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Protein

Pre-mRNA-processing factor 39

Gene

PRPF39

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Experimental evidence at protein leveli

Functioni

Involved in pre-mRNA splicing.By similarity

GO - Biological processi

Complete GO annotation...

Keywords - Biological processi

mRNA processing, mRNA splicing

Names & Taxonomyi

Protein namesi
Recommended name:
Pre-mRNA-processing factor 39
Alternative name(s):
PRP39 homolog
Gene namesi
Name:PRPF39
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 14

Organism-specific databases

HGNCiHGNC:20314. PRPF39.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Organism-specific databases

PharmGKBiPA142671127.

Polymorphism and mutation databases

BioMutaiPRPF39.
DMDMi223590245.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 669669Pre-mRNA-processing factor 39PRO_0000259648Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei44 – 441PhosphoserineCombined sources

Keywords - PTMi

Phosphoprotein

Proteomic databases

EPDiQ86UA1.
MaxQBiQ86UA1.
PaxDbiQ86UA1.
PeptideAtlasiQ86UA1.
PRIDEiQ86UA1.

PTM databases

iPTMnetiQ86UA1.
PhosphoSiteiQ86UA1.

Expressioni

Gene expression databases

BgeeiQ86UA1.
CleanExiHS_PRPF39.
ExpressionAtlasiQ86UA1. baseline and differential.
GenevisibleiQ86UA1. HS.

Organism-specific databases

HPAiHPA001176.

Interactioni

Protein-protein interaction databases

BioGridi120347. 14 interactions.
IntActiQ86UA1. 6 interactions.
STRINGi9606.ENSP00000348010.

Structurei

3D structure databases

ProteinModelPortaliQ86UA1.
SMRiQ86UA1. Positions 86-215.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Repeati109 – 14133HAT 1Add
BLAST
Repeati143 – 17533HAT 2Add
BLAST
Repeati183 – 21836HAT 3Add
BLAST
Repeati220 – 25334HAT 4Add
BLAST
Repeati333 – 36533HAT 5Add
BLAST
Repeati367 – 39933HAT 6Add
BLAST
Repeati404 – 43633HAT 7Add
BLAST

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi665 – 6684Poly-Pro

Sequence similaritiesi

Belongs to the PRP39 family.Curated
Contains 7 HAT repeats.Curated

Keywords - Domaini

Repeat

Phylogenomic databases

eggNOGiKOG1258. Eukaryota.
ENOG410XPVR. LUCA.
GeneTreeiENSGT00390000005033.
HOGENOMiHOG000010277.
HOVERGENiHBG082194.
InParanoidiQ86UA1.
KOiK13217.
OMAiTGWVYLL.
OrthoDBiEOG7ZSHSM.
PhylomeDBiQ86UA1.
TreeFamiTF314746.

Family and domain databases

Gene3Di1.25.40.10. 2 hits.
InterProiIPR003107. HAT.
IPR011990. TPR-like_helical_dom.
[Graphical view]
SMARTiSM00386. HAT. 7 hits.
[Graphical view]
SUPFAMiSSF48452. SSF48452. 2 hits.

Sequences (2)i

Sequence statusi: Complete.

