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CLP1 Gene

protein-coding   GIFtS: 57
GCID: GC11P057425

Cleavage And Polyadenylation Factor I Subunit 1

(Previous names: CLP1, cleavage and polyadenylation factor I subunit, homolog...)
  See CLP1-related disease
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
Cleavage And Polyadenylation Factor I Subunit 11 2     CLP1, Cleavage And Polyadenylation Factor I Subunit, Homolog (S.
Cerevisiae)1
Polyadenylation Factor Clp12 3     Polyribonucleotide 5'-Hydroxyl-Kinase1
Polynucleotide Kinase Clp12 3     ATP/GTP-Binding Protein2
Pre-MRNA Cleavage Complex II Protein Clp12 3     CLP1, Cleavage And Polyadenylation Factor I Subunit, Homolog2
HEAB2 3     hClp12
EC 2.7.1.783 8     Homolog Of Yeast CFIA Subunit Clp1p2
ATP/GTPbinding Protein1     Polyribonucleotide 5'-Hydroxyl-Kinase Clp12

External Ids:    HGNC: 169991   Entrez Gene: 109782   Ensembl: ENSG000001724097   OMIM: 6087575   UniProtKB: Q929893   

Export aliases for CLP1 gene to outside databases

Previous GC identifers: GC11P057182 GC11P053774


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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GeneCards Summary for CLP1 Gene:
CLP1 (cleavage and polyadenylation factor I subunit 1) is a protein-coding gene. Diseases associated with CLP1 include pontocerebellar hypoplasia, type 10. GO annotations related to this gene include ATP-dependent polyribonucleotide 5'-hydroxyl-kinase activity and ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity.

UniProtKB/Swiss-Prot: CLP1_HUMAN, Q92989
Function: Polynucleotide kinase that can phosphorylate the 5'-hydroxyl groups of double-stranded RNA (dsRNA),
single-stranded RNA (ssRNA), double-stranded DNA (dsDNA) and double-stranded DNA:RNA hybrids. dsRNA is
phosphorylated more efficiently than dsDNA, and the RNA component of a DNA:RNA hybrid is phosphorylated more
efficiently than the DNA component. Appears to have roles in both tRNA splicing and mRNA 3'-end formation.
Component of the tRNA splicing endonuclease complex. Phosphorylates the 5'-terminus of the tRNA 3'-exon during
tRNA splicing; this phosphorylation event is a prerequisite for the subsequent ligation of the two exon halves
and the production of a mature tRNA. Component of the pre-mRNA cleavage complex II (CF-II), which seems to be
required for mRNA 3'-end formation. Also phosphorylates the 5'-terminus of exogenously introduced short
interfering RNAs (siRNAs), which is a necessary prerequisite for their incorporation into the RNA-induced
silencing complex (RISC). However, endogenous siRNAs and microRNAs (miRNAs) that are produced by the cleavage of
dsRNA precursors by DICER1 already contain a 5'-phosphate group, so this protein may be dispensible for normal
RNA-mediated gene silencing




(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence at NCBI GenBank:
NC_000011.9  NT_167190.2  NC_018922.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the CLP1 gene promoter:
         C/EBPbeta   GCNF   Arnt   AREB6   CREB   IRF-2   NRF-2   deltaCREB   GCNF-1   GCNF-2   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmids (see all 2): CLP1 promoter sequence
   Search Chromatin IP Primers for CLP1

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat CLP1


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 11q12   Ensembl cytogenetic band:  11q12.1   HGNC cytogenetic band: 11q12.1

CLP1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
CLP1 gene location

GeneLoc information about chromosome 11         GeneLoc Exon Structure

GeneLoc location for GC11P057425:  view genomic region     (about GC identifiers)

