Human Gene PRPF40A (ENST00000545856.8_15) from GENCODE V47lift37

JavaScript is disabled in your web browser

You must have JavaScript enabled in your web browser to use the Genome Browser

Description: pre-mRNA processing factor 40 homolog A, transcript variant 22 (from RefSeq NM_001395481.1)
Gencode Transcript: ENST00000545856.8_15
Gencode Gene: ENSG00000196504.21_18
Transcript (Including UTRs)
Position: hg19 chr2:153,508,246-153,573,975 Size: 65,730 Total Exon Count: 26 Strand: -
Coding Region
Position: hg19 chr2:153,512,820-153,573,953 Size: 61,134 Coding Exon Count: 26

Page Index	Sequence and Links	UniProtKB Comments	Primers	MalaCards	CTD
Gene Alleles	RNA-Seq Expression	Microarray Expression	RNA Structure	Protein Structure	Other Species
GO Annotations	mRNA Descriptions	Other Names	Model Information	Methods

Data last updated at UCSC: 2024-08-22 23:36:26

Sequence and Links to Tools and Databases

Genomic Sequence (chr2:153,508,246-153,573,975)			mRNA (may differ from genome)		Protein (972 aa)
Gene Sorter	Genome Browser	Other Species FASTA	VisiGene	Gene interactions	Table Schema
AlphaFold	BioGPS	Ensembl	ExonPrimer	GeneCards	HGNC
Malacards	MGI	PubMed	UniProtKB	Wikipedia

Comments and Description Text from UniProtKB


	ID: F5H578_HUMAN DESCRIPTION: SubName: Full=Pre-mRNA-processing factor 40 homolog A; Flags: Fragment; CAUTION: The sequence shown here is derived from an Ensembl automatic analysis pipeline and should be considered as preliminary data.

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

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 C006780 bisphenol A C016403 2,4-dinitrotoluene C023514 2,6-dinitrotoluene C030370 2-methoxy-5-(2',3',4'-trimethoxyphenyl)tropone D001564 Benzo(a)pyrene D019256 Cadmium Chloride D002737 Chloroprene D016572 Cyclosporine D004041 Dietary Fats D004052 Diethylnitrosamine 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

Region	Fold Energy	Bases	Energy/Base	Display As
5' UTR	-0.10	22	-0.005	Picture	PostScript	Text
3' UTR	-1050.40	4574	-0.230	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

InterPro Domains: Graphical view of domain structure
IPR002713 - FF_domain
IPR001202 - WW_Rsp5_WWP

Pfam Domains:
PF00397 - WW domain
PF01846 - FF domain

SCOP Domains:
81698 - FF domain
81995 - beta-sandwich domain of Sec23/24
51045 - WW domain

ModBase Predicted Comparative 3D Structure on F5H578


Front	Top	Side

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.

Mouse	Rat	Zebrafish	D. melanogaster	C. elegans	S. cerevisiae
No ortholog	No ortholog	No ortholog	No ortholog	No ortholog	No ortholog
Gene Details	Gene Details
Gene Sorter	Gene Sorter
	RGD

Gene Ontology (GO) Annotations with Structured Vocabulary


	Cellular Component: GO:0005829 cytosol GO:0016607 nuclear speck

Descriptions from all associated GenBank mRNAs


	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. 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.

Other Names for This Gene


	Alternate Gene Symbols: ENST00000545856.1, ENST00000545856.2, ENST00000545856.3, ENST00000545856.4, ENST00000545856.5, ENST00000545856.6, ENST00000545856.7, F5H578, F5H578_HUMAN, NM_001395481, PRPF40A , uc324wtt.1, uc324wtt.2 UCSC ID: ENST00000545856.8_15 RefSeq Accession: NM_001365597.4 Protein: F5H578

Gene Model Information


	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.