PRPF38A Gene
protein-coding GIFtS: 49
GCID: GC01P052870
|
|
PRP38 pre-mRNA processing factor 38 (yeast) domain containing...
| |
Aliases
for PRPF38A gene
(According to
1HGNC,
2Entrez Gene,
3UniProtKB/Swiss-Prot,
4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc,
7Ensembl,
8DME,
9miRBase,
and/or 10fRNAdb)
About This Section
|
| Aliases |
|---|
| PRP38 Pre-MRNA Processing Factor 38 (Yeast) Domain Containing A1 2 | | Prp381 2 | | FLJ149361 | | RP5-965L7.12 | | Pre-MRNA-Splicing Factor 38A2 |
Export aliases for PRPF38A gene to outside databasesPrevious GC identifers: GC01P052583 GC01P052642 GC01P050986 |
Summaries
for PRPF38A gene(According to Entrez Gene,
Tocris Bioscience,
Wikipedia's
Gene Wiki,
PharmGKB,
UniProtKB/Swiss-Prot,
and/or
UniProtKB/TrEMBL)
About This Section
|
UniProtKB/Swiss-Prot: PR38A_HUMAN, Q8NAV1Function: May be required for pre-mRNA splicing (Potential)
|
Genomic Views
for PRPF38A gene
(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 69),
Regulatory elements and Epigenetics data according to
QIAGEN,
SABiosciences, and/or
SwitchGear Genomics)
About This Section
| RefSeq DNA sequence:- NC_000001.10 NC_018912.1 NT_032977.9
Regulatory elements:
 SABiosciences Regulatory transcription factor binding sites in the PRPF38A gene promoter:
Pbx1a POU3F2 (N-Oct-5b) POU3F2 (N-Oct-5a) STAT5A POU3F2 Meis-1b Gfi-1 Meis-1a Meis-1 ATF6
Other transcription factors
Search SABiosciences Chromatin IP Primers for PRPF38A
Epigenetics:
| | QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat PRPF38A |
Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track
Entrez Gene cytogenetic band: 1p32.3 Ensembl cytogenetic band: 1p32.3 HGNC cytogenetic band: 1p32.3PRPF38A Gene in genomic location: bands according to Ensembl, locations according to
 (and/or Entrez Gene and/or Ensembl if different)
GeneLoc information about chromosome 1 GeneLoc Exon Structure GeneLoc location for GC01P052870: view genomic region
(about GC identifiers)
Start:
|
52,870,219 bp from pter |
End:
|
52,883,992 bp from pter |
Size:
|
13,774 bases |
Orientation:
|
plus strand |
|
Proteins
for PRPF38A gene
(According to
1UniProtKB,
HORDE,
neXtProt,
Ensembl,
and/or Reactome,
Modification sites according to 2PhosphoSitePlus,
Specific Peptides from DME,
Protein expression images according to data from SPIRE MOPED and PaxDb,
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, and/or
Uscn,
Biochemical Assays by
EMD Millipore,
R&D Systems,
OriGene,
GenScript,
Cell Signaling Technology,
Enzo Life Sciences, and/or
Uscn,
Ontologies according to Gene
Ontology Consortium 01 Mar 2013 and
Entrez Gene,
Antibodies by
EMD Millipore,
R&D Systems,
GenScript,
Cell Signaling Technology,
OriGene,
Novus Biologicals,
Thermo Fisher Scientific,
Abcam, and/or
Uscn)
About This Section
|
UniProtKB/Swiss-Prot: PR38A_HUMAN, Q8NAV1 (See
protein sequence)Recommended Name: Pre-mRNA-splicing factor 38A Size: 312 amino acids; 37477 Da
Subcellular location: Nucleus (Potential)
Sequence caution: Sequence=BAB55405.1; Type=Erroneous initiation;
