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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 Deadenylation-dependent mRNA decay and Translational Control. GO annotations related to this gene include poly(A) RNA binding and 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).

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

Genomics for PATL1 Gene

Regulatory Elements for PATL1 Gene

Enhancers for PATL1 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH11F059220 1.1 FANTOM5 ENCODE 15.9 +446.2 446225 4.7 CTCF JUN CEBPB JUNB EP300 NR2F2 RFX5 JUND ZNF512 FOS PATL1 MPEG1 DTX4 OR4D6 OR5A2 OR5A1 OR5AN1 FAM111A OSBP RN7SL42P
GH11F059753 1.5 FANTOM5 ENCODE 9.4 -86.6 -86647 4.3 HDGF PKNOX1 ARID4B SIN3A DMAP1 ZNF2 ZNF143 ZNF207 FOS DEK STX3 PATL1 LOC101927226 MS4A6A OSBP FABP5P7
GH11F059270 1.4 FANTOM5 Ensembl ENCODE 8 +396.0 396040 4.4 PKNOX1 ESRRA BMI1 EBF1 RELA EED ZNF143 ETV6 CREM CHD2 STX3 PATL1 MPEG1 OSBP FAM111A GC11M059264 ENSG00000214797
GH11F059215 1.2 FANTOM5 ENCODE 8.8 +451.9 451872 2.5 PKNOX1 TBL1XR1 BMI1 EGR1 ETV6 RCOR1 CREM CBFB JUNB TBX21 DTX4 MPEG1 PATL1 FAM111A OSBP RN7SL42P WARSP1
GH11F059197 1.5 FANTOM5 Ensembl ENCODE 6.3 +469.9 469910 3.0 TBP PKNOX1 MXI1 MAX YBX1 CEBPG BMI1 EBF1 ZBTB40 RELA DTX4 OR5A2 OR5AN1 MPEG1 PATL1 OR4D6 FAM111A GC11M058947
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around PATL1 on UCSC Golden Path with GeneCards custom track

Promoters for PATL1 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000109392 -60 3001 HDGF PKNOX1 CREB3L1 MLX WRNIP1 ARID4B SIN3A YY1 SLC30A9 ZNF207

Genomic Location for PATL1 Gene

Chromosome:
11
Start:
59,636,716 bp from pter
End:
59,669,040 bp from pter
Size:
32,325 bases
Orientation:
Minus strand

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

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for PATL1 Gene

No data available for DME Specific Peptides for PATL1 Gene

Domains & Families for PATL1 Gene

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

No data available for Gene Families for PATL1 Gene

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
GO:0044822 poly(A) RNA binding IDA 22658674
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

Inhibitory RNA Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , 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

Gene Ontology (GO) - Cellular Components for PATL1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000932 cytoplasmic mRNA processing 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

Transcripts for PATL1 Gene

Unigene Clusters for PATL1 Gene

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

Inhibitory RNA Products

Flow Cytometry 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 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.
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 and mRNA differential expression in normal tissues 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 34 35
  • 99.35 (n)
dog
(Canis familiaris)
Mammalia PATL1 34 35
  • 92.81 (n)
mouse
(Mus musculus)
Mammalia Patl1 34 16 35
  • 92.68 (n)
rat
(Rattus norvegicus)
Mammalia Patl1 34
  • 92.38 (n)
cow
(Bos Taurus)
Mammalia PATL1 34 35
  • 91.6 (n)
oppossum
(Monodelphis domestica)
Mammalia PATL1 35
  • 89 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia -- 35
  • 86 (a)
OneToMany
-- 35
  • 83 (a)
OneToMany
chicken
(Gallus gallus)
Aves PATL1 35
  • 79 (a)
OneToOne
OSBP 34
  • 71.79 (n)
lizard
(Anolis carolinensis)
Reptilia PATL1 35
  • 80 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia patl1 34
  • 63.78 (n)
African clawed frog
(Xenopus laevis)
Amphibia Xl.6630 34
zebrafish
(Danio rerio)
Actinopterygii patl1 34 35
  • 57.29 (n)
wufa11d04 34
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.8716 34
sea squirt
(Ciona savignyi)
Ascidiacea -- 35
  • 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 Sequence Context AA Info Type
rs1009425 -- 59,639,685(+) CATGG(A/G)TAATG intron-variant
rs1009712 -- 59,642,493(-) agctg(G/T)ccatc intron-variant
rs1055215 -- 59,639,664(+) TAAAA(A/G)ATGGT intron-variant
rs10627707 -- 59,652,150(+) CTCTC(-/TT)TGTTA intron-variant
rs111432802 -- 59,668,783(+) CCGCC(C/T)CCTGC intron-variant, upstream-variant-2KB

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

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

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)

Relevant External Links 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
  • hepatitic c virus
- elite association - COSMIC cancer census association via MalaCards
Search PATL1 in MalaCards View complete list of genes associated with diseases

Relevant External Links for PATL1

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
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. … Diez J. (Biochim. Biophys. Acta 2007) 2 3 4 64
  2. RNA-related nuclear functions of human Pat1b, the P-body mRNA decay factor. (PMID: 22090346) Marnef A. … Standart N. (Mol. Biol. Cell 2012) 3 4 64
  3. The human Pat1b protein: a novel mRNA deadenylation factor identified by a new immunoprecipitation technique. (PMID: 20852261) Totaro A. … Achsel T. (Nucleic Acids Res. 2011) 3 4 64
  4. The C-terminal alpha-alpha superhelix of Pat is required for mRNA decapping in metazoa. (PMID: 20543818) Braun J.E. … Izaurralde E. (EMBO J. 2010) 3 4 64
  5. Human Pat1b connects deadenylation with mRNA decapping and controls the assembly of processing bodies. (PMID: 20584987) Ozgur S. … Stoecklin G. (Mol. Cell. Biol. 2010) 3 4 64

Products for PATL1 Gene

Sources for PATL1 Gene

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