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Aliases for PATL1 Gene

Aliases for PATL1 Gene

  • Protein Associated With Topoisomerase II Homolog 1 (Yeast) 2 3
  • Pat1b 3 4 6
  • Protein PAT1 Homolog B 3 4
  • PAT1-Like Protein 1 3 4
  • HPat1b 3 4
  • 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 (Protein Associated With Topoisomerase II Homolog 1 (Yeast)) is a Protein Coding gene. Among its related pathways are Gene Expression and Deadenylation-dependent mRNA decay. GO annotations related to this gene include RNA binding and poly(G) 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

Epigenetics Products

  • DNA Methylation CpG Assay Predesigned for Pyrosequencing in human,mouse,rat

Genomic Location for PATL1 Gene

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

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
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

Proteomics data for PATL1 Gene at MOPED

Post-translational modifications for PATL1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for PATL1 Gene

ENSEMBL proteins:
Reactome Protein details:
REFSEQ proteins:

Antibody Products

  • Cell Signaling Technology (CST) Antibodies for PATL1 (PATL1)

No data available for DME Specific Peptides for PATL1 Gene

Domains 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 :
  • Q86TB9
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 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

Animal Model Products

CRISPR Products

miRNA for PATL1 Gene

miRTarBase miRNAs that target PATL1

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for PATL1

In Situ Assay Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Phenotypes , Animal Models , Transcription Factor Targeting 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
Jensen Localization Image for PATL1 Gene COMPARTMENTS Subcellular localization image for PATL1 gene
Compartment Confidence
nucleus 5
cytosol 4

Gene Ontology (GO) - Cellular Components for PATL1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000932 cytoplasmic mRNA processing body IDA 20543818
GO:0005634 nucleus --
GO:0005829 cytosol TAS --
GO:0016605 PML body IEA --
GO:0016607 nuclear speck IEA --
genes like me logo Genes that share ontologies with PATL1: view

Pathways for PATL1 Gene

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

Pathways by source 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:0000288 nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay TAS --
GO:0000290 deadenylation-dependent decapping of nuclear-transcribed mRNA IDA 20584987
GO:0010467 gene expression TAS --
GO:0016070 RNA metabolic process --
GO:0016071 mRNA metabolic process --
genes like me logo Genes that share ontologies with PATL1: view

Transcripts for PATL1 Gene

Unigene Clusters for PATL1 Gene

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

CRISPR Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for PATL1

Primer 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 for PATL1 Gene

Protein differential expression in normal tissues for PATL1 Gene

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

Integrated Proteomics: protein expression from ProteomicsDB, PaxDb, MOPED, and MaxQB for PATL1 Gene

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 expressions with PATL1: view

Expression partners for PATL1 Gene

In Situ Assay 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
cow
(Bos Taurus)
Mammalia PATL1 35
  • 91.6 (n)
  • 95.45 (a)
PATL1 36
  • 96 (a)
OneToOne
dog
(Canis familiaris)
Mammalia PATL1 35
  • 92.81 (n)
  • 96.88 (a)
PATL1 36
  • 97 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Patl1 35
  • 92.68 (n)
  • 96.49 (a)
Patl1 16
Patl1 36
  • 96 (a)
OneToOne
chimpanzee
(Pan troglodytes)
Mammalia PATL1 35
  • 99.35 (n)
  • 99.22 (a)
PATL1 36
  • 99 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Patl1 35
  • 92.38 (n)
  • 95.97 (a)
oppossum
(Monodelphis domestica)
Mammalia PATL1 36
  • 89 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia -- 36
  • 86 (a)
OneToMany
-- 36
  • 83 (a)
OneToMany
chicken
(Gallus gallus)
Aves OSBP 35
  • 71.79 (n)
  • 79.7 (a)
PATL1 36
  • 79 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia PATL1 36
  • 80 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia patl1 35
  • 63.78 (n)
  • 63.64 (a)
African clawed frog
(Xenopus laevis)
Amphibia Xl.6630 35
zebrafish
(Danio rerio)
Actinopterygii patl1 35
  • 57.29 (n)
  • 55.52 (a)
wufa11d04 35
patl1 36
  • 46 (a)
OneToOne
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.8716 35
sea squirt
(Ciona savignyi)
Ascidiacea -- 36
  • 32 (a)
OneToMany
Species with no ortholog for PATL1:
  • 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

Selected 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 MAF
rs4040 -- 59,637,777(+) ATTAA(G/T)TACAA utr-variant-3-prime
rs13891 -- 59,637,786(+) AAGAT(A/T)GAACA utr-variant-3-prime
rs525107 -- 59,666,960(-) GTCTT(G/T)GGAGG missense, reference
rs525990 -- 59,666,869(-) ACATT(G/T)GGGTC missense, reference
rs1009425 -- 59,639,685(+) CATGG(A/G)TAATG intron-variant

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

Variant ID Type Subtype PubMed ID
nsv832172 CNV Loss 17160897
esv2469731 CNV Insertion 19546169
nsv819971 CNV Loss 19587683

Relevant External Links for PATL1 Gene

HapMap Linkage Disequilibrium report
PATL1

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

Disorders for PATL1 Gene

No disorders were found for PATL1 Gene.

No data available for MalaCards , OMIM , UniProtKB/Swiss-Prot , University of Copenhagen DISEASES , Novoseek inferred disease relationships , Genatlas and External Links 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
  2. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T. … Sugano S. (Nat. Genet. 2004) 3 4
  3. 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
  4. 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
  5. Distinct functions of maternal and somatic Pat1 protein paralogs. (PMID: 20826699) Marnef A. … Standart N. (RNA 2010) 3 4

Products for PATL1 Gene

Sources for PATL1 Gene

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