Start:
57,416,465 bp from pter      End:
57,429,340 bp from pter
Size:
12,876 bases      Orientation:
plus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, Cloud-Clone Corp., and/or eBioscience,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., and/or eBioscience, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: CLP1_HUMAN, Q92989 (See protein sequence)
Recommended Name: Polyribonucleotide 5'-hydroxyl-kinase Clp1  
Size: 425 amino acids; 47646 Da
Cofactor: Magnesium, manganese or nickel
Subunit: Component of the tRNA splicing endonuclease complex, composed of CLP1, TSEN2, TSEN15, TSEN34 and TSEN54.
Component of pre-mRNA cleavage complex II (CF-II). Also associates with numerous components of the pre-mRNA
cleavage complex I (CF-I/CFIm), including NUDT21, CPSF2, CPSF3, CPSF6 and CPSF7. Interacts with CSTF2 and SYMPK
Secondary accessions: B2R7J6 B4DTI8
Alternative splicing: 2 isoforms:  Q92989-1   Q92989-2   

Explore the universe of human proteins at neXtProt for CLP1: NX_Q92989

Explore proteomics data for CLP1 at MOPED

Post-translational modifications: 

  • Ubiquitination2 at Lys127
  • Modification sites at PhosphoSitePlus
  • Selected DME Specific Peptides for CLP1 (Q92989) (see all 14)
     RDLPHFVRT  NRRASVSGC  CRLLLNYAVR  LSPAPRPLPK 


    See CLP1 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins (2 alternative transcripts): 
    NP_001136069.1  NP_006822.1  

    ENSEMBL proteins: 
     ENSP00000435287   ENSP00000433406   ENSP00000434995   ENSP00000431744   ENSP00000436066  
     ENSP00000304704  
    Reactome Protein details: Q92989

    CLP1 Human Recombinant Protein Products:

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    OriGene MassSpec for CLP1
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    Novus Biologicals CLP1 Proteins
    Novus Biologicals CLP1 Lysates
    Browse Sino Biological Recombinant Proteins
    Browse Sino Biological Cell Lysates
    Browse ProSpec Recombinant Proteins
    Cloud-Clone Corp. Proteins for CLP1

     
    Search eBioscience for Proteins for CLP1 

    CLP1 Antibody Products:

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    LSBio Antibodies in human, mouse, rat for CLP1

    CLP1 Assay Products:

    Browse Kits and Assays available from EMD Millipore
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    Browse Enzo Life Sciences for kits & assays
    Cloud-Clone Corp. ELISAs for CLP1
    Cloud-Clone Corp. CLIAs for CLP1
    Search eBioscience for ELISAs for CLP1 


    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    3 InterPro protein domains:
     IPR010655 Pre-mRNA_cleavage_cplxII_Clp1
     IPR028606 Clp1
     IPR027417 P-loop_NTPase

    Graphical View of Domain Structure for InterPro Entry Q92989

    ProtoNet protein and cluster: Q92989

    1 Blocks protein domain: IPB010655 Pre-mRNA cleavage complex II Clp1

    UniProtKB/Swiss-Prot: CLP1_HUMAN, Q92989
    Similarity: Belongs to the Clp1 family. Clp1 subfamily


    Find genes that share domains with CLP1           About GenesLikeMe


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: CLP1_HUMAN, Q92989
    Function: Polynucleotide kinase that can phosphorylate the 5'-hydroxyl groups of double-stranded RNA (dsRNA),
    single-stranded RNA (ssRNA), double-stranded DNA (dsDNA) and double-stranded DNA:RNA hybrids. dsRNA is
    phosphorylated more efficiently than dsDNA, and the RNA component of a DNA:RNA hybrid is phosphorylated more
    efficiently than the DNA component. Appears to have roles in both tRNA splicing and mRNA 3'-end formation.
    Component of the tRNA splicing endonuclease complex. Phosphorylates the 5'-terminus of the tRNA 3'-exon during
    tRNA splicing; this phosphorylation event is a prerequisite for the subsequent ligation of the two exon halves
    and the production of a mature tRNA. Component of the pre-mRNA cleavage complex II (CF-II), which seems to be
    required for mRNA 3'-end formation. Also phosphorylates the 5'-terminus of exogenously introduced short
    interfering RNAs (siRNAs), which is a necessary prerequisite for their incorporation into the RNA-induced
    silencing complex (RISC). However, endogenous siRNAs and microRNAs (miRNAs) that are produced by the cleavage of
    dsRNA precursors by DICER1 already contain a 5'-phosphate group, so this protein may be dispensible for normal
    RNA-mediated gene silencing
    Catalytic activity: ATP + 5'-dephospho-DNA = ADP + 5'-phospho-DNA
    Catalytic activity: ATP + 5'-dephospho-RNA = ADP + 5'-phospho-RNA

