Human Gene PRPF40A (uc002tyh.4)
  Description: Homo sapiens PRP40 pre-mRNA processing factor 40 homolog A (S. cerevisiae) (PRPF40A), mRNA.
Transcript (Including UTRs)
   Position: hg19 chr2:153,508,107-153,573,975 Size: 65,869 Total Exon Count: 26 Strand: -
Coding Region
   Position: hg19 chr2:153,512,820-153,573,953 Size: 61,134 Coding Exon Count: 26 

Page IndexSequence and LinksPrimersGenetic AssociationsMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr2:153,508,107-153,573,975)mRNA (may differ from genome)Protein (930 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMalacards
MGIOMIMPubMedReactomeUniProtKBWikipedia
BioGrid CRISPR DB

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): PRPF40A
CDC HuGE Published Literature: PRPF40A
Positive Disease Associations: Atrial Natriuretic Factor , CD40 Ligand , Follicle Stimulating Hormone
Related Studies:
  1. Atrial Natriuretic Factor
    Emelia J Benjamin et al. BMC medical genetics 2007, Genome-wide association with select biomarker traits in the Framingham Heart Study., BMC medical genetics. [PubMed 17903293]
    The Framingham GWAS represents a resource to describe potentially novel genetic influences on systemic biomarker variability. The newly described associations will need to be replicated in other studies.
  2. CD40 Ligand
    Emelia J Benjamin et al. BMC medical genetics 2007, Genome-wide association with select biomarker traits in the Framingham Heart Study., BMC medical genetics. [PubMed 17903293]
    The Framingham GWAS represents a resource to describe potentially novel genetic influences on systemic biomarker variability. The newly described associations will need to be replicated in other studies.
  3. CD40 Ligand
    Emelia J Benjamin et al. BMC medical genetics 2007, Genome-wide association with select biomarker traits in the Framingham Heart Study., BMC medical genetics. [PubMed 17903293]
    The Framingham GWAS represents a resource to describe potentially novel genetic influences on systemic biomarker variability. The newly described associations will need to be replicated in other studies.
           more ... click here to view the complete list

-  MalaCards Disease Associations
  MalaCards Gene Search: PRPF40A
Diseases sorted by gene-association score: rett syndrome (5)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 24.98 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 481.29 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR 0.00220.000 Picture PostScript Text
3' UTR -1143.404713-0.243 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  Pfam Domains:
PF00397 - WW domain
PF01846 - FF domain

SCOP Domains:
81698 - FF domain
51045 - WW domain

ModBase Predicted Comparative 3D Structure on O75400-2
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The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologGenome BrowserNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
  Ensembl   
  Protein Sequence   
  Alignment   

