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Protein

Pre-mRNA-processing factor 6

Gene

PRPF6

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Involved in pre-mRNA splicing as component of the U4/U6-U5 tri-snRNP complex, one of the building blocks of the spliceosome. Enhances dihydrotestosterone-induced transactivation activity of AR, as well as dexamethasone-induced transactivation activity of NR3C1, but does not affect estrogen-induced transactivation.1 Publication

GO - Molecular functioni

  • androgen receptor binding Source: MGI
  • poly(A) RNA binding Source: UniProtKB
  • ribonucleoprotein complex binding Source: BHF-UCL
  • RNA binding Source: MGI
  • transcription coactivator activity Source: MGI

GO - Biological processi

  • mRNA splicing, via spliceosome Source: UniProtKB
  • positive regulation of transcription from RNA polymerase II promoter Source: MGI
  • RNA localization Source: MGI
  • RNA splicing Source: UniProtKB
  • RNA splicing, via transesterification reactions Source: UniProtKB
  • spliceosomal complex assembly Source: UniProtKB
  • spliceosomal tri-snRNP complex assembly Source: BHF-UCL
Complete GO annotation...

Keywords - Biological processi

mRNA processing, mRNA splicing

Enzyme and pathway databases

BioCyciZFISH:ENSG00000101161-MONOMER.
ReactomeiR-HSA-72163. mRNA Splicing - Major Pathway.
R-HSA-72165. mRNA Splicing - Minor Pathway.
SignaLinkiO94906.

Names & Taxonomyi

Protein namesi
Recommended name:
Pre-mRNA-processing factor 6
Alternative name(s):
Androgen receptor N-terminal domain-transactivating protein 1
Short name:
ANT-1
PRP6 homolog
U5 snRNP-associated 102 kDa protein
Short name:
U5-102 kDa protein
Gene namesi
Name:PRPF6
Synonyms:C20orf14
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 20

Organism-specific databases

HGNCiHGNC:15860. PRPF6.

Subcellular locationi

GO - Cellular componenti

  • catalytic step 2 spliceosome Source: UniProtKB
  • membrane Source: UniProtKB
  • nuclear speck Source: UniProtKB-SubCell
  • nucleoplasm Source: HPA
  • nucleus Source: MGI
  • spliceosomal complex Source: UniProtKB
  • U4/U6 x U5 tri-snRNP complex Source: BHF-UCL
  • U5 snRNP Source: BHF-UCL
Complete GO annotation...

Keywords - Cellular componenti

Nucleus, Spliceosome

Pathology & Biotechi

Involvement in diseasei

Retinitis pigmentosa 60 (RP60)1 Publication
The disease may be caused by mutations affecting the gene represented in this entry. Cells from RP60 patients show intron retention for pre-mRNA bearing specific splicing signals.
Disease descriptionA retinal dystrophy belonging to the group of pigmentary retinopathies. Retinitis pigmentosa is characterized by retinal pigment deposits visible on fundus examination and primary loss of rod photoreceptor cells followed by secondary loss of cone photoreceptors. Patients typically have night vision blindness and loss of midperipheral visual field. As their condition progresses, they lose their far peripheral visual field and eventually central vision as well.
See also OMIM:613983
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_065768729R → W in RP60; mislocalized in Cajal bodies; partial loss of localization in splicing speckles. 1 PublicationCorresponds to variant rs387907100dbSNPEnsembl.1

Keywords - Diseasei

Disease mutation, Retinitis pigmentosa

Organism-specific databases

DisGeNETi24148.
MalaCardsiPRPF6.
MIMi613983. phenotype.
OpenTargetsiENSG00000101161.
Orphaneti791. Retinitis pigmentosa.
PharmGKBiPA25682.

Polymorphism and mutation databases

BioMutaiPRPF6.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002057591 – 941Pre-mRNA-processing factor 6Add BLAST941

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei143PhosphoserineCombined sources1
Modified residuei180PhosphothreonineCombined sources1
Modified residuei266PhosphothreonineCombined sources1
Modified residuei275PhosphothreonineCombined sources1
Modified residuei279PhosphoserineCombined sources1

Keywords - PTMi

Phosphoprotein

Proteomic databases

EPDiO94906.
MaxQBiO94906.
PaxDbiO94906.
PeptideAtlasiO94906.
PRIDEiO94906.