         Enzyme Number (IUBMB): EC 2.7.1.781 2

         Gene Ontology (GO): 4 molecular function terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005524ATP binding TAS8896421
    GO:0046404ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity IEA--
    GO:0051733polydeoxyribonucleotide kinase activity IDA17495927
    GO:0051736ATP-dependent polyribonucleotide 5'-hydroxyl-kinase activity IDA17495927
         
    Find genes that share ontologies with CLP1           About GenesLikeMe


    Phenotypes:
         12 MGI mutant phenotypes (inferred from 3 alleles(MGI details for Clp1):
     behavior/neurological  cellular  growth/size/body  integument  mortality/aging 
     muscle  nervous system  no phenotypic analysis  other  respiratory system 
     skeleton  tumorigenesis 

    Find genes that share phenotypes with CLP1           About GenesLikeMe

    Animal Models:
       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for CLP1
       inGenious Targeting Laboratory: Contact us about creating complex and humanized mouse models for CLP1

       genOway customized KO model: permanent, tissue-specific or time-controlled inactivation for CLP1
       genOway customized Knockin model: humanization, point mutation, expression monitoring, etc. for CLP1

    miRNA
    Products:
        
    miRTarBase miRNAs that target CLP1:
    hsa-mir-98-5p (MIRT027594)

    Block miRNA regulation of human, mouse, rat CLP1 using miScript Target Protectors
    Selected qRT-PCR Assays for microRNAs that regulate CLP1 (see all 10):
    hsa-miR-98 hsa-let-7d hsa-let-7c hsa-let-7i hsa-let-7g hsa-let-7e hsa-miR-3927 hsa-let-7b
    SwitchGear 3'UTR luciferase reporter plasmidCLP1 3' UTR sequence
    Inhib. RNA
    Products:
        
    OriGene RNAi products in human, mouse, rat for CLP1
    Predesigned siRNA for gene silencing in human, mouse, rat CLP1

    Gene Editing
    Products:
    DNA2.0 Custom Protein Engineering Service for CLP1

    Clone
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    OriGene clones in human, mouse for CLP1 (see all 12)
    OriGene ORF clones in mouse, rat for CLP1
    OriGene custom cloning services - gene synthesis, subcloning, mutagenesis, variant library, vector shuttling
    GenScript: all cDNA clones in your preferred vector (see all 2): CLP1 (NM_006831)
    Browse Sino Biological Human cDNA Clones
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for CLP1
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat CLP1

    Cell Line
    Products:
         
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    Browse ESI BIO Cell Lines and PureStem Progenitors for CLP1 
    In Situ Assay
    Products:
       

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for CLP1


    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from UniProtKB/Swiss-Prot
    CLP1_HUMAN, Q92989: Nucleus
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    nucleus5
    cytosol2
    extracellular1
    mitochondrion1
    peroxisome1
    plasma membrane1

    Gene Ontology (GO): 5 cellular component terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000214tRNA-intron endonuclease complex IDA17495927
    GO:0005634nucleus IDA--
    GO:0005654nucleoplasm TAS--
    GO:0005730NOT nucleolus IDA--
    GO:0005849mRNA cleavage factor complex IEA--

    Find genes that share ontologies with CLP1           About GenesLikeMe


    (SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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    SuperPaths for CLP1 About    
    See pathways by source

    SuperPathContained pathways About
    1mRNA Splicing - Major Pathway
    mRNA Splicing - Major Pathway0.78
    mRNA Splicing0.78
    Processing of Capped Intron-Containing Pre-mRNA0.78
    mRNA processing0.44
    2RNA Polymerase II Transcription Termination
    RNA Polymerase II Transcription Termination0.80
    Processing of Capped Intronless Pre-mRNA0.52
    Cleavage of Growing Transcript in the Termination Region0.80
    Processing of Intronless Pre-mRNAs0.00
    mRNA 3-end processing0.80
    3Formation of RNA Pol II elongation complex
    RNA Polymerase II Transcription0.60
    4Gene Expression
    Gene Expression0.40
    5mRNA surveillance pathway
    mRNA surveillance pathway


