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Protein

Heterogeneous nuclear ribonucleoprotein U

Gene

HNRNPU

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

Functioni

Component of the CRD-mediated complex that promotes MYC mRNA stabilization. Binds to pre-mRNA. Has high affinity for scaffold-attached region (SAR) DNA. Binds to double- and single-stranded DNA and RNA. Plays a role in the circadian regulation of the core clock component ARNTL/BMAL1 transcription (By similarity).By similarity1 Publication

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi504 – 511ATPSequence analysis8

GO - Molecular functioni

  • ATP binding Source: UniProtKB-KW
  • core promoter binding Source: UniProtKB
  • DNA binding Source: ProtInc
  • enhancer binding Source: Ensembl
  • poly(G) binding Source: Ensembl
  • ribonucleoprotein complex binding Source: Ensembl
  • RNA binding Source: UniProtKB
  • telomerase RNA binding Source: BHF-UCL

GO - Biological processi

  • cardiac muscle cell development Source: Ensembl
  • cellular response to dexamethasone stimulus Source: Ensembl
  • circadian regulation of gene expression Source: UniProtKB
  • CRD-mediated mRNA stabilization Source: UniProtKB
  • mRNA splicing, via spliceosome Source: Reactome
  • negative regulation of telomere maintenance via telomerase Source: BHF-UCL
  • osteoblast differentiation Source: UniProtKB
  • positive regulation of DNA topoisomerase (ATP-hydrolyzing) activity Source: Ensembl
  • positive regulation of gene expression Source: Ensembl
  • RNA metabolic process Source: Reactome
  • RNA processing Source: ProtInc

Keywordsi

Molecular functionDNA-binding, Ribonucleoprotein, RNA-binding
Biological processBiological rhythms, mRNA processing, mRNA splicing
LigandATP-binding, Nucleotide-binding

Enzyme and pathway databases

ReactomeiR-HSA-72163. mRNA Splicing - Major Pathway.
R-HSA-72203. Processing of Capped Intron-Containing Pre-mRNA.
SIGNORiQ00839.

Names & Taxonomyi

Protein namesi
Recommended name:
Heterogeneous nuclear ribonucleoprotein U
Short name:
hnRNP U
Alternative name(s):
Scaffold attachment factor A
Short name:
SAF-A
p120
pp120
Gene namesi
Name:HNRNPU
Synonyms:HNRPU, SAFA, U21.1
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 1

Organism-specific databases

EuPathDBiHostDB:ENSG00000153187.16.
HGNCiHGNC:5048. HNRNPU.

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Keywords - Cellular componenti

Cytoplasm, Nucleus, Spliceosome

Pathology & Biotechi

Involvement in diseasei

Epileptic encephalopathy, early infantile, 54 (EIEE54)2 Publications
The disease is caused by mutations affecting the gene represented in this entry.
Disease descriptionA form of epileptic encephalopathy, a heterogeneous group of severe childhood onset epilepsies characterized by refractory seizures, neurodevelopmental impairment, and poor prognosis. Development is normal prior to seizure onset, after which cognitive and motor delays become apparent.
See also OMIM:617391
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_078622171 – 825Missing in EIEE54. 1 PublicationAdd BLAST655
Natural variantiVAR_078623805 – 825Missing in EIEE54; unknown pathological significance. 1 PublicationAdd BLAST21

Keywords - Diseasei

Disease mutation, Epilepsy

Organism-specific databases

DisGeNETi3192.
MIMi617391. phenotype.
OpenTargetsiENSG00000153187.
PharmGKBiPA162391486.