PTM databases

iPTMnetiO94906.
PhosphoSitePlusiO94906.
SwissPalmiO94906.

Expressioni

Tissue specificityi

Widely expressed.1 Publication

Gene expression databases

BgeeiENSG00000101161.
CleanExiHS_PRPF6.
GenevisibleiO94906. HS.

Organism-specific databases

HPAiHPA047106.

Interactioni

Subunit structurei

Associates with the U5 snRNP particle. Component of the U4/U6-U5 tri-snRNP complex composed of the U4, U6 and U5 snRNAs and at least PRPF3, PRPF4, PRPF6, PRPF8, PRPF31, SNRNP200, TXNL4A, SNRNP40, DDX23, CD2BP2, PPIH, SNU13, EFTUD2, SART1 and USP39, LSm proteins LSm2-8 and Sm proteins. Interacts with ARAF1. Identified in the spliceosome C complex. Interacts with AR and NR3C1, but not ESR1, independently of the presence of hormones.5 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
ARAFP103984EBI-536755,EBI-365961
CD2BP2O954005EBI-536755,EBI-768015
IKQ131232EBI-536755,EBI-713456
PRPF31Q8WWY32EBI-536755,EBI-1567797

GO - Molecular functioni

  • androgen receptor binding Source: MGI

Protein-protein interaction databases

BioGridi117298. 101 interactors.
DIPiDIP-29006N.
IntActiO94906. 41 interactors.
MINTiMINT-260551.
STRINGi9606.ENSP00000266079.

Structurei

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3JCRelectron microscopy7.00G1-941[»]
ProteinModelPortaliO94906.
SMRiO94906.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Repeati384 – 416HAT 1Add BLAST33
Repeati418 – 444HAT 2Add BLAST27
Repeati445 – 476HAT 3Add BLAST32
Repeati554 – 586HAT 4Add BLAST33
Repeati588 – 620HAT 5Add BLAST33
Repeati622 – 654HAT 6Add BLAST33
Repeati689 – 721HAT 7Add BLAST33
Repeati723 – 755HAT 8Add BLAST33
Repeati855 – 887HAT 9Add BLAST33

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi67 – 72Poly-Asp6

Sequence similaritiesi

Contains 9 HAT repeats.Curated

Keywords - Domaini

Repeat

Phylogenomic databases

eggNOGiKOG0495. Eukaryota.
ENOG410XRKD. LUCA.
GeneTreeiENSGT00550000075016.
HOVERGENiHBG023330.
InParanoidiO94906.
KOiK12855.
OMAiRQRFYAV.
OrthoDBiEOG091G01F5.
PhylomeDBiO94906.
TreeFamiTF105743.

Family and domain databases

Gene3Di1.25.40.10. 4 hits.
InterProiIPR003107. HAT.
IPR010491. PRP1_N.
IPR013026. TPR-contain_dom.
IPR011990. TPR-like_helical_dom.
IPR019734. TPR_repeat.
[Graphical view]
PfamiPF06424. PRP1_N. 1 hit.
PF13181. TPR_8. 1 hit.
[Graphical view]
SMARTiSM00386. HAT. 13 hits.
SM00028. TPR. 3 hits.
[Graphical view]
SUPFAMiSSF48452. SSF48452. 4 hits.

Sequences (2)i

Sequence statusi: Complete.

This entry describes 2 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: O94906-1) [UniParc]FASTAAdd to basket