-  Descriptions from all associated GenBank mRNAs
  LF383498 - JP 2014500723-A/191001: Polycomb-Associated Non-Coding RNAs.
LF205694 - JP 2014500723-A/13197: Polycomb-Associated Non-Coding RNAs.
LF347181 - JP 2014500723-A/154684: Polycomb-Associated Non-Coding RNAs.
LF347182 - JP 2014500723-A/154685: Polycomb-Associated Non-Coding RNAs.
LF347183 - JP 2014500723-A/154686: Polycomb-Associated Non-Coding RNAs.
LF347184 - JP 2014500723-A/154687: Polycomb-Associated Non-Coding RNAs.
LF347185 - JP 2014500723-A/154688: Polycomb-Associated Non-Coding RNAs.
LF347186 - JP 2014500723-A/154689: Polycomb-Associated Non-Coding RNAs.
AF151059 - Homo sapiens HSPC225 mRNA, complete cds.
AK000592 - Homo sapiens cDNA FLJ20585 fis, clone KAT09510.
BC027178 - Homo sapiens PRP40 pre-mRNA processing factor 40 homolog A (S. cerevisiae), mRNA (cDNA clone IMAGE:4343048), partial cds.
JD410260 - Sequence 391284 from Patent EP1572962.
JD245454 - Sequence 226478 from Patent EP1572962.
JD243919 - Sequence 224943 from Patent EP1572962.
JD236540 - Sequence 217564 from Patent EP1572962.
AK021621 - Homo sapiens cDNA FLJ11559 fis, clone HEMBA1003098, highly similar to Homo sapiens NY-REN-6 antigen mRNA.
JD510462 - Sequence 491486 from Patent EP1572962.
AF155096 - Homo sapiens NY-REN-6 antigen mRNA, partial cds.
JD304057 - Sequence 285081 from Patent EP1572962.
AK315187 - Homo sapiens cDNA, FLJ96168, Homo sapiens formin binding protein 3 (FNBP3), mRNA.
KJ902849 - Synthetic construct Homo sapiens clone ccsbBroadEn_12243 PRPF40A gene, encodes complete protein.
LF347187 - JP 2014500723-A/154690: Polycomb-Associated Non-Coding RNAs.
LF347188 - JP 2014500723-A/154691: Polycomb-Associated Non-Coding RNAs.
LF347189 - JP 2014500723-A/154692: Polycomb-Associated Non-Coding RNAs.
AK298547 - Homo sapiens cDNA FLJ59286 partial cds, highly similar to Pre-mRNA-processing factor 40 homolog A.
LF347190 - JP 2014500723-A/154693: Polycomb-Associated Non-Coding RNAs.
LF347195 - JP 2014500723-A/154698: Polycomb-Associated Non-Coding RNAs.
LF347196 - JP 2014500723-A/154699: Polycomb-Associated Non-Coding RNAs.
LF347197 - JP 2014500723-A/154700: Polycomb-Associated Non-Coding RNAs.
JD448817 - Sequence 429841 from Patent EP1572962.
LF347199 - JP 2014500723-A/154702: Polycomb-Associated Non-Coding RNAs.
LF347202 - JP 2014500723-A/154705: Polycomb-Associated Non-Coding RNAs.
LF347203 - JP 2014500723-A/154706: Polycomb-Associated Non-Coding RNAs.
LF347204 - JP 2014500723-A/154707: Polycomb-Associated Non-Coding RNAs.
LF347205 - JP 2014500723-A/154708: Polycomb-Associated Non-Coding RNAs.
BC073138 - Homo sapiens cDNA clone IMAGE:6528230, partial cds.
AK024810 - Homo sapiens cDNA: FLJ21157 fis, clone CAS09937.
AF049528 - Homo sapiens huntingtin-interacting protein HYPA/FBP11 (HYPA) mRNA, partial cds.
AF049523 - Homo sapiens huntingtin-interacting protein HYPA/FBP11 (HYPA) mRNA, partial cds.
BC000273 - Homo sapiens PRP40 pre-mRNA processing factor 40 homolog A (yeast), mRNA (cDNA clone IMAGE:3356968).
BC011788 - Homo sapiens PRP40 pre-mRNA processing factor 40 homolog A (S. cerevisiae), mRNA (cDNA clone IMAGE:4026200), partial cds.
BC029414 - Homo sapiens PRP40 pre-mRNA processing factor 40 homolog A (S. cerevisiae), mRNA (cDNA clone IMAGE:4733897), partial cds.
LF347206 - JP 2014500723-A/154709: Polycomb-Associated Non-Coding RNAs.
LF347207 - JP 2014500723-A/154710: Polycomb-Associated Non-Coding RNAs.
