from Mutant Phenotype
more info
PubMed 
cell motility IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of phosphoprotein phosphatase activity IEA
Inferred from Electronic Annotation
more info
 
stress fiber assembly IMP
Inferred from Mutant Phenotype
more info
PubMed 
Component Evidence Code Pubs
cell junction IEA
Inferred from Electronic Annotation
more info
 
cytosol ISS
Inferred from Sequence or Structural Similarity
more info
 
nucleus ISS
Inferred from Sequence or Structural Similarity
more info
 
synapse IEA
Inferred from Electronic Annotation
more info
 

General protein information

Preferred Names
phosphatase and actin regulator 1
Names
RPEL repeat containing 1

NCBI Reference Sequences (RefSeq)

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_001242648.2NP_001229577.1  phosphatase and actin regulator 1 isoform a

    See identical proteins and their annotated locations for NP_001229577.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1, 2, 3 and 4 all encode isoform a.
    Source sequence(s)
    AA809685, AK290017, AK295263, AL008729
    Consensus CDS
    CCDS75401.1
    UniProtKB/Swiss-Prot
    Q9C0D0
    UniProtKB/TrEMBL
    B4DHU0
    Related
    ENSP00000329880.8, OTTHUMP00000016044, ENST00000332995.11, OTTHUMT00000039880
    Conserved Domains (2) summary
    smart00707
    Location:461485
    RPEL; Repeat in Drosophila CG10860, human KIAA0680 and C. elegans F26H9.2
    pfam02755
    Location:139161
    RPEL; RPEL repeat
  2. NM_001322308.1NP_001309237.1  phosphatase and actin regulator 1 isoform a

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR compared to variant 1. Variants 1, 2, 3 and 4 all encode isoform a.
    Source sequence(s)
    AA809685, AK290017, AK295263, AL008729
    Consensus CDS
    CCDS75401.1
    UniProtKB/Swiss-Prot
    Q9C0D0
    UniProtKB/TrEMBL
    B4DHU0
    Conserved Domains (2) summary
    smart00707
    Location:461485
    RPEL; Repeat in Drosophila CG10860, human KIAA0680 and C. elegans F26H9.2
    pfam02755
    Location:139161
    RPEL; RPEL repeat
  3. NM_001322309.1NP_001309238.1  phosphatase and actin regulator 1 isoform a

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) differs in the 5' UTR compared to variant 1. Variants 1, 2, 3 and 4 all encode isoform a.
    Source sequence(s)
    AA809685, AK290017, AL008729, CR746945
    Consensus CDS
    CCDS75401.1
    UniProtKB/Swiss-Prot
    Q9C0D0
    Conserved Domains (2) summary
    smart00707
    Location:461485
    RPEL; Repeat in Drosophila CG10860, human KIAA0680 and C. elegans F26H9.2
    pfam02755
    Location:139161
    RPEL; RPEL repeat
  4. NM_001322310.1NP_001309239.1  phosphatase and actin regulator 1 isoform b

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) differs in the 5' UTR and includes an additional in-frame exon in the central coding region, compared to variant 1, resulting in an isoform (b) that is longer than isoform a.
    Source sequence(s)
    AA809685, AK290017, AK295263, AL008729
    UniProtKB/Swiss-Prot
    Q9C0D0
    UniProtKB/TrEMBL
    B4DHU0
    Conserved Domains (3) summary
    smart00707
    Location:530554
    RPEL; Repeat in Drosophila CG10860, human KIAA0680 and C. elegans F26H9.2
    pfam02755
    Location:139161
    RPEL; RPEL repeat
    cl25800
    Location:196311
    GGN; Gametogenetin
  5. NM_001322311.1NP_001309240.1  phosphatase and actin regulator 1 isoform c

    Status: REVIEWED

    Description
    Transcript Variant: This variant (6) lacks several 5' exons but contains an alternate 5' terminal exon, and it thus differs in the 5' UTR and initiates translation from a downstream in-frame start codon, compared to variant 1. The encoded isoform (c) is shorter at the N-terminus, compared to isoform a. Both variants 6 and 7 encode isoform c.
    Source sequence(s)
    AA809685, AL008729, AL598323, BC101526
    UniProtKB/Swiss-Prot
    Q9C0D0
    Conserved Domains (2) summary
    smart00707
    Location:369393
    RPEL; Repeat in Drosophila CG10860, human KIAA0680 and C. elegans F26H9.2
    pfam02755
    Location:4769
    RPEL; RPEL repeat
  6. NM_001322312.1NP_001309241.1  phosphatase and actin regulator 1 isoform c

    Status: REVIEWED

    Description
    Transcript Variant: This variant (7) lacks several 5' exons but contains an alternate 5' terminal exon, and it thus differs in the 5' UTR and initiates translation from a downstream in-frame start codon, compared to variant 1. The encoded isoform (c) is shorter at the N-terminus, compared to isoform a. Both variants 6 and 7 encode isoform c.
    Source sequence(s)
    AA809685, AL008729, BC101526, DB201185
    UniProtKB/Swiss-Prot
    Q9C0D0
    Conserved Domains (2) summary
    smart00707
    Location:369393
    RPEL; Repeat in Drosophila CG10860, human KIAA0680 and C. elegans F26H9.2
    pfam02755
    Location:4769
    RPEL; RPEL repeat
  7. NM_001322313.1NP_001309242.1  phosphatase and actin regulator 1 isoform d