Polymorphism and mutation databases

BioMutaiHNRNPU.
DMDMi254763463.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemovedCombined sources3 Publications
ChainiPRO_00000818722 – 825Heterogeneous nuclear ribonucleoprotein UAdd BLAST824

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei2N-acetylserine; partialCombined sources2 Publications1
Modified residuei4PhosphoserineCombined sources1
Modified residuei17N6-acetyllysineBy similarity1
Modified residuei21N6-acetyllysineBy similarity1
Modified residuei59PhosphoserineCombined sources1
Modified residuei66PhosphoserineCombined sources1
Modified residuei186N6-acetyllysineBy similarity1
Modified residuei187ADP-ribosylserine1 Publication1
Modified residuei255CitrullineBy similarity1
Modified residuei265N6-acetyllysine; alternateCombined sources1
Cross-linki265Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO1); alternateCombined sources
Cross-linki265Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2); alternateCombined sources
Modified residuei266PhosphotyrosineBy similarity1
Modified residuei267PhosphoserineCombined sources1
Modified residuei271PhosphoserineCombined sources1
Modified residuei286PhosphothreonineCombined sources1
Modified residuei352N6-acetyllysineCombined sources1
Cross-linki495Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources
Modified residuei516N6-acetyllysine; alternateCombined sources1
Cross-linki516Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2); alternateCombined sources
Modified residuei524N6-acetyllysine; alternateCombined sources1
Cross-linki524Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2); alternateCombined sources
Modified residuei532PhosphothreonineCombined sources1
Cross-linki536Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources
Modified residuei551N6-acetyllysineCombined sources1
Modified residuei565N6-acetyllysine; alternateCombined sources1
Cross-linki565Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2); alternateCombined sources
Cross-linki574Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources
Modified residuei582PhosphothreonineCombined sources1
Cross-linki609Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources
Cross-linki626Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources
Modified residuei635N6-acetyllysine; alternateCombined sources1
Cross-linki635Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2); alternateCombined sources
Cross-linki664Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources
Cross-linki670Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources
Modified residuei702Omega-N-methylarginineCombined sources1
Modified residuei715Asymmetric dimethylarginineBy similarity1
Modified residuei720Asymmetric dimethylarginineBy similarity1
Modified residuei727Asymmetric dimethylarginineBy similarity1
Modified residuei733Asymmetric dimethylarginine; alternateCombined sources1
Modified residuei733Omega-N-methylarginine; alternateBy similarity1
Modified residuei739Asymmetric dimethylarginine; alternateCombined sources1
Modified residuei739Dimethylated arginine; in A2780 ovarian carcinoma cell line1 Publication1
Modified residuei739Omega-N-methylarginine; alternateCombined sources1
Modified residuei755Asymmetric dimethylarginineCombined sources1
Modified residuei762Asymmetric dimethylarginineCombined sources1
Modified residuei814N6-acetyllysine; alternateCombined sources1
Cross-linki814Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2); alternateCombined sources
Isoform Short (identifier: Q00839-2)
Modified residuei215N6-acetyllysineCombined sources1

Post-translational modificationi

Extensively phosphorylated.1 Publication
Arg-739 is dimethylated, probably to asymmetric dimethylarginine.1 Publication
Citrullinated by PADI4.By similarity

Keywords - PTMi

Acetylation, ADP-ribosylation, Citrullination, Isopeptide bond, Methylation, Phosphoprotein, Ubl conjugation

Proteomic databases

EPDiQ00839.
MaxQBiQ00839.
PaxDbiQ00839.
PeptideAtlasiQ00839.
PRIDEiQ00839.

PTM databases

iPTMnetiQ00839.
PhosphoSitePlusiQ00839.
SwissPalmiQ00839.

Expressioni

Gene expression databases

BgeeiENSG00000153187.
CleanExiHS_HNRNPU.
ExpressionAtlasiQ00839. baseline and differential.
GenevisibleiQ00839. HS.

Organism-specific databases

HPAiCAB011532.
HPA041057.
HPA058707.

