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Protein

Pre-mRNA-processing factor 40 homolog A

Gene

PRPF40A

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

Functioni

Binds to WASL/N-WASP and suppresses its translocation from the nucleus to the cytoplasm, thereby inhibiting its cytoplasmic function (By similarity). Plays a role in the regulation of cell morphology and cytoskeletal organization. Required in the control of cell shape and migration. May play a role in cytokinesis. May be involved in pre-mRNA splicing.By similarity1 Publication

GO - Molecular functioni

  • poly(A) RNA binding Source: UniProtKB
  • RNA binding Source: GO_Central

GO - Biological processi

  • cell cycle Source: UniProtKB-KW
  • cell division Source: UniProtKB-KW
  • cell migration Source: UniProtKB
  • cytoskeleton organization Source: UniProtKB
  • mRNA splicing, via spliceosome Source: GO_Central
  • regulation of cell shape Source: UniProtKB
  • regulation of cytokinesis Source: UniProtKB
Complete GO annotation...

Keywords - Biological processi

Cell cycle, Cell division, mRNA processing, mRNA splicing

Enzyme and pathway databases

ReactomeiR-HSA-72163. mRNA Splicing - Major Pathway.
SignaLinkiO75400.

Names & Taxonomyi

Protein namesi
Recommended name:
Pre-mRNA-processing factor 40 homolog A
Alternative name(s):
Fas ligand-associated factor 1
Formin-binding protein 11
Formin-binding protein 3
Huntingtin yeast partner A
Huntingtin-interacting protein 10
Short name:
HIP-10
Huntingtin-interacting protein A
Renal carcinoma antigen NY-REN-6
Gene namesi
Name:PRPF40A
Synonyms:FBP11, FLAF1, FNBP3, HIP10, HYPA
ORF Names:HSPC225
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 2

Organism-specific databases

HGNCiHGNC:16463. PRPF40A.

Subcellular locationi

GO - Cellular componenti

  • cytoplasm Source: HPA
  • membrane Source: UniProtKB
  • nuclear matrix Source: UniProtKB
  • nuclear speck Source: UniProtKB-SubCell
  • nucleoplasm Source: HPA
  • U1 snRNP Source: GO_Central
  • U2-type prespliceosome Source: GO_Central
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Organism-specific databases

DisGeNETi55660.
OpenTargetsiENSG00000196504.
PharmGKBiPA28195.

Polymorphism and mutation databases

BioMutaiPRPF40A.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000760851 – 957Pre-mRNA-processing factor 40 homolog AAdd BLAST957

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei9Omega-N-methylarginineBy similarity1
Modified residuei34PhosphoserineCombined sources1
Modified residuei151PhosphoserineCombined sources1
Modified residuei196N6-acetyllysineCombined sources1
Cross-linki241Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources
Modified residuei345PhosphothreonineCombined sources1
Modified residuei373PhosphothreonineCombined sources1
Modified residuei723PhosphoserineCombined sources1
Modified residuei787PhosphoserineCombined sources1
Modified residuei883PhosphoserineCombined sources1
Modified residuei885PhosphoserineCombined sources1
Modified residuei888PhosphoserineCombined sources1
Modified residuei932PhosphothreonineCombined sources1
Modified residuei933PhosphoserineCombined sources1
Modified residuei935PhosphoserineCombined sources1
Modified residuei938PhosphoserineCombined sources1
Isoform 2 (identifier: O75400-2)
Modified residuei17Omega-N-methylarginineCombined sources1
Modified residuei24Omega-N-methylarginineCombined sources1
Modified residuei47Omega-N-methylarginineCombined sources1
Isoform 5 (identifier: O75400-5)
Modified residuei17Omega-N-methylarginineCombined sources1
Modified residuei24Omega-N-methylarginineCombined sources1
Modified residuei47Omega-N-methylarginineCombined sources1

Keywords - PTMi

Acetylation, Isopeptide bond, Methylation, Phosphoprotein, Ubl conjugation

Proteomic databases

EPDiO75400.
MaxQBiO75400.
PaxDbiO75400.
PeptideAtlasiO75400.
PRIDEiO75400.