Secondary accessions: Q96JW1 Q9BVZ8Alternative splicing: 2 isoforms: Q8NAV1-1 Q8NAV1-2 Explore the universe of human proteins at neXtProt for PRPF38A: NX_Q8NAV1
Post-translational modifications:
View modification sites using PhosphoSitePlus2View neXtProt modification sites for NX_Q8NAV1
PRPF38A Protein expression data from MOPED and PaxDb: About this image 
REFSEQ proteins: NP_116253.2
ENSEMBL proteins: ENSP00000257181
Human Recombinant Protein Products for PRPF38A:
Gene Ontology (GO): 1 cellular component term (GO ID links to tree view): About this table | GO ID | Qualified GO term | Evidence | PubMed IDs |
|---|
| GO:0005681 | spliceosomal complex |
IEA | -- |
PRPF38A for ontologies About GeneDecksing
PRPF38A Antibody Products:
Assay Products for PRPF38A: |
Protein
Domains /
Families
for PRPF38A gene(According to InterPro, ProtoNet,
UniProtKB, and/or BLOCKS,
Sets of similar genes according to GeneDecks)
About This Section
|
PRPF38A for domains About GeneDecksing
2 InterPro domains/families:Graphical View of Domain Structure for InterPro Entry Q8NAV1ProtoNet protein and cluster: Q8NAV1 UniProtKB/Swiss-Prot: PR38A_HUMAN, Q8NAV1Similarity: Belongs to the PRP38 family |
Function
for PRPF38A gene
(According to 1UniProtKB,
Genatlas,
LifeMap Discovery™,
IUBMB, and/or
2DME,
Human phenotypes from GenomeRNAi,
Animal models from MGI Mar 06 2013,
inGenious Targeting Laboratory,
bound targets from SABiosciences,
miRNA Gene Targets from miRTarBase,
shRNA from
OriGene,
Sirion Biotech,
RNAi from
EMD Millipore,
siRNAs from
OriGene,
QIAGEN,
microRNA from QIAGEN,
Gene Editing from DNA2.0,
Sirion Biotech,
Clones from EMD Millipore,
OriGene,
SwitchGear Genomics,
GenScript,
Sino Biological,
DNA2.0,
and Vector BioLabs,
Cell Lines from GenScript,
LifeMap BioReagents,
Sirion Biotech,
In Situ Hybridization Assays from Advanced Cell Diagnostics,
Ontologies according to Gene Ontology Consortium 01 Mar 2013 via
Entrez Gene.)
About This Section
|
Molecular Function:
UniProtKB/Swiss-Prot Summary: PR38A_HUMAN, Q8NAV1Function: May be required for pre-mRNA splicing (Potential)Phenotypes:
2 GenomeRNAi human phenotypes for PRPF38A:
Animal Models:
Clone
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OriGene untagged cDNA clones in CMV expression vector in human, mouse, rat for PRPF38A
OriGene custom cloning services - gene synthesis, subcloning, mutagenesis,
variant library, vector shuttling 
| |  | GenScript: all cDNA clones in your preferred vector: PRPF38A (NM_032864) | |  | Browse Sino Biological Human cDNA Clones | |  | DNA2.0 Custom Codon Optimized Gene
Synthesis Service for PRPF38A | |  | Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat PRPF38A |
In Situ Assay
Products: |
 | Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for PRPF38A |
|
Pathways & Interactions
for PRPF38A gene
(Pathways according to
EMD Millipore,
R&D Systems,
Cell Signaling Technology,
KEGG,
PharmGKB,
BioSystems,
Reactome,
Tocris Bioscience,
GeneGo (Thomson Reuters),
QIAGEN,
and/or UniProtKB,
Sets of similar genes according to GeneDecks,
Interaction Networks according to
SABiosciences,
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 Mar 2013 via
Entrez Gene).