U70667 - Human Fas-ligand associated factor 1 mRNA, partial cds.
LF347210 - JP 2014500723-A/154713: Polycomb-Associated Non-Coding RNAs.
AF049524 - Homo sapiens huntingtin-interacting protein HYPA/FBP11 (HYPA) mRNA, partial cds.
LF347211 - JP 2014500723-A/154714: Polycomb-Associated Non-Coding RNAs.
LF347222 - JP 2014500723-A/154725: Polycomb-Associated Non-Coding RNAs.
LF347223 - JP 2014500723-A/154726: Polycomb-Associated Non-Coding RNAs.
MA619075 - JP 2018138019-A/191001: Polycomb-Associated Non-Coding RNAs.
MA582758 - JP 2018138019-A/154684: Polycomb-Associated Non-Coding RNAs.
MA582759 - JP 2018138019-A/154685: Polycomb-Associated Non-Coding RNAs.
MA582760 - JP 2018138019-A/154686: Polycomb-Associated Non-Coding RNAs.
MA582761 - JP 2018138019-A/154687: Polycomb-Associated Non-Coding RNAs.
MA582762 - JP 2018138019-A/154688: Polycomb-Associated Non-Coding RNAs.
MA582763 - JP 2018138019-A/154689: Polycomb-Associated Non-Coding RNAs.
MA582764 - JP 2018138019-A/154690: Polycomb-Associated Non-Coding RNAs.
MA582765 - JP 2018138019-A/154691: Polycomb-Associated Non-Coding RNAs.
MA582766 - JP 2018138019-A/154692: Polycomb-Associated Non-Coding RNAs.
MA582767 - JP 2018138019-A/154693: Polycomb-Associated Non-Coding RNAs.
MA582772 - JP 2018138019-A/154698: Polycomb-Associated Non-Coding RNAs.
MA582773 - JP 2018138019-A/154699: Polycomb-Associated Non-Coding RNAs.
MA582774 - JP 2018138019-A/154700: Polycomb-Associated Non-Coding RNAs.
MA582776 - JP 2018138019-A/154702: Polycomb-Associated Non-Coding RNAs.
MA582779 - JP 2018138019-A/154705: Polycomb-Associated Non-Coding RNAs.
MA582780 - JP 2018138019-A/154706: Polycomb-Associated Non-Coding RNAs.
MA582781 - JP 2018138019-A/154707: Polycomb-Associated Non-Coding RNAs.
MA582782 - JP 2018138019-A/154708: Polycomb-Associated Non-Coding RNAs.
MA582783 - JP 2018138019-A/154709: Polycomb-Associated Non-Coding RNAs.
MA582784 - JP 2018138019-A/154710: Polycomb-Associated Non-Coding RNAs.
MA582787 - JP 2018138019-A/154713: Polycomb-Associated Non-Coding RNAs.
MA582788 - JP 2018138019-A/154714: Polycomb-Associated Non-Coding RNAs.
MA582799 - JP 2018138019-A/154725: Polycomb-Associated Non-Coding RNAs.
MA582800 - JP 2018138019-A/154726: Polycomb-Associated Non-Coding RNAs.
MA441271 - JP 2018138019-A/13197: Polycomb-Associated Non-Coding RNAs.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa03040 - Spliceosome

Reactome (by CSHL, EBI, and GO)

Protein O75400 (Reactome details) participates in the following event(s):

R-HSA-72107 Formation of the Spliceosomal E complex
R-HSA-72127 Formation of the Spliceosomal B Complex
R-HSA-72124 Formation of the Spliceosomal A Complex
R-HSA-72163 mRNA Splicing - Major Pathway
R-HSA-72172 mRNA Splicing
R-HSA-72203 Processing of Capped Intron-Containing Pre-mRNA
R-HSA-8953854 Metabolism of RNA

-  Other Names for This Gene
  Alternate Gene Symbols: FBP11, FLAF1, FNBP3, HIP10, HSPC225, HYPA, NM_017892, NP_060362, O75400-2
UCSC ID: uc002tyh.4
RefSeq Accession: NM_017892
Protein: O75400-2, splice isoform of O75400 CCDS: CCDS46430.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_017892.3
exon count: 26CDS single in 3' UTR: no RNA size: 7528
ORF size: 2793CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 5724.00frame shift in genome: no % Coverage: 100.00
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.