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Aliases for PATL1 Gene

Aliases for PATL1 Gene

  • PAT1 Homolog 1, Processing Body MRNA Decay Factor 2 3 5
  • Protein PAT1 Homolog B 3 4
  • PAT1-Like Protein 1 3 4
  • HPat1b 3 4
  • Pat1b 3 4
  • Protein Associated With Topoisomerase II Homolog 1 (Yeast) 2
  • Protein Associated With Topoisomerase II Homolog 1 3
  • Protein PAT1 Homolog 1 3

External Ids for PATL1 Gene

Previous GeneCards Identifiers for PATL1 Gene

  • GC11M059161
  • GC11M059404
  • GC11M055751

Summaries for PATL1 Gene

GeneCards Summary for PATL1 Gene

PATL1 (PAT1 Homolog 1, Processing Body MRNA Decay Factor) is a Protein Coding gene. Diseases associated with PATL1 include Hepatitis C Virus. Among its related pathways are Gene Expression and Deadenylation-dependent mRNA decay. Gene Ontology (GO) annotations related to this gene include poly(U) RNA binding. An important paralog of this gene is PATL2.

UniProtKB/Swiss-Prot for PATL1 Gene

  • RNA-binding protein involved in deadenylation-dependent decapping of mRNAs, leading to the degradation of mRNAs. Acts as a scaffold protein that connects deadenylation and decapping machinery. Required for cytoplasmic mRNA processing body (P-body) assembly. In case of infection, required for translation and replication of hepatitis C virus (HCV).

Additional gene information for PATL1 Gene

No data available for Entrez Gene Summary , CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PATL1 Gene

Genomics for PATL1 Gene

GeneHancer (GH) Regulatory Elements for PATL1 Gene

Promoters and enhancers for PATL1 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH11I059666 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 563.1 +0.3 313 3.8 HDGF PKNOX1 FOXA2 SMAD1 MLX ARNT ARID4B SIN3A YY1 SLC30A9 PATL1 LOC105369318 STX3 LOC101927226 ENSG00000255008 MS4A6A
GH11I059544 Enhancer 1.8 FANTOM5 Ensembl ENCODE dbSUPER 44.9 +119.9 119932 8.8 FEZF1 DMAP1 IRF4 YY1 SLC30A9 ZNF213 E2F8 ZNF416 ZNF143 ZNF548 GC11M059554 GC11P059550 TRV-TAC1-1 TRV-TAC2-1 ENSG00000269570 LOC101927226 PATL1 ENSG00000255008 FAM111A-DT STX3
GH11I059141 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 21.3 +524.9 524947 5 HDGF PKNOX1 FOXA2 ARID4B SIN3A DMAP1 ZNF2 YY1 E2F8 ZNF207 FAM111A ENSG00000255381 FAM111A-DT LOC100422399 ENSG00000269570 LOC101927226 PATL1 STX3 ENSG00000255008 OR5A2
GH11I059809 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 19.2 -141.5 -141514 2.2 PKNOX1 CLOCK SMAD1 ARNT ZFP64 ARID4B SIN3A DMAP1 ZNF2 IRF4 MRPL16 LOC101927226 PATL1 FAM111A-DT FAM111A STX3 GC11P059803 GC11P059703
GH11I059106 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE dbSUPER 12.3 +561.2 561177 3.4 PKNOX1 ZFP64 ARID4B SIN3A FEZF1 DMAP1 E2F8 ATF7 KLF7 ZNF548 FAM111B ENSG00000269570 ENSG00000255008 LOC101927226 ZFP91 PATL1 STX3 ENSG00000255299 FAM111A FABP5P7
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around PATL1 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the PATL1 gene promoter:

Genomic Locations for PATL1 Gene

Genomic Locations for PATL1 Gene
chr11:59,636,716-59,669,040
(GRCh38/hg38)
Size:
32,325 bases
Orientation:
Minus strand
chr11:59,404,189-59,436,511
(GRCh37/hg19)

Genomic View for PATL1 Gene

Genes around PATL1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PATL1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PATL1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PATL1 Gene

Proteins for PATL1 Gene

  • Protein details for PATL1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q86TB9-PATL1_HUMAN
    Recommended name:
    Protein PAT1 homolog 1
    Protein Accession:
    Q86TB9
    Secondary Accessions:
    • B3KXT9
    • Q2TA86
    • Q6P166
    • Q8N9M6
    • Q8NI63

    Protein attributes for PATL1 Gene

    Size:
    770 amino acids
    Molecular mass:
    86850 Da
    Quaternary structure:
    • Interacts (via region A) with DDX6/RCK. Interacts (via region H and region C) with LSM1 and LSM4. Interacts (via region N) with DCP1A, DCP2, EDC3, EDC4 and XRN1. Interacts with the CCR4-NOT complex. Interacts with the Lsm-containing SMN-Sm protein complex.
    SequenceCaution:
    • Sequence=CAD89916.1; Type=Erroneous initiation; Note=Translation N-terminally shortened.; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for PATL1 Gene