About This Section
|
Unified GeneCards pathways About this table
See pathways by source
| Super-pathway | contained gene-specific pathways |
|---|
| 1 | mRNA Splicing - Major Pathway | |
Pathway sources
See GeneCards unified pathways
Show all pathways
1 
Kegg Pathway (Kegg details for PRPF38A):
PRPF38A for pathways About GeneDecksing
Interactions:
Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for PRPF38A
STRING Interaction
Network Preview (showing 5 interactants - click image to see 15)
5/19 Interacting proteins for PRPF38A (Q8NAV12, 3 ENSP000002571814) via UniProtKB, MINT, STRING, and/or I2D (see all 19)About this table
Gene Ontology (GO): 2 biological process terms (GO ID links to tree view): About this table
PRPF38A for ontologies About GeneDecksing
|
Drugs & Compounds
for PRPF38A gene(Chemical Compounds according to UniProtKB, Enzo Life Sciences,
EMD Millipore, Tocris Bioscience
HMDB,
BitterDB, and/or
Novoseek, and Drugs according to
DrugBank,
Enzo Life Sciences, and/or
PharmGKB, with drugs/clinical trials/news
search links to CenterWatch)
About This Section
|
 Browse Tocris compounds for PRPF38A
Search CenterWatch for drugs/clinical trials and news about PRPF38A / PR38A
|
Transcripts
for PRPF38A gene(Secondary structures according to
fRNAdb,
GenBank/EMBL/DDBJ Accessions according to
Unigene
(Build 235 Homo sapiens; Mar 10 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,
RNAi Products from
EMD Millipore,
siRNAs from
OriGene,
QIAGEN,
shRNA from
OriGene,
Sirion Biotech,
microRNA from QIAGEN,
Tagged/untagged cDNA clones from
OriGene,
SwitchGear Genomics,
GenScript,
DNA2.0,
Vector BioLabs,
Primers from
OriGene,
SABiosciences, and/or
QIAGEN
)
About This Section
|
REFSEQ mRNAs for PRPF38A gene (2 alternative transcripts): NM_032284.2 NM_032864.3 Unigene Cluster for PRPF38A: PRP38 pre-mRNA processing factor 38 (yeast) domain containing A Hs.5301 [show with all ESTs]Unigene Representative Sequence: NM_0328643 Ensembl transcripts including schematic representations, and UCSC links where relevant: ENST00000257181(uc001ctv.4 uc001ctw.4) ENST00000487160 ENST00000474048
Clone
Products: | | OriGene Myc/DDK tagged cDNA clones in CMV expression vector in human, mouse, rat for PRPF38A (see all 3)
OriGene untagged cDNA clones in CMV expression vector in human, mouse, rat for PRPF38A
OriGene custom cloning services - gene synthesis, subcloning, mutagenesis,
variant library, vector shuttling
| | | GenScript: all cDNA clones in your preferred vector: PRPF38A (NM_032864) | | | DNA2.0 Custom Codon Optimized Gene
Synthesis Service for PRPF38A | | | Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat PRPF38A |
Additional cDNA sequence: AK027842.1 AK092038.1 AK315621.1 BC000777.2 BC063655.1 BC105004.1 BC105006.1 8 DOTS entries: DT.95271536 DT.95107639 DT.95271537 DT.121336855 DT.92011978 DT.121280878 DT.75168164 DT.91652210 24/132 AceView cDNA sequences (see all 132): BE326913 BC000777 BM751076 AI056919 AX747327 BE646153 BX327847 BU615655 AA354564 AA255731 AA825904 CR607179 AL541043 BE313907 AI421240 BE857095 CB122845 AA761710 BQ424525 AA262655 CA865760 NM_032864 CD368320 BU632867
GeneLoc Exon Structure
4 Alternative Splicing Database (ASD) splice patterns (SP) for PRPF38A About this scheme
| ExUns: | 1a | · | 1b | · | 1c | ^ | 2 | ^ | 3a | · | 3b | ^ | 4a | · | 4b | · | 4c | ^ | 5 | ^ | 6 | ^ | 7 | ^ | 8 | ^ | 9 | ^ | 10 | ^ | 11a | · | 11b |
|---|
|
| SP1: | | | | | | | - | | | | | | | | | | - | | | | | | | | | | | | | | | | | | |
| SP2: | | | | | | | | | | | - | | - | | - | | - | | - | | | | | | | | | | | | | | | | |
| SP3: | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
| SP4: | | | | | | | - | | | | | | | | | | | | | | | | | | | | | | | | | | | |
ECgene alternative splicing isoforms for PRPF38A
|
Expression
for PRPF38A gene
(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™,