PTM databases

iPTMnetiO75400.
PhosphoSitePlusiO75400.
SwissPalmiO75400.

Miscellaneous databases

PMAP-CutDBO75400.

Expressioni

Tissue specificityi

Expressed in the brain cortex (at protein level). Widely expressed.2 Publications

Gene expression databases

BgeeiENSG00000196504.
CleanExiHS_PRPF40A.
ExpressionAtlasiO75400. baseline and differential.
GenevisibleiO75400. HS.

Organism-specific databases

HPAiHPA038272.
HPA038273.

Interactioni

Subunit structurei

Interacts with the N-terminus of HTT. Interacts with the phosphorylated C-terminal domain of POLR2A. Interacts with AKAP8L, SF1, SRPK1, CARD8, ATBF1 and MECP2 (By similarity). Interacts through the WW domains with formin proline-rich regions and with WASL/N-WASP (By similarity).By similarity

Binary interactionsi

WithEntry#Exp.IntActNotes
CHD3Q128732EBI-473291,EBI-523590
HTTP4285815EBI-473291,EBI-466029
NKAPQ8N5F72EBI-473291,EBI-721539
RBM39Q144983EBI-5280197,EBI-395290
SDCBPO005603EBI-5280197,EBI-727004
SDCBP2Q9H1903EBI-5280197,EBI-742426
SF1Q156373EBI-473291,EBI-744603
SF3A1Q154592EBI-473291,EBI-1054743

Protein-protein interaction databases

BioGridi120792. 189 interactors.
IntActiO75400. 94 interactors.
MINTiMINT-1180299.
STRINGi9606.ENSP00000386458.

Structurei

Secondary structure

1957
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi136 – 138Combined sources3
Turni142 – 145Combined sources4
Beta strandi146 – 151Combined sources6
Turni152 – 154Combined sources3
Beta strandi155 – 160Combined sources6
Turni161 – 164Combined sources4
Beta strandi165 – 169Combined sources5
Helixi172 – 174Combined sources3
Helixi177 – 183Combined sources7
Beta strandi186 – 191Combined sources6
Beta strandi197 – 201Combined sources5
Turni202 – 205Combined sources4
Beta strandi206 – 209Combined sources4
Helixi213 – 216Combined sources4
Beta strandi218 – 220Combined sources3
Helixi393 – 406Combined sources14
Beta strandi411 – 413Combined sources3
Helixi415 – 423Combined sources9
Helixi426 – 430Combined sources5
Helixi434 – 447Combined sources14
Helixi743 – 755Combined sources13
Helixi767 – 774Combined sources8
Helixi778 – 781Combined sources4
Helixi786 – 804Combined sources19

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1UZCNMR-A381-450[»]
1YWINMR-A142-173[»]
1YWJNMR-A142-173[»]
1ZR7NMR-A146-173[»]
2CQNNMR-A743-806[»]
2DYFNMR-A146-173[»]
2KZGNMR-A381-450[»]
2L5FNMR-A133-220[»]
2L9VNMR-A381-450[»]
2LKSNMR-A391-439[»]
ProteinModelPortaliO75400.
SMRiO75400.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiO75400.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini140 – 173WW 1PROSITE-ProRule annotationAdd BLAST34
Domaini181 – 214WW 2PROSITE-ProRule annotationAdd BLAST34
Domaini393 – 447FF 1Add BLAST55
Domaini460 – 514FF 2Add BLAST55
Domaini527 – 587FF 3Add BLAST61
Domaini607 – 667FF 4Add BLAST61
Domaini672 – 727FF 5Add BLAST56
Domaini742 – 799FF 6Add BLAST58

Domaini

The WW domains are essential for localization to nuclear speckles.By similarity

Sequence similaritiesi

Belongs to the PRPF40 family.Curated
Contains 6 FF domains.Curated
Contains 2 WW domains.PROSITE-ProRule annotation

Keywords - Domaini

Repeat

Phylogenomic databases

eggNOGiKOG0152. Eukaryota.
COG5104. LUCA.
GeneTreeiENSGT00820000127014.
HOVERGENiHBG059634.
InParanoidiO75400.
KOiK12821.
OMAiYSKQEEC.
OrthoDBiEOG091G06F8.
PhylomeDBiO75400.
TreeFamiTF318732.