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

Isoform 1 (identifier: Q86UA1-1) [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
MQNSHMDEYR NSSNGSTGNS SEVVVEHPTD FSTEIMNVTE MEQSPDDSPN
60 70 80 90 100
VNASTEETEM ASAVDLPVTL TETEANFPPE YEKFWKTVEN NPQDFTGWVY
110 120 130 140 150
LLQYVEQENH LMAARKAFDR FFIHYPYCYG YWKKYADLEK RHDNIKPSDE
160 170 180 190 200
VYRRGLQAIP LSVDLWIHYI NFLKETLDPG DPETNNTIRG TFEHAVLAAG
210 220 230 240 250
TDFRSDRLWE MYINWENEQG NLREVTAIYD RILGIPTQLY SHHFQRFKEH
260 270 280 290 300
VQNNLPRDLL TGEQFIQLRR ELASVNGHSG DDGPPGDDLP SGIEDITDPA
310 320 330 340 350
KLITEIENMR HRIIEIHQEM FNYNEHEVSK RWTFEEGIKR PYFHVKPLEK
360 370 380 390 400
AQLKNWKEYL EFEIENGTHE RVVVLFERCV ISCALYEEFW IKYAKYMENH
410 420 430 440 450
SIEGVRHVFS RACTIHLPKK PMVHMLWAAF EEQQGNINEA RNILKTFEEC
460 470 480 490 500
VLGLAMVRLR RVSLERRHGN LEEAEHLLQD AIKNAKSNNE SSFYAVKLAR
510 520 530 540 550
HLFKIQKNLP KSRKVLLEAI ERDKENTKLY LNLLEMEYSG DLKQNEENIL
560 570 580 590 600
NCFDKAVHGS LPIKMRITFS QRKVEFLEDF GSDVNKLLNA YDEHQTLLKE
610 620 630 640 650
QDSLKRKAEN GSEEPEEKKA HTEDTTSSST QMIDGDLQAN QAVYNYSAWY
660
QYNYQNPWNY GQYYPPPPT
Length:669
Mass (Da):78,430
Last modified:February 10, 2009 - v3
Checksum:i6213DEF58C536744
GO
Isoform 2 (identifier: Q86UA1-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-396: Missing.
     652-669: YNYQNPWNYGQYYPPPPT → VSLHNYNSLFIDVISIN

Note: No experimental confirmation available.
Show »
Length:272
Mass (Da):31,494
Checksum:iE69EF57F46C0564D
GO

Sequence cautioni

The sequence AAI25127.1 differs from that shown. Reason: Erroneous initiation. Curated
The sequence AAI25128.1 differs from that shown. Reason: Erroneous initiation. Curated

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti312 – 3121R → G in AAI25128 (PubMed:15489334).Curated

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei1 – 396396Missing in isoform 2. 1 PublicationVSP_021496Add
BLAST
Alternative sequencei652 – 66918YNYQN…PPPPT → VSLHNYNSLFIDVISIN in isoform 2. 1 PublicationVSP_021497Add
BLAST

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK001990 mRNA. Translation: BAA92024.1.
AL121809 Genomic DNA. No translation available.
BC051886 mRNA. Translation: AAH51886.1.
BC125126 mRNA. Translation: AAI25127.1. Different initiation.
BC125127 mRNA. Translation: AAI25128.1. Different initiation.
CCDSiCCDS9682.2. [Q86UA1-1]
RefSeqiNP_060392.3. NM_017922.3. [Q86UA1-1]
UniGeneiHs.274337.

Genome annotation databases

EnsembliENST00000355765; ENSP00000348010; ENSG00000185246. [Q86UA1-1]
GeneIDi55015.
KEGGihsa:55015.
UCSCiuc001wvz.4. human. [Q86UA1-1]

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK001990 mRNA. Translation: BAA92024.1.
AL121809 Genomic DNA. No translation available.
BC051886 mRNA. Translation: AAH51886.1.
BC125126 mRNA. Translation: AAI25127.1. Different initiation.
BC125127 mRNA. Translation: AAI25128.1. Different initiation.
CCDSiCCDS9682.2. [Q86UA1-1]
RefSeqiNP_060392.3. NM_017922.3. [Q86UA1-1]
UniGeneiHs.274337.

3D structure databases

ProteinModelPortaliQ86UA1.
SMRiQ86UA1. Positions 86-215.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi120347. 14 interactions.
IntActiQ86UA1. 6 interactions.
STRINGi9606.ENSP00000348010.

PTM databases

iPTMnetiQ86UA1.
PhosphoSiteiQ86UA1.

Polymorphism and mutation databases

BioMutaiPRPF39.
DMDMi223590245.