plus additional links to
Genevestigator, and/or
SOURCE, and/or
BioGPS, and/or
UniProtKB,
PCR Arrays from
SABiosciences,
Primers from
OriGene,
SABiosciences, and/or
QIAGEN,
In Situ Hybridization Assays from Advanced Cell Diagnostics)
About This Section
| PRPF38A expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS
CGAP TAG: GCCTCCTGTG
About this image
See PRPF38A Protein Expression from SPIRE MOPED and PaxDB
Genevestigator expression for PRPF38A
SOURCE GeneReport for Unigene cluster: Hs.5301
SABiosciences Custom PCR Arrays for PRPF38A
Primer
Products: | | OriGene genome-wide validated SYBR primer pairs in human, mouse, rat for PRPF38A
Browse OriGene validated miRNA SYBR primer pairs
| | | SABiosciences RT2 qPCR Primer Assay in human, mouse, rat PRPF38A | | | QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat PRPF38A | | | QIAGEN QuantiFast Probe-based Assays in human, mouse, rat PRPF38A | In Situ
Assay Products: |
| Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for PRPF38A |
Orthologs
for PRPF38A gene
(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)
About This Section
|
This gene was present in the common ancestor of eukaryotes.
Orthologs for PRPF38A gene from 8/34 species (see all 34) About this table
| Organism |
Taxonomic
classification |
Gene |
Description |
Human
Similarity |
Orthology
Type |
Details |
chicken
(Gallus gallus) |
Aves |
PRPF38A1 |
PRP38 pre-mRNA processing factor 38 (yeast) domain more |
79.59(n)
97.76(a) |
|
771795 XM_001234244.2 XP_001234245.1 |
lizard
(Anolis carolinensis) |
Reptilia |
PRPF38A6 |
-- |
96(a) |
1 ↔ 1 |
4(114575606-114580026) |
African clawed frog
(Xenopus laevis) |
Amphibia |
Xl.18232 |
Xenopus laevis transcribed sequence with moderate similarity more |
76.02(n) |
|
CA973499.1 |
zebrafish
(Danio rerio) |
Actinopterygii |
570529392 |
-- |
75.39(n) |
|
334840 57052939 |
fruit fly
(Drosophila melanogaster) |
Insecta |
Prp381 |
pre-mRNA processing factor 38 |
58.33(n)
59.67(a) |
|
35934 NM_136619.2 NP_610463.2 |
worm
(Caenorhabditis elegans) |
Secernentea |
CELE_D1054.141 |
Protein D1054.14 |
51.18(n)
53.2(a) |
|
179499 NM_073361.2 NP_505762.1 |
thale cress
(Arabidopsis thaliana) |
eudicotyledons |
AT2G406501 |
pre-mRNA-splicing factor 38A |
52.9(n)
51.94(a) |
|
818660 NM_129627.2 NP_565937.1 |
rice
(Oryza sativa) |
Liliopsida |
Os.68132 |
Oryza sativa (japonica cultivar-group) cDNA clone0 more |
73.4(n) |
|
AK064099.1 |
ENSEMBL Gene Tree for PRPF38A (if available)
TreeFam Gene Tree for PRPF38A (if available) |
Paralogs
for PRPF38A gene(Paralogs according to
1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
About This Section
| Paralogs for PRPF38A gene
- SNRNP272
PRPF38A for paralogs About GeneDecksing
3 Pseudogenes.org Pseudogenes for PRPF38A
PGOHUM00000238671 PGOHUM00000238679 PGOHUM00000260557
|
Genomic Variants
for PRPF38A gene(SNPs/Variants according to the
1NCBI SNP Database,
2Ensembl,
3PupaSUITE,
UniProtKB, 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) and the Locus Specific Mutation
Databases (LSDB), Blood group antigen gene mutations by BGMUT,
Resequencing Primers from QIAGEN,
Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
About This Section
|
| Genomic Data | Transcription Related Data | Allele Frequencies | | SNP ID | Valid | Clinical
significance | Chr 1 pos | Sequence | # | AA
Chg | Type | More | # | Allele
freq | Pop | Total
sample | More |
|---|
HapMap Linkage Disequilibrium report for PRPF38A (52870219 - 52883992 bp)
Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
Database of Genomic Variants (DGV) variations for PRPF38A: -- | SABiosciences Cancer Mutation PCR Assays |
| | QIAGEN SeqTarget long-range PCR primers in human, mouse, rat for resequencing PRPF38A |
|
Disorders
/ Diseases
for PRPF38A gene
(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.)