Interactioni

Subunit structurei

Identified in the spliceosome C complex. Component of the coding region determinant (CRD)-mediated complex, composed of DHX9, HNRNPU, IGF2BP1, SYNCRIP and YBX1. Identified in a IGF2BP1-dependent mRNP granule complex containing untranslated mRNAs. Interacts with IGF2BP1, IGF2BP2, IGF2BP3 and ERBB4. Ligand for CR2. Interacts with CRY1 (By similarity). Interacts with UBQLN2 (PubMed:25616961). Interacts with GEMIN5 (PubMed:25911097).By similarity8 Publications

Binary interactionsi

Show more details

Protein-protein interaction databases

BioGridi109433. 524 interactors.
CORUMiQ00839.
DIPiDIP-684N.
IntActiQ00839. 319 interactors.
MINTiMINT-1654412.
STRINGi9606.ENSP00000283179.

Structurei

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1ZRJNMR-A23-42[»]
ProteinModelPortaliQ00839.
SMRiQ00839.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ00839.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini8 – 42SAPPROSITE-ProRule annotationAdd BLAST35
Domaini267 – 464B30.2/SPRYPROSITE-ProRule annotationAdd BLAST198

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni714 – 739RNA-binding RGG-box1 PublicationAdd BLAST26

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi2 – 160Asp/Glu-rich (acidic)Add BLAST159
Compositional biasi84 – 94Poly-GluAdd BLAST11
Compositional biasi161 – 209Gln-richAdd BLAST49
Compositional biasi703 – 825Gly-richAdd BLAST123
Compositional biasi740 – 750Poly-GlyAdd BLAST11

Phylogenomic databases

eggNOGiENOG410IR1W. Eukaryota.
ENOG410Y1WQ. LUCA.
GeneTreeiENSGT00390000020210.
HOGENOMiHOG000253920.
HOVERGENiHBG061101.
InParanoidiQ00839.
KOiK12888.
OMAiQAFNQSW.
OrthoDBiEOG091G041T.
PhylomeDBiQ00839.
TreeFamiTF317301.

Family and domain databases

Gene3Di1.10.720.30. 1 hit.
InterProiView protein in InterPro
IPR001870. B30.2/SPRY.
IPR013320. ConA-like_dom.
IPR026745. hnRNP_U.
IPR027417. P-loop_NTPase.
IPR003034. SAP_dom.
IPR003877. SPRY_dom.
PANTHERiPTHR12381:SF63. PTHR12381:SF63. 1 hit.
PfamiView protein in Pfam
PF02037. SAP. 1 hit.
PF00622. SPRY. 1 hit.
SMARTiView protein in SMART
SM00513. SAP. 1 hit.
SM00449. SPRY. 1 hit.
SUPFAMiSSF49899. SSF49899. 1 hit.
SSF52540. SSF52540. 1 hit.
SSF68906. SSF68906. 1 hit.
PROSITEiView protein in PROSITE
PS50188. B302_SPRY. 1 hit.
PS50800. SAP. 1 hit.