Family and domain databases

Gene3Di1.10.10.440. 5 hits.
InterProiIPR002713. FF_domain.
IPR001202. WW_dom.
[Graphical view]
PfamiPF01846. FF. 5 hits.
PF00397. WW. 2 hits.
[Graphical view]
SMARTiSM00441. FF. 5 hits.
SM00456. WW. 2 hits.
[Graphical view]
SUPFAMiSSF51045. SSF51045. 2 hits.
SSF81698. SSF81698. 5 hits.
PROSITEiPS51676. FF. 6 hits.
PS01159. WW_DOMAIN_1. 2 hits.
PS50020. WW_DOMAIN_2. 2 hits.
[Graphical view]

Sequences (4)i

Sequence statusi: Complete.

This entry describes 4 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: O75400-1) [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
MRPGTGAERG GLMVSEMESH PPSQGPGDGE RRLSGSSLCS GSWVSADGFL
60 70 80 90 100
RRRPSMGHPG MHYAPMGMHP MGQRANMPPV PHGMMPQMMP PMGGPPMGQM
110 120 130 140 150
PGMMSSVMPG MMMSHMSQAS MQPALPPGVN SMDVAAGTAS GAKSMWTEHK
160 170 180 190 200
SPDGRTYYYN TETKQSTWEK PDDLKTPAEQ LLSKCPWKEY KSDSGKPYYY
210 220 230 240 250
NSQTKESRWA KPKELEDLEG YQNTIVAGSL ITKSNLHAMI KAEESSKQEE
260 270 280 290 300
CTTTSTAPVP TTEIPTTMST MAAAEAAAAV VAAAAAAAAA AAAANANAST
310 320 330 340 350
SASNTVSGTV PVVPEPEVTS IVATVVDNEN TVTISTEEQA QLTSTPAIQD
360 370 380 390 400
QSVEVSSNTG EETSKQETVA DFTPKKEEEE SQPAKKTYTW NTKEEAKQAF
410 420 430 440 450
KELLKEKRVP SNASWEQAMK MIINDPRYSA LAKLSEKKQA FNAYKVQTEK
460 470 480 490 500
EEKEEARSKY KEAKESFQRF LENHEKMTST TRYKKAEQMF GEMEVWNAIS
510 520 530 540 550
ERDRLEIYED VLFFLSKKEK EQAKQLRKRN WEALKNILDN MANVTYSTTW
560 570 580 590 600
SEAQQYLMDN PTFAEDEELQ NMDKEDALIC FEEHIRALEK EEEEEKQKSL
610 620 630 640 650
LRERRRQRKN RESFQIFLDE LHEHGQLHSM SSWMELYPTI SSDIRFTNML
660 670 680 690 700
GQPGSTALDL FKFYVEDLKA RYHDEKKIIK DILKDKGFVV EVNTTFEDFV
710 720 730 740 750
AIISSTKRST TLDAGNIKLA FNSLLEKAEA REREREKEEA RKMKRKESAF
760 770 780 790 800
KSMLKQAAPP IELDAVWEDI RERFVKEPAF EDITLESERK RIFKDFMHVL
810 820 830 840 850
EHECQHHHSK NKKHSKKSKK HHRKRSRSRS GSDSDDDDSH SKKKRQRSES
860 870 880 890 900
RSASEHSSSA ESERSYKKSK KHKKKSKKRR HKSDSPESDA EREKDKKEKD
910 920 930 940 950
RESEKDRTRQ RSESKHKSPK KKTGKDSGNW DTSGSELSEG ELEKRRRTLL

EQLDDDQ
Length:957
Mass (Da):108,805
Last modified:August 22, 2003 - v2
Checksum:i8874D0C1CE1FCDAF
GO
Isoform 2 (identifier: O75400-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-1: M → MCSGSGRRRSSLSPTM
     14-55: Missing.