    Status: REVIEWED

    Description
    Transcript Variant: This variant (8) lacks several 5' exons but contains an alternate 5' terminal exon, and it thus differs in the 5' UTR and initiates translation from a downstream in-frame start codon, and it also includes an additional in-frame exon in the central coding region, compared to variant 1. The encoded isoform (d) is shorter at the N-terminus, compared to isoform a.
    Source sequence(s)
    AA809685, AK290017, AK295263, AL008729, BX952169, DB201185
    UniProtKB/Swiss-Prot
    Q9C0D0
    UniProtKB/TrEMBL
    B4DHU0
    Conserved Domains (3) summary
    smart00707
    Location:438462
    RPEL; Repeat in Drosophila CG10860, human KIAA0680 and C. elegans F26H9.2
    pfam02755
    Location:4769
    RPEL; RPEL repeat
    cl25800
    Location:104219
    GGN; Gametogenetin
  8. NM_001322314.1NP_001309243.1  phosphatase and actin regulator 1 isoform e

    Status: REVIEWED

    Description
    Transcript Variant: This variant (9) lacks several 5' exons but contains an alternate 5' terminal exon, and it thus differs in the 5' UTR and initiates translation from an alternate start codon, and it also includes an additional in-frame exon in the central coding region, compared to variant 1. The encoded isoform (e) has a distinct N-terminus and is longer than isoform a.
    Source sequence(s)
    AA809685, AK290017, AK295263, AL008729, AL591682, BX952169
    UniProtKB/Swiss-Prot
    Q9C0D0
    UniProtKB/TrEMBL
    B4DHU0
    Conserved Domains (2) summary
    smart00707
    Location:531555
    RPEL; Repeat in Drosophila CG10860, human KIAA0680 and C. elegans F26H9.2
    pfam02755
    Location:141162
    RPEL; RPEL repeat
  9. NM_030948.3NP_112210.1  phosphatase and actin regulator 1 isoform a

    See identical proteins and their annotated locations for NP_112210.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes isoform a. Variants 1, 2, 3 and 4 all encode isoform a.
    Source sequence(s)
    AA809685, AK295263, AL008729, BC101526, DA253448
    Consensus CDS
    CCDS75401.1
    UniProtKB/Swiss-Prot
    Q9C0D0
    UniProtKB/TrEMBL
    B4DHU0
    Related
    ENSP00000368655.1, OTTHUMP00000016040, ENST00000379350.5, OTTHUMT00000039876
    Conserved Domains (2) summary
    smart00707
    Location:461485
    RPEL; Repeat in Drosophila CG10860, human KIAA0680 and C. elegans F26H9.2
    pfam02755
    Location:139161
    RPEL; RPEL repeat

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000006.12 Reference GRCh38.p12 Primary Assembly

    Range
    12716635..13290462
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017010457.2XP_016865946.1  phosphatase and actin regulator 1 isoform X2

  2. XM_017010461.2XP_016865950.1  phosphatase and actin regulator 1 isoform X5

  3. XM_017010455.2XP_016865944.1  phosphatase and actin regulator 1 isoform X2

  4. XM_017010460.2XP_016865949.1  phosphatase and actin regulator 1 isoform X5

  5. XM_017010454.2XP_016865943.1  phosphatase and actin regulator 1 isoform X2

  6. XM_017010459.2XP_016865948.1  phosphatase and actin regulator 1 isoform X5

  7. XM_005248934.3XP_005248991.1  phosphatase and actin regulator 1 isoform X3

    See identical proteins and their annotated locations for XP_005248991.1

    Conserved Domains (3) summary
    smart00707
    Location:530554
    RPEL; Repeat in Drosophila CG10860, human KIAA0680 and C. elegans F26H9.2
    pfam02755
    Location:139161
    RPEL; RPEL repeat
    cl25800
    Location:196311
    GGN; Gametogenetin
  8. XM_017010456.2XP_016865945.1  phosphatase and actin regulator 1 isoform X2

  9. XM_017010462.2XP_016865951.1  phosphatase and actin regulator 1 isoform X5

  10. XM_017010466.2XP_016865955.1  phosphatase and actin regulator 1 isoform X7

  11. XM_017010469.2XP_016865958.1  phosphatase and actin regulator 1 isoform X8

  12. XM_017010465.2XP_016865954.1  phosphatase and actin regulator 1 isoform X7

  13. XM_017010467.2XP_016865956.1  phosphatase and actin regulator 1 isoform X8

  14. XM_017010452.2XP_016865941.1  phosphatase and actin regulator 1 isoform X1

  15. XM_017010458.2XP_016865947.1  phosphatase and actin regulator 1 isoform X4

  16. XM_017010464.2XP_016865953.1  phosphatase and actin regulator 1 isoform X6

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