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
Data last updated at UCSC: 2013-06-14
Sequence and Links to Tools and Databases
Primer design for this transcript
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: 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.
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.
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.
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MalaCards Disease Associations
Comparative Toxicogenomics Database (CTD)
Common Gene Haplotype Alleles
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RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
Microarray Expression Data
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mRNA Secondary Structure of 3' and 5' UTRs
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
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.
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
Other Names for This Gene
Alternate Gene Symbols: FBP11, FLAF1, FNBP3, HIP10, HSPC225, HYPA, NM_017892, NP_060362, O75400-2UCSC ID: uc002tyh.4RefSeq 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:
26 CDS single in 3' UTR:
no
RNA size:
7528
ORF size:
2793 CDS single in intron:
no
Alignment % ID:
100.00
txCdsPredict score:
5724.00 frame 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
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Methods, Credits, and Use Restrictions
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