    Alternative splice isoforms for PATL1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for PATL1 Gene

Post-translational modifications for PATL1 Gene

No Post-translational modifications

Other Protein References for PATL1 Gene

No data available for DME Specific Peptides for PATL1 Gene

Domains & Families for PATL1 Gene

Gene Families for PATL1 Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for PATL1 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for PATL1 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q86TB9

UniProtKB/Swiss-Prot:

PATL1_HUMAN :
  • The region A, also named N-term, mediates the interaction with DDX6/RCK and is required for cytoplasmic mRNA processing body assembly.
  • Belongs to the PAT1 family.
Domain:
  • The region A, also named N-term, mediates the interaction with DDX6/RCK and is required for cytoplasmic mRNA processing body assembly.
  • The region C, also named Pat-C, is required for RNA-binding and mediates the binding with the Lsm-containing SMN-Sm protein complex and the decapping machinery. It folds into an alpha-alpha superhelix, exposing conserved and basic residues on one side of the domain.
Family:
  • Belongs to the PAT1 family.
genes like me logo Genes that share domains with PATL1: view

Function for PATL1 Gene

Molecular function for PATL1 Gene

UniProtKB/Swiss-Prot Function:
RNA-binding protein involved in deadenylation-dependent decapping of mRNAs, leading to the degradation of mRNAs. Acts as a scaffold protein that connects deadenylation and decapping machinery. Required for cytoplasmic mRNA processing body (P-body) assembly. In case of infection, required for translation and replication of hepatitis C virus (HCV).

Gene Ontology (GO) - Molecular Function for PATL1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003723 RNA binding IEA,IDA 20543818
GO:0005515 protein binding IPI 20543818
GO:0008266 poly(U) RNA binding IDA 20826699
GO:0034046 poly(G) binding IDA 20826699
genes like me logo Genes that share ontologies with PATL1: view
genes like me logo Genes that share phenotypes with PATL1: view

Animal Models for PATL1 Gene

MGI Knock Outs for PATL1:

Animal Model Products

CRISPR Products

Inhibitory RNA Products

No data available for Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for PATL1 Gene

Localization for PATL1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PATL1 Gene

Cytoplasm, P-body. Nucleus. Nucleus, PML body. Nucleus speckle. Note=Predominantly cytoplasmic. Shuttles between the nucleus and the cytoplasm in a CRM1-dependent manner. Enriched in splicing speckles. Localization to nuclear foci and speckles requires active transcription. Excluded from the nucleolus.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for PATL1 gene
Compartment Confidence
nucleus 5
cytosol 5

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytoplasmic bodies (3)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for PATL1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000932 P-body IEA,IDA 20543818
GO:0005634 nucleus IEA --
GO:0005737 cytoplasm IEA --
GO:0005829 cytosol TAS --
GO:0016605 PML body IEA --
genes like me logo Genes that share ontologies with PATL1: view

Pathways & Interactions for PATL1 Gene

genes like me logo Genes that share pathways with PATL1: view

Pathways by source for PATL1 Gene

1 Cell Signaling Technology pathway for PATL1 Gene
1 KEGG pathway for PATL1 Gene

Gene Ontology (GO) - Biological Process for PATL1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000290 deadenylation-dependent decapping of nuclear-transcribed mRNA IDA 20584987
GO:0033962 cytoplasmic mRNA processing body assembly IDA 20584987
GO:0043928 exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay TAS --
genes like me logo Genes that share ontologies with PATL1: view

No data available for SIGNOR curated interactions for PATL1 Gene

Drugs & Compounds for PATL1 Gene

No Compound Related Data Available

Transcripts for PATL1 Gene

Unigene Clusters for PATL1 Gene

Protein associated with topoisomerase II homolog 1 (yeast):
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Alternative Splicing Database (ASD) splice patterns (SP) for PATL1 Gene

ExUns: 1a · 1b ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11a · 11b ^ 12 ^ 13 ^ 14a · 14b ^ 15 ^ 16a · 16b ^ 17a · 17b ^ 18 ^ 19
SP1: -
SP2: - - - -
SP3:

Relevant External Links for PATL1 Gene

GeneLoc Exon Structure for
PATL1
ECgene alternative splicing isoforms for
PATL1

Expression for PATL1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for PATL1 Gene

Protein differential expression in normal tissues from HIPED for PATL1 Gene

This gene is overexpressed in Serum (28.3), Liver, secretome (6.4), and Placenta (6.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for PATL1 Gene



Protein tissue co-expression partners for PATL1 Gene

NURSA nuclear receptor signaling pathways regulating expression of PATL1 Gene:

PATL1

SOURCE GeneReport for Unigene cluster for PATL1 Gene:

Hs.591960

mRNA Expression by UniProt/SwissProt for PATL1 Gene:

Q86TB9-PATL1_HUMAN
Tissue specificity: Ubiquitous.