    Find genes that share SuperPaths with CLP1           About GenesLikeMe

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways


    1 BioSystems Pathway for CLP1
        mRNA processing

    4 Reactome Pathways for CLP1
        mRNA Splicing - Major Pathway
    mRNA 3'-end processing
    Processing of Intronless Pre-mRNAs
    Cleavage of Growing Transcript in the Termination Region


    1 Kegg Pathway  (Kegg details for CLP1):
        mRNA surveillance pathway

        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for CLP1
    Interactions:

        Search GeneGlobe Interaction Network for CLP1

    STRING Interaction Network Preview (showing 5 interactants - click image to see 25)

    Selected Interacting proteins for CLP1 (Q929892, 3 ENSP000003047044) via UniProtKB, MINT, STRING, and/or I2D (see all 688)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    CPSF2Q9P2I02, 3, ENSP000002988754MINT-7945693 I2D: score=1 STRING: ENSP00000298875
    CPSF3Q9UKF62, 3, ENSP000002381124MINT-7945693 I2D: score=1 STRING: ENSP00000238112
    CPSF7Q8N6842, 3, ENSP000003454124MINT-7945693 I2D: score=1 STRING: ENSP00000345412
    NUDT21O438093, ENSP000003002914I2D: score=3 STRING: ENSP00000300291
    CPSF6Q166303, ENSP000003917744I2D: score=1 STRING: ENSP00000391774
    About this table

    Gene Ontology (GO): Selected biological process terms (see all 9):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000398mRNA splicing, via spliceosome TAS--
    GO:0006366transcription from RNA polymerase II promoter TAS--
    GO:0006369termination of RNA polymerase II transcription TAS--
    GO:0006388tRNA splicing, via endonucleolytic cleavage and ligation IDA17495927
    GO:0008380RNA splicing TAS--

    Find genes that share ontologies with CLP1           About GenesLikeMe



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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    Browse Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    Browse Tocris compounds for CLP1



    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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    REFSEQ mRNAs for CLP1 gene (2 alternative transcripts): 
    NM_001142597.1  NM_006831.2  

    Unigene Cluster for CLP1:

    Cleavage and polyadenylation factor I subunit 1
    Hs.523687  [show with all ESTs]
    Unigene Representative Sequence: U73524
    6 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000529773 ENST00000529430 ENST00000533682(uc001nkw.3 uc010rjw.2 uc009yml.3)
    ENST00000533905 ENST00000525602 ENST00000302731
    miRNA
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    Block miRNA regulation of human, mouse, rat CLP1 using miScript Target Protectors
    Selected qRT-PCR Assays for microRNAs that regulate CLP1 (see all 10):
    hsa-miR-98 hsa-let-7d hsa-let-7c hsa-let-7i hsa-let-7g hsa-let-7e hsa-miR-3927 hsa-let-7b
    SwitchGear 3'UTR luciferase reporter plasmidCLP1 3' UTR sequence
    Inhib. RNA
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    Predesigned siRNA for gene silencing in human, mouse, rat CLP1
    Clone
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    OriGene ORF clones in mouse, rat for CLP1
    OriGene custom cloning services - gene synthesis, subcloning, mutagenesis, variant library, vector shuttling
    GenScript: all cDNA clones in your preferred vector (see all 2): CLP1 (NM_006831)
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for CLP1
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat CLP1
    Primer
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    OriGene qPCR primer pairs and template standards for CLP1
    OriGene qSTAR qPCR primer pairs in human, mouse for CLP1
    Pre-validated RT2 qPCR Primer Assay in human, mouse, rat CLP1
      QuantiTect SYBR Green Assays in human, mouse, rat CLP1
      QuantiFast Probe-based Assays in human, mouse, rat CLP1

    Additional mRNA sequence: 

    AK300232.1 AK313007.1 BC000446.1 U73524.1 

    5 DOTS entries:

    DT.416520  DT.97822953  DT.100670080  DT.100748469  DT.95358805 

    Selected AceView cDNA sequences (see all 134):