Show »
Length:930
Mass (Da):105,927
Checksum:i6AFC2E30F4FAEB47
GO
Isoform 3 (identifier: O75400-3) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     220-237: Missing.

Show »
Length:939
Mass (Da):106,907
Checksum:i05527BF2FC5C9449
GO
Isoform 5 (identifier: O75400-5) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-1: M → MCSGSGRRRSSLSPTM
     14-55: Missing.
     127-128: PG → LN
     129-957: Missing.

Note: Probable target of nonsense-mediated mRNA decay.Combined sources
Show »
Length:101
Mass (Da):10,697
Checksum:i2C254F75EDA2059D
GO

Sequence cautioni

The sequence AAC27501 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.Curated
The sequence AAC27502 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.Curated
The sequence AAC27506 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.Curated
The sequence AAD42862 differs from that shown. Reason: Frameshift at position 953.Curated
The sequence AAF36145 differs from that shown. Reason: Frameshift at several positions.Curated
The sequence AAH11788 differs from that shown. Contaminating sequence. Potential poly-A sequence starting in position 409.Curated
The sequence BAA91277 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.Curated
The sequence BAB15016 differs from that shown.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti372 – 373FT → LL in AAB93495 (Ref. 5) Curated2
Sequence conflicti433K → N in AAC27501 (PubMed:9700202).Curated1
Sequence conflicti433K → N in AAC27506 (PubMed:9700202).Curated1
Sequence conflicti787S → P in BAA91277 (PubMed:14702039).Curated1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_0407811M → MCSGSGRRRSSLSPTM in isoform 2 and isoform 5. 3 Publications1
Alternative sequenceiVSP_00804714 – 55Missing in isoform 2 and isoform 5. 3 PublicationsAdd BLAST42
Alternative sequenceiVSP_040782127 – 128PG → LN in isoform 5. 1 Publication2
Alternative sequenceiVSP_040783129 – 957Missing in isoform 5. 1 PublicationAdd BLAST829
Alternative sequenceiVSP_008048220 – 237Missing in isoform 3. 1 PublicationAdd BLAST18

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AC012443 Genomic DNA. No translation available.
AC079344 Genomic DNA. No translation available.
AK000592 mRNA. Translation: BAA91277.1. Different initiation.
AK024810 mRNA. Translation: BAB15016.1. Sequence problems.
AF049523 mRNA. Translation: AAC27501.1. Different initiation.
AF049524 mRNA. Translation: AAC27502.1. Different initiation.
AF049528 mRNA. Translation: AAC27506.1. Different initiation.
BC011788 mRNA. Translation: AAH11788.1. Sequence problems.
BC027178 mRNA. Translation: AAH27178.1.
U70667 mRNA. Translation: AAB93495.1.
AF155096 mRNA. Translation: AAD42862.1. Frameshift.
AF151059 mRNA. Translation: AAF36145.1. Frameshift.
CCDSiCCDS46430.1. [O75400-2]
RefSeqiNP_060362.3. NM_017892.3. [O75400-2]
UniGeneiHs.643580.

Genome annotation databases

EnsembliENST00000410080; ENSP00000386458; ENSG00000196504. [O75400-2]
GeneIDi55660.
KEGGihsa:55660.
UCSCiuc002tyh.5. human. [O75400-1]