About This Section
|
PRPF38A for disorders About GeneDecksing
1  disease for PRPF38A: About MalaCardsmalaria
Export disorders for PRPF38A gene to outside databases
|
Publications
for PRPF38A gene (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)
About This Section
|
PubMed articles for PRPF38A gene, integrated from 9 sources (see all 20):
(articles sorted by number of sources associating them with PRPF38A) | |  | Utopia: connect your pdf to the dynamic
world of online information |
- Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (2004)
- Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1, 3 Strausberg R.L....Marra M.A. (2002)
- Initial characterization of the human central proteome. (PubMed id 21269460)2 Burkard T.R.... Colinge J. (2011)
- A proteome-wide, quantitative survey of in vivo ubiqui tylation sites reveals widespread regulatory roles. (PubMed id 21890473)1 Wagner S.A....Choudhary C. (2011)
- A directed protein interaction network for investigat ing intracellular signal transduction. (PubMed id 21900206)1 Vinayagam A....Wanker E.E. (2011)
- The Brd4 extraterminal domain confers transcription a ctivation independent of pTEFb by recruiting multiple proteins, including NSD3. (PubMed id 21555454)1 Rahman S....Howley P.M. (2011)
- Systematic and quantitative assessment of the ubiquiti n-modified proteome. (PubMed id 21906983)1 Kim W....Gygi S.P. (2011)
- System-wide temporal characterization of the proteome and phosphoproteome of human embryonic stem cell differentiation. (PubMed id 21406692)2 Rigbolt K.T....Blagoev B. (2011)
- Interactions of pathological hallmark proteins: tubul in polymerization promoting protein/p25, beta-amyloid, and alpha-synuclein. (PubMed id 21832049)1 OlA!h J....OvA!di J. (2011)
- Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis. (PubMed id 20068231)2 Olsen J.V....Mann M. (2010)
|
External Searches for PRPF38A gene
(in PubMed,
OMIM, and NCBI Bookshelf)
About This Section
|
|
Genome Databases showing PRPF38A gene
(According to
Entrez Gene,
HGNC,
AceView,
euGenes,
Ensembl,
miRBase,
ECgene,
Kegg,
and/or
H-InvDB)
About This Section
|
|
Other Databases showing PRPF38A gene
(According to HUGE)
About This Section
| -- |
Specialized Databases showing PRPF38A gene(According to PharmGKB,
ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
About This Section
|
| Name | Description |
| PharmGKB entry for PRPF38A | Pharmacogenomics, SNPs, Pathways |
|
| | |
About This Section
| Patent Information for PRPF38A gene:
Search GeneIP for patents involving PRPF38A
GeneCards and IP:
Japan Patent Office Licenses GeneCards European Patent Office Licenses GeneCards Improving the IP Search
|
Products
for PRPF38A gene(Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, SABiosciences, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Uscn, Thermo Fisher Scientific, Gene Editing from DNA2.0 and Sirion Biotech, Clones from EMD Millipore, OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript, LifeMap BioReagents, and Sirion Biotech, PCR Arrays from SABiosciences, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, and/or
Enzo Life Sciences, In Situ Hybridization Assays from
Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory)
About This Section
|
 | |
 | |
 |
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| | | | | Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for PRPF38A |
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