    BQ574764 AI474298 BC000446 AW072178 CA441446 AI016679 AW004029 AI962399 
    AW273932 BM929461 AI128497 AA878365 BF110257 AI498305 AI243334 BM721809 
    W67856 BF433054 AI738527 AW025380 T34517 AA412207 AA188172 AI085352 

    GeneLoc Exon Structure

    3 Alternative Splicing Database (ASD) splice patterns (SP) for CLP1    About this scheme

    ExUns: 1a · 1b · 1c ^ 2a · 2b · 2c · 2d ^ 3a · 3b
    SP1:                                                      
    SP2:                                -     -               
    SP3:                    -                                 


    ECgene alternative splicing isoforms for CLP1

    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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    CLP1 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: AGACTGTAAT
    CLP1 Expression
    About this image


    CLP1 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 5) fully expand
     
     Intermediate Mesoderm (Gastrulation Derivatives)    fully expand to see all 2 entries
             Mesonephric cells Mesonephros
             Mesonephros
     
     Kidney (Urinary System)
             Metanephros
     
     Gonad
             Mesonephric cells Mesonephros
     
     Testis (Reproductive System)
     
     Bone (Muscoskeletal System)
    CLP1 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    CLP1 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.523687
        Custom PCR Arrays for CLP1
    Primer
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    OriGene qPCR primer pairs and template standards for CLP1
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    QuantiFast Probe-based Assays in human, mouse, rat CLP1
    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for CLP1

    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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    This gene was present in the common ancestor of eukaryotes.

    Orthologs for CLP1 gene from Selected species (see all 18)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Clp11 , 5 CLP1, cleavage and polyadenylation factor I subunit, more5
    CLP1, cleavage and polyadenylation factor I subunit1
    90.04(n)1
    98.59(a)1
      2 (49.45 cM)5
    989851  NM_133840.21  NP_598601.11 
     847231225 
    chicken
    (Gallus gallus)
    Aves CLP11 CLP1, cleavage and polyadenylation factor I subunit, more 79.69(n)
    93.18(a)
      423131  NM_001012292.1  NP_001012292.1 
    lizard
    (Anolis carolinensis)
    Reptilia CLP16
    cleavage and polyadenylation factor I subunit 1
    94(a)
    1 ↔ 1
    1(91588369-91592959)
    African clawed frog
    (Xenopus laevis)
    Amphibia CA790819.12   -- 74.71(n)    CA790819.1 
    zebrafish
    (Danio rerio)
    Actinopterygii LOC5656211 polyribonucleotide 5'-hydroxyl-kinase Clp1-like 71.03(n)
    81.11(a)
      565621  XM_688892.5  XP_693984.3 
    fruit fly
    (Drosophila melanogaster)
    Insecta cbc1 crowded by cid 58.76(n)
    56.97(a)
      36494  NM_137032.3  NP_610876.1 
    worm
    (Caenorhabditis elegans)
    Secernentea clpf-11 clpf-1 51.34(n)
    48.9(a)
      175442  NM_001047393.2  NP_001040858.1 
    baker's yeast
    (Saccharomyces cerevisiae)
    Saccharomycetes CLP1(YOR250C)4 Subunit of cleavage factor I (CFI), involved in both more   --   15(802307-800970) 854424  NP_014893.1 
    thale cress
    (Arabidopsis thaliana)
    eudicotyledons CLPS31 CLPS3 48.77(n)
    42.89(a)
      819626  NM_202491.1  NP_974220.1 
    rice
    (Oryza sativa)
    Liliopsida Os02g02175001 Os02g0217500 48.36(n)
    39.81(a)
      4328733  NM_001052834.1  NP_001046299.1 


    ENSEMBL Gene Tree for CLP1 (if available)
    TreeFam Gene Tree for CLP1 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section

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    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
    About This Section