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide

        10         20         30         40         50
MNKKKKPFLG MPAPLGYVPG LGRGATGFTT RSDIGPARDA NDPVDDRHAP
60 70 80 90 100
PGKRTVGDQM KKNQAADDDD EDLNDTNYDE FNGYAGSLFS SGPYEKDDEE
110 120 130 140 150
ADAIYAALDK RMDERRKERR EQREKEEIEK YRMERPKIQQ QFSDLKRKLA
160 170 180 190 200
EVTEEEWLSI PEVGDARNKR QRNPRYEKLT PVPDSFFAKH LQTGENHTSV
210 220 230 240 250
DPRQTQFGGL NTPYPGGLNT PYPGGMTPGL MTPGTGELDM RKIGQARNTL
260 270 280 290 300
MDMRLSQVSD SVSGQTVVDP KGYLTDLNSM IPTHGGDIND IKKARLLLKS
310 320 330 340 350
VRETNPHHPP AWIASARLEE VTGKLQVARN LIMKGTEMCP KSEDVWLEAA
360 370 380 390 400
RLQPGDTAKA VVAQAVRHLP QSVRIYIRAA ELETDIRAKK RVLRKALEHV
410 420 430 440 450
PNSVRLWKAA VELEEPEDAR IMLSRAVECC PTSVELWLAL ARLETYENAR
460 470 480 490 500
KVLNKARENI PTDRHIWITA AKLEEANGNT QMVEKIIDRA ITSLRANGVE
510 520 530 540 550
INREQWIQDA EECDRAGSVA TCQAVMRAVI GIGIEEEDRK HTWMEDADSC
560 570 580 590 600
VAHNALECAR AIYAYALQVF PSKKSVWLRA AYFEKNHGTR ESLEALLQRA
610 620 630 640 650
VAHCPKAEVL WLMGAKSKWL AGDVPAARSI LALAFQANPN SEEIWLAAVK
660 670 680 690 700
LESENDEYER ARRLLAKARS SAPTARVFMK SVKLEWVQDN IRAAQDLCEE
710 720 730 740 750
ALRHYEDFPK LWMMKGQIEE QKEMMEKARE AYNQGLKKCP HSTPLWLLLS
760 770 780 790 800
RLEEKIGQLT RARAILEKSR LKNPKNPGLW LESVRLEYRA GLKNIANTLM
810 820 830 840 850
AKALQECPNS GILWSEAIFL EARPQRRTKS VDALKKCEHD PHVLLAVAKL
860 870 880 890 900
FWSQRKITKA REWFHRTVKI DSDLGDAWAF FYKFELQHGT EEQQEEVRKR
910 920 930 940
CESAEPRHGE LWCAVSKDIA NWQKKIGDIL RLVAGRIKNT F
Length:941
Mass (Da):106,925
Last modified:May 1, 1999 - v1
Checksum:i91C2F1ADCA439BE9
GO
Isoform 2 (identifier: O94906-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     637-676: Missing.

Note: No experimental confirmation available.
Show »
Length:901
Mass (Da):102,429
Checksum:i23ADD30A75374402
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti20G → W in AAD01798 (PubMed:10848612).Curated1
Sequence conflicti223P → R in AAD01798 (PubMed:10848612).Curated1
Sequence conflicti284H → R in BAG50938 (PubMed:14702039).Curated1
Sequence conflicti421I → T in BAG36962 (PubMed:14702039).Curated1

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_069766477N → S Very rare variant found in a family with neuronal ceroid lipofuscinosis carrying a causative mutation in DNAJC5; uncertain role as a disease phenotype modifier. 1 Publication1
Natural variantiVAR_065768729R → W in RP60; mislocalized in Cajal bodies; partial loss of localization in splicing speckles. 1 PublicationCorresponds to variant rs387907100dbSNPEnsembl.1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_041857637 – 676Missing in isoform 2. 1 PublicationAdd BLAST40

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB019219 mRNA. Translation: BAA37140.1.
AF221842 mRNA. Translation: AAF66128.1.
AF026031 mRNA. Translation: AAD01798.1.
AK001554 mRNA. Translation: BAG50938.1.
AK314310 mRNA. Translation: BAG36962.1.
AL356790, AL118506, AL355803 Genomic DNA. Translation: CAH71582.1.
AL118506, AL355803, AL356790 Genomic DNA. Translation: CAI21906.1.
AL355803, AL118506, AL356790 Genomic DNA. Translation: CAC16610.2.
BC001666 mRNA. Translation: AAH01666.1.
AL137320 mRNA. Translation: CAB70695.1.
CCDSiCCDS13550.1. [O94906-1]
PIRiT46386.
RefSeqiNP_036601.2. NM_012469.3. [O94906-1]
UniGeneiHs.31334.