Evidence on tissue expression from TISSUES for PATL1 Gene

  • Liver(4.4)
  • Muscle(4.4)
  • Eye(4.1)
  • Nervous system(2.3)
genes like me logo Genes that share expression patterns with PATL1: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for PATL1 Gene

Orthologs for PATL1 Gene

This gene was present in the common ancestor of chordates.

Orthologs for PATL1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia PATL1 33 34
  • 99.35 (n)
dog
(Canis familiaris)
Mammalia PATL1 33 34
  • 92.81 (n)
mouse
(Mus musculus)
Mammalia Patl1 33 16 34
  • 92.68 (n)
rat
(Rattus norvegicus)
Mammalia Patl1 33
  • 92.38 (n)
cow
(Bos Taurus)
Mammalia PATL1 33 34
  • 91.6 (n)
oppossum
(Monodelphis domestica)
Mammalia PATL1 34
  • 89 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia -- 34
  • 86 (a)
OneToMany
-- 34
  • 83 (a)
OneToMany
chicken
(Gallus gallus)
Aves PATL1 34
  • 79 (a)
OneToOne
OSBP 33
  • 71.79 (n)
lizard
(Anolis carolinensis)
Reptilia PATL1 34
  • 80 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia patl1 33
  • 63.78 (n)
African clawed frog
(Xenopus laevis)
Amphibia Xl.6630 33
zebrafish
(Danio rerio)
Actinopterygii patl1 33 34
  • 57.29 (n)
wufa11d04 33
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.8716 33
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 32 (a)
OneToMany
Species where no ortholog for PATL1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for PATL1 Gene

ENSEMBL:
Gene Tree for PATL1 (if available)
TreeFam:
Gene Tree for PATL1 (if available)

Paralogs for PATL1 Gene

Paralogs for PATL1 Gene

(1) SIMAP similar genes for PATL1 Gene using alignment to 1 proteins:

Pseudogenes.org Pseudogenes for PATL1 Gene

genes like me logo Genes that share paralogs with PATL1: view

Variants for PATL1 Gene

Sequence variations from dbSNP and Humsavar for PATL1 Gene

SNP ID Clin Chr 11 pos Variation AA Info Type
rs1000041207 -- 59,642,766(-) T/G intron_variant
rs1000096781 -- 59,650,125(-) A/G intron_variant
rs1000150316 -- 59,639,398(-) A/G intron_variant
rs1000502710 -- 59,655,066(-) C/T intron_variant
rs1000567887 -- 59,647,210(-) A/T intron_variant

Structural Variations from Database of Genomic Variants (DGV) for PATL1 Gene

Variant ID Type Subtype PubMed ID
esv2469731 CNV insertion 19546169
nsv1070038 CNV deletion 25765185
nsv819971 CNV loss 19587683
nsv832172 CNV loss 17160897

Variation tolerance for PATL1 Gene

Residual Variation Intolerance Score: 46.4% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.30; 41.14% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for PATL1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
PATL1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PATL1 Gene

Disorders for PATL1 Gene

MalaCards: The human disease database

(1) MalaCards diseases for PATL1 Gene - From: GeneCards

Disorder Aliases PubMed IDs
hepatitis c virus
  • hepatitis c virus, susceptibility to
- elite association - COSMIC cancer census association via MalaCards
Search PATL1 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for PATL1

genes like me logo Genes that share disorders with PATL1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for PATL1 Gene

Publications for PATL1 Gene

  1. Identification of PatL1, a human homolog to yeast P body component Pat1. (PMID: 17936923) Scheller N … Díez J (Biochimica et biophysica acta 2007) 2 3 4 58
  2. RNA-related nuclear functions of human Pat1b, the P-body mRNA decay factor. (PMID: 22090346) Marnef A … Standart N (Molecular biology of the cell 2012) 3 4 58
  3. The human Pat1b protein: a novel mRNA deadenylation factor identified by a new immunoprecipitation technique. (PMID: 20852261) Totaro A … Achsel T (Nucleic acids research 2011) 3 4 58
  4. The C-terminal alpha-alpha superhelix of Pat is required for mRNA decapping in metazoa. (PMID: 20543818) Braun JE … Izaurralde E (The EMBO journal 2010) 3 4 58
  5. Human Pat1b connects deadenylation with mRNA decapping and controls the assembly of processing bodies. (PMID: 20584987) Ozgur S … Stoecklin G (Molecular and cellular biology 2010) 3 4 58

Products for PATL1 Gene

Sources for PATL1 Gene

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