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    Selected SNPs for CLP1 (see all 146)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 11 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1905271331,2
    --57423331(+) CTCGCA/GCTGTC 2 -- us2k10--------
    rs1817884541,2
    C--57423357(+) CAGTGC/GCAGGA 2 -- us2k10--------
    rs17838221,2
    C,F--57423367(-) TGAGCT/CGAGAT 2 -- us2k13Minor allele frequency- C:0.33NA 6
    rs1851216311,2
    --57423576(+) TACAGA/GCGTGA 2 -- us2k10--------
    rs1886986371,2
    --57423745(+) CAGGCA/GCCCGC 2 -- us2k10--------
    rs1812788721,2
    --57423811(+) GTCAGC/GCTGGT 2 -- us2k10--------
    rs1854789741,2
    --57423824(+) CGAACC/TCCTGA 2 -- us2k10--------
    rs116076021,2
    H--57423887(+) gagccA/Cccgcg 2 -- us2k10--------
    rs1463067291,2
    C--57423902(+) GCCTAA/GATGTT 2 -- us2k10--------
    rs16135921,2
    C,F,H--57424000(+) tatctT/Gagtct 2 -- us2k124Minor allele frequency- G:0.29NS EA NA WA CSA 2352

    HapMap Linkage Disequilibrium report for CLP1 (57416465 - 57429340 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 3 variations for CLP1:    About this table    
    Variant IDTypeSubtypePubMed ID
    nsv832164CNV Loss17160897
    nsv508633CNV Loss20534489
    nsv832163CNV Gain17160897

    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing CLP1
    DNA2.0 Custom Variant and Variant Library Synthesis for CLP1

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    OMIM gene information: 608757    OMIM disorders: --

    1 disease for CLP1:    
    About MalaCards
    pontocerebellar hypoplasia, type 10


    Find genes that share disorders with CLP1           About GenesLikeMe


    Export disorders for CLP1 gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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    PubMed articles for CLP1 gene, integrated from 10 sources (see all 19):
    (articles sorted by number of sources associating them with CLP1)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Human pre-mRNA cleavage factor II(m) contains homologs of yeast proteins and bridges two other cleavage factors. (PubMed id 11060040)1, 2, 3 de Vries H....Keller W. (EMBO J. 2000)
    2. AF10 is split by MLL and HEAB, a human homolog to a putative Caenorhabditis elegans ATP/GTP-binding protein in an invins(10;11)(p12;q23q12). (PubMed id 8896421)1, 2, 3 Tanabe S.... Rowley J.D. (Blood 1996)
    3. Human RNA 5'-kinase (hClp1) can function as a tRNA splicing enzyme in vivo. (PubMed id 18648070)1, 2, 9 Ramirez A.... Schwer B. (RNA 2008)
    4. The human RNA kinase hClp1 is active on 3' transfer RNA exons and short interfering RNAs. (PubMed id 17495927)1, 2, 9 Weitzer S. and Martinez J. (Nature 2007)
    5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S.... Malek J. (Genome Res. 2004)
    6. Identification of a human endonuclease complex reveals a link between tRNA splicing and pre-mRNA 3' end formation. (PubMed id 15109492)1, 2 Paushkin S.V.... Trotta C.R. (Cell 2004)
    7. Pathway Analysis of ChIP-Seq-Based NRF1 Target Genes Suggests a Logical Hypothesis of their Involvement in the Pathogenesis of Neurodegenerative Diseases. (PubMed id 24250222)1 Satoh J....Yamamoto Y. (Gene Regul Syst Bio 2013)
    8. N-terminal acetylome analyses and functional insights of the N- terminal acetyltransferase NatB. (PubMed id 22814378)2 Van Damme P....Aldabe R. (Proc. Natl. Acad. Sci. U.S.A. 2012)
    9. Systematic and quantitative assessment of the ubiquitin-modified proteome. (PubMed id 21906983)1 Kim W....Gygi S.P. (Mol. Cell 2011)
    10. Interactions of pathological hallmark proteins: tubulin polymerization promoting protein/p25, beta-amyloid, and alpha-synuclein. (PubMed id 21832049)1 OlA!h J....OvA!di J. (J. Biol. Chem. 2011)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
    Aliases
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 10978 HGNC: 16999 AceView: HEAB Ensembl:ENSG00000172409 euGenes: HUgn10978
    ECgene: CLP1 Kegg: 10978 H-InvDB: CLP1

    (According to HUGE)
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    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
    About This Section

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    NameDescription
    PharmGKB entry for CLP1 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section

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    Patent Information for CLP1 gene:
    Search GeneIP for patents involving CLP1

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



    (Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, eBioscience, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
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