Genome annotation databases

EnsembliENST00000266079; ENSP00000266079; ENSG00000101161. [O94906-1]
GeneIDi24148.
KEGGihsa:24148.
UCSCiuc002yho.4. human. [O94906-1]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB019219 mRNA. Translation: BAA37140.1.
AF221842 mRNA. Translation: AAF66128.1.
AF026031 mRNA. Translation: AAD01798.1.
AK001554 mRNA. Translation: BAG50938.1.
AK314310 mRNA. Translation: BAG36962.1.
AL356790, AL118506, AL355803 Genomic DNA. Translation: CAH71582.1.
AL118506, AL355803, AL356790 Genomic DNA. Translation: CAI21906.1.
AL355803, AL118506, AL356790 Genomic DNA. Translation: CAC16610.2.
BC001666 mRNA. Translation: AAH01666.1.
AL137320 mRNA. Translation: CAB70695.1.
CCDSiCCDS13550.1. [O94906-1]
PIRiT46386.
RefSeqiNP_036601.2. NM_012469.3. [O94906-1]
UniGeneiHs.31334.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3JCRelectron microscopy7.00G1-941[»]
ProteinModelPortaliO94906.
SMRiO94906.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi117298. 101 interactors.
DIPiDIP-29006N.
IntActiO94906. 41 interactors.
MINTiMINT-260551.
STRINGi9606.ENSP00000266079.

PTM databases

iPTMnetiO94906.
PhosphoSitePlusiO94906.
SwissPalmiO94906.

Polymorphism and mutation databases

BioMutaiPRPF6.

Proteomic databases

EPDiO94906.
MaxQBiO94906.
PaxDbiO94906.
PeptideAtlasiO94906.
PRIDEiO94906.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000266079; ENSP00000266079; ENSG00000101161. [O94906-1]
GeneIDi24148.
KEGGihsa:24148.
UCSCiuc002yho.4. human. [O94906-1]

Organism-specific databases

CTDi24148.
DisGeNETi24148.
GeneCardsiPRPF6.
GeneReviewsiPRPF6.
HGNCiHGNC:15860. PRPF6.
HPAiHPA047106.
MalaCardsiPRPF6.
MIMi613979. gene.
613983. phenotype.
neXtProtiNX_O94906.
OpenTargetsiENSG00000101161.
Orphaneti791. Retinitis pigmentosa.
PharmGKBiPA25682.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG0495. Eukaryota.
ENOG410XRKD. LUCA.
GeneTreeiENSGT00550000075016.
HOVERGENiHBG023330.
InParanoidiO94906.
KOiK12855.
OMAiRQRFYAV.
OrthoDBiEOG091G01F5.
PhylomeDBiO94906.
TreeFamiTF105743.

Enzyme and pathway databases

BioCyciZFISH:ENSG00000101161-MONOMER.
ReactomeiR-HSA-72163. mRNA Splicing - Major Pathway.
R-HSA-72165. mRNA Splicing - Minor Pathway.
SignaLinkiO94906.

Miscellaneous databases

ChiTaRSiPRPF6. human.
GeneWikiiPRPF6.
GenomeRNAii24148.
PROiO94906.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000101161.
CleanExiHS_PRPF6.
GenevisibleiO94906. HS.

Family and domain databases

Gene3Di1.25.40.10. 4 hits.
InterProiIPR003107. HAT.
IPR010491. PRP1_N.
IPR013026. TPR-contain_dom.
IPR011990. TPR-like_helical_dom.
IPR019734. TPR_repeat.
[Graphical view]
PfamiPF06424. PRP1_N. 1 hit.
PF13181. TPR_8. 1 hit.
[Graphical view]
SMARTiSM00386. HAT. 13 hits.
SM00028. TPR. 3 hits.
[Graphical view]
SUPFAMiSSF48452. SSF48452. 4 hits.
ProtoNetiSearch...

Entry informationi

Entry nameiPRP6_HUMAN
AccessioniPrimary (citable) accession number: O94906
Secondary accession number(s): B2RAR5
, B3KMC6, O95109, Q5VXS5, Q9H3Z1, Q9H4T9, Q9H4U8, Q9NTE6
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 19, 2002
Last sequence update: May 1, 1999
Last modified: November 30, 2016
This is version 167 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. Human chromosome 20
    Human chromosome 20: entries, gene names and cross-references to MIM
  2. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  3. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  4. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  5. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  6. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.