Proteomic databases

EPDiQ86UA1.
MaxQBiQ86UA1.
PaxDbiQ86UA1.
PeptideAtlasiQ86UA1.
PRIDEiQ86UA1.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000355765; ENSP00000348010; ENSG00000185246. [Q86UA1-1]
GeneIDi55015.
KEGGihsa:55015.
UCSCiuc001wvz.4. human. [Q86UA1-1]

Organism-specific databases

CTDi55015.
GeneCardsiPRPF39.
H-InvDBHIX0011621.
HGNCiHGNC:20314. PRPF39.
HPAiHPA001176.
MIMi614907. gene.
neXtProtiNX_Q86UA1.
PharmGKBiPA142671127.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG1258. Eukaryota.
ENOG410XPVR. LUCA.
GeneTreeiENSGT00390000005033.
HOGENOMiHOG000010277.
HOVERGENiHBG082194.
InParanoidiQ86UA1.
KOiK13217.
OMAiTGWVYLL.
OrthoDBiEOG7ZSHSM.
PhylomeDBiQ86UA1.
TreeFamiTF314746.

Miscellaneous databases

GenomeRNAii55015.
PROiQ86UA1.
SOURCEiSearch...

Gene expression databases

BgeeiQ86UA1.
CleanExiHS_PRPF39.
ExpressionAtlasiQ86UA1. baseline and differential.
GenevisibleiQ86UA1. HS.

Family and domain databases

Gene3Di1.25.40.10. 2 hits.
InterProiIPR003107. HAT.
IPR011990. TPR-like_helical_dom.
[Graphical view]
SMARTiSM00386. HAT. 7 hits.
[Graphical view]
SUPFAMiSSF48452. SSF48452. 2 hits.
ProtoNetiSearch...

Publicationsi

  1. "Complete sequencing and characterization of 21,243 full-length human cDNAs."
    Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R., Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H., Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S.
    , Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K., Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S., Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O., Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H., Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B., Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H., Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O., Isogai T., Sugano S.
    Nat. Genet. 36:40-45(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
    Tissue: Placenta.
  2. "The DNA sequence and analysis of human chromosome 14."
    Heilig R., Eckenberg R., Petit J.-L., Fonknechten N., Da Silva C., Cattolico L., Levy M., Barbe V., De Berardinis V., Ureta-Vidal A., Pelletier E., Vico V., Anthouard V., Rowen L., Madan A., Qin S., Sun H., Du H.
    , Pepin K., Artiguenave F., Robert C., Cruaud C., Bruels T., Jaillon O., Friedlander L., Samson G., Brottier P., Cure S., Segurens B., Aniere F., Samain S., Crespeau H., Abbasi N., Aiach N., Boscus D., Dickhoff R., Dors M., Dubois I., Friedman C., Gouyvenoux M., James R., Madan A., Mairey-Estrada B., Mangenot S., Martins N., Menard M., Oztas S., Ratcliffe A., Shaffer T., Trask B., Vacherie B., Bellemere C., Belser C., Besnard-Gonnet M., Bartol-Mavel D., Boutard M., Briez-Silla S., Combette S., Dufosse-Laurent V., Ferron C., Lechaplais C., Louesse C., Muselet D., Magdelenat G., Pateau E., Petit E., Sirvain-Trukniewicz P., Trybou A., Vega-Czarny N., Bataille E., Bluet E., Bordelais I., Dubois M., Dumont C., Guerin T., Haffray S., Hammadi R., Muanga J., Pellouin V., Robert D., Wunderle E., Gauguet G., Roy A., Sainte-Marthe L., Verdier J., Verdier-Discala C., Hillier L.W., Fulton L., McPherson J., Matsuda F., Wilson R., Scarpelli C., Gyapay G., Wincker P., Saurin W., Quetier F., Waterston R., Hood L., Weissenbach J.
    Nature 421:601-607(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  3. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
    The MGC Project Team
    Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
    Tissue: Uterus.
  4. Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  5. "An enzyme assisted RP-RPLC approach for in-depth analysis of human liver phosphoproteome."
    Bian Y., Song C., Cheng K., Dong M., Wang F., Huang J., Sun D., Wang L., Ye M., Zou H.
    J. Proteomics 96:253-262(2014) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-44, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Liver.

Entry informationi

Entry nameiPRP39_HUMAN
AccessioniPrimary (citable) accession number: Q86UA1
Secondary accession number(s): Q08AL1, Q08AL2, Q9NUU5
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 31, 2006
Last sequence update: February 10, 2009
Last modified: July 6, 2016
This is version 108 of the entry and version 3 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

Complete proteome, Reference proteome

Documents

  1. Human chromosome 14
    Human chromosome 14: 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. 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.