Sequences (2)i

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

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

Isoform Long (identifier: Q00839-1) [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
MSSSPVNVKK LKVSELKEEL KKRRLSDKGL KAELMERLQA ALDDEEAGGR
60 70 80 90 100
PAMEPGNGSL DLGGDSAGRS GAGLEQEAAA GGDEEEEEEE EEEEGISALD
110 120 130 140 150
GDQMELGEEN GAAGAADSGP MEEEEAASED ENGDDQGFQE GEDELGDEEE
160 170 180 190 200
GAGDENGHGE QQPQPPATQQ QQPQQQRGAA KEAAGKSSGP TSLFAVTVAP
210 220 230 240 250
PGARQGQQQA GGKKKAEGGG GGGRPGAPAA GDGKTEQKGG DKKRGVKRPR
260 270 280 290 300
EDHGRGYFEY IEENKYSRAK SPQPPVEEED EHFDDTVVCL DTYNCDLHFK
310 320 330 340 350
ISRDRLSASS LTMESFAFLW AGGRASYGVS KGKVCFEMKV TEKIPVRHLY
360 370 380 390 400
TKDIDIHEVR IGWSLTTSGM LLGEEEFSYG YSLKGIKTCN CETEDYGEKF
410 420 430 440 450
DENDVITCFA NFESDEVELS YAKNGQDLGV AFKISKEVLA GRPLFPHVLC
460 470 480 490 500
HNCAVEFNFG QKEKPYFPIP EEYTFIQNVP LEDRVRGPKG PEEKKDCEVV
510 520 530 540 550
MMIGLPGAGK TTWVTKHAAE NPGKYNILGT NTIMDKMMVA GFKKQMADTG
560 570 580 590 600
KLNTLLQRAP QCLGKFIEIA ARKKRNFILD QTNVSAAAQR RKMCLFAGFQ
610 620 630 640 650
RKAVVVCPKD EDYKQRTQKK AEVEGKDLPE HAVLKMKGNF TLPEVAECFD
660 670 680 690 700
EITYVELQKE EAQKLLEQYK EESKKALPPE KKQNTGSKKS NKNKSGKNQF
710 720 730 740 750
NRGGGHRGRG GFNMRGGNFR GGAPGNRGGY NRRGNMPQRG GGGGGSGGIG
760 770 780 790 800
YPYPRAPVFP GRGSYSNRGN YNRGGMPNRG NYNQNFRGRG NNRGYKNQSQ
810 820
GYNQWQQGQF WGQKPWSQHY HQGYY
Length:825
Mass (Da):90,584
Last modified:July 28, 2009 - v6
Checksum:i5D4EC4188436831F
GO
Isoform Short (identifier: Q00839-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     213-231: Missing.

Show »
Length:806
Mass (Da):88,980
Checksum:iBCE1AD365501EDC1
GO

Sequence cautioni

The sequence AAC19382 differs from that shown. Aberrant splicing.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti603A → V in AAH07950 (PubMed:15489334).Curated1

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_078622171 – 825Missing in EIEE54. 1 PublicationAdd BLAST655
Natural variantiVAR_014712712F → L2 PublicationsCorresponds to variant dbSNP:rs1052660Ensembl.1
Natural variantiVAR_078623805 – 825Missing in EIEE54; unknown pathological significance. 1 PublicationAdd BLAST21

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_005846213 – 231Missing in isoform Short. 3 PublicationsAdd BLAST19

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X65488 mRNA. Translation: CAA46472.1.
AF068846 mRNA. Translation: AAC19382.1. Sequence problems.
BX323046 Genomic DNA. No translation available.
BC003367 mRNA. Translation: AAH03367.1.
BC003621 mRNA. Translation: AAH03621.1.
BC007950 mRNA. Translation: AAH07950.2.
BC024767 mRNA. Translation: AAH24767.1.
BC034925 mRNA. Translation: AAH34925.1.
CCDSiCCDS31081.1. [Q00839-2]
CCDS41479.1. [Q00839-1]
PIRiS22765.
RefSeqiNP_004492.2. NM_004501.3. [Q00839-2]
NP_114032.2. NM_031844.2. [Q00839-1]
XP_016856604.1. XM_017001115.1. [Q00839-1]
XP_016856605.1. XM_017001116.1. [Q00839-1]
XP_016856606.1. XM_017001117.1. [Q00839-2]
UniGeneiHs.106212.
Hs.411490.
Hs.743421.

Genome annotation databases

EnsembliENST00000444376; ENSP00000393151; ENSG00000153187. [Q00839-2]
ENST00000640218; ENSP00000491215; ENSG00000153187. [Q00839-1]
GeneIDi3192.
KEGGihsa:3192.
UCSCiuc001iaz.2. human. [Q00839-1]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Similar proteinsi

Entry informationi

Entry nameiHNRPU_HUMAN
AccessioniPrimary (citable) accession number: Q00839
Secondary accession number(s): O75507
, Q8N174, Q96HY9, Q9BQ09
Entry historyiIntegrated into UniProtKB/Swiss-Prot: April 1, 1993
Last sequence update: July 28, 2009
Last modified: September 27, 2017
This is version 199 of the entry and version 6 of the sequence. See 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 1
    Human chromosome 1: 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