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AC012443 Genomic DNA. No translation available.
AC079344 Genomic DNA. No translation available.
AK000592 mRNA. Translation: BAA91277.1. Different initiation.
AK024810 mRNA. Translation: BAB15016.1. Sequence problems.
AF049523 mRNA. Translation: AAC27501.1. Different initiation.
AF049524 mRNA. Translation: AAC27502.1. Different initiation.
AF049528 mRNA. Translation: AAC27506.1. Different initiation.
BC011788 mRNA. Translation: AAH11788.1. Sequence problems.
BC027178 mRNA. Translation: AAH27178.1.
U70667 mRNA. Translation: AAB93495.1.
AF155096 mRNA. Translation: AAD42862.1. Frameshift.
AF151059 mRNA. Translation: AAF36145.1. Frameshift.
CCDSiCCDS46430.1. [O75400-2]
RefSeqiNP_060362.3. NM_017892.3. [O75400-2]
UniGeneiHs.643580.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1UZCNMR-A381-450[»]
1YWINMR-A142-173[»]
1YWJNMR-A142-173[»]
1ZR7NMR-A146-173[»]
2CQNNMR-A743-806[»]
2DYFNMR-A146-173[»]
2KZGNMR-A381-450[»]
2L5FNMR-A133-220[»]
2L9VNMR-A381-450[»]
2LKSNMR-A391-439[»]
ProteinModelPortaliO75400.
SMRiO75400.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi120792. 189 interactors.
IntActiO75400. 94 interactors.
MINTiMINT-1180299.
STRINGi9606.ENSP00000386458.

PTM databases

iPTMnetiO75400.
PhosphoSitePlusiO75400.
SwissPalmiO75400.

Polymorphism and mutation databases

BioMutaiPRPF40A.

Proteomic databases

EPDiO75400.
MaxQBiO75400.
PaxDbiO75400.
PeptideAtlasiO75400.
PRIDEiO75400.

Protocols and materials databases

DNASUi55660.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000410080; ENSP00000386458; ENSG00000196504. [O75400-2]
GeneIDi55660.
KEGGihsa:55660.
UCSCiuc002tyh.5. human. [O75400-1]

Organism-specific databases

CTDi55660.
DisGeNETi55660.
GeneCardsiPRPF40A.
HGNCiHGNC:16463. PRPF40A.
HPAiHPA038272.
HPA038273.
MIMi612941. gene.
neXtProtiNX_O75400.
OpenTargetsiENSG00000196504.
PharmGKBiPA28195.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG0152. Eukaryota.
COG5104. LUCA.
GeneTreeiENSGT00820000127014.
HOVERGENiHBG059634.
InParanoidiO75400.
KOiK12821.
OMAiYSKQEEC.
OrthoDBiEOG091G06F8.
PhylomeDBiO75400.
TreeFamiTF318732.

Enzyme and pathway databases

ReactomeiR-HSA-72163. mRNA Splicing - Major Pathway.
SignaLinkiO75400.

Miscellaneous databases

ChiTaRSiPRPF40A. human.
EvolutionaryTraceiO75400.
GeneWikiiPRPF40A.
GenomeRNAii55660.
PMAP-CutDBO75400.
PROiO75400.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000196504.
CleanExiHS_PRPF40A.
ExpressionAtlasiO75400. baseline and differential.
GenevisibleiO75400. HS.

Family and domain databases

Gene3Di1.10.10.440. 5 hits.
InterProiIPR002713. FF_domain.
IPR001202. WW_dom.
[Graphical view]
PfamiPF01846. FF. 5 hits.
PF00397. WW. 2 hits.
[Graphical view]
SMARTiSM00441. FF. 5 hits.
SM00456. WW. 2 hits.
[Graphical view]
SUPFAMiSSF51045. SSF51045. 2 hits.
SSF81698. SSF81698. 5 hits.
PROSITEiPS51676. FF. 6 hits.
PS01159. WW_DOMAIN_1. 2 hits.
PS50020. WW_DOMAIN_2. 2 hits.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiPR40A_HUMAN
AccessioniPrimary (citable) accession number: O75400
Secondary accession number(s): O43856
, O75404, Q8TBQ1, Q9H782, Q9NWU9, Q9P0Q2, Q9Y5A8
Entry historyi
Integrated into UniProtKB/Swiss-Prot: August 22, 2003
Last sequence update: August 22, 2003
Last modified: November 30, 2016
This is version 168 of the entry and version 2 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, Reference proteome

Documents

  1. Human chromosome 2
    Human chromosome 2: entries, gene names and cross-references to MIM
  2. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  4. 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.