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Protein

U3 small nucleolar RNA-associated protein 4 homolog

Gene

UTP4

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

Functioni

May be a transcriptional regulator. Acts as a positive regulator of HIVEP1 which specifically binds to the DNA sequence 5'-GGGACTTTCC-3' found in enhancer elements of numerous viral promoters such as those of HIV-1, SV40, or CMV. Ribosome biogenesis factor involved in small subunit (SSU) pre-rRNA processing at sites A', A0, 1 and 2b.2 Publications

GO - Molecular functioni

  • poly(A) RNA binding Source: UniProtKB

GO - Biological processi

  • maturation of SSU-rRNA Source: UniProtKB
  • regulation of transcription, DNA-templated Source: UniProtKB
  • rRNA processing Source: Reactome
  • transcription, DNA-templated Source: UniProtKB-KW
Complete GO annotation...

Keywords - Biological processi

rRNA processing, Transcription, Transcription regulation

Enzyme and pathway databases

ReactomeiR-HSA-6790901. rRNA modification in the nucleus and cytosol.
R-HSA-6791226. Major pathway of rRNA processing in the nucleolus and cytosol.
SignaLinkiQ969X6.

Names & Taxonomyi

Protein namesi
Recommended name:
U3 small nucleolar RNA-associated protein 4 homolog
Alternative name(s):
Cirhin
UTP4 small subunit processome component
Gene namesi
Name:UTP4Imported
Synonyms:CIRH1A, cPERP-E1 Publication, KIAA1988
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 16

Organism-specific databases

HGNCiHGNC:1983. UTP4.

Subcellular locationi

GO - Cellular componenti

  • chromosome Source: UniProtKB
  • fibrillar center Source: UniProtKB
  • nucleolus Source: UniProtKB
  • nucleoplasm Source: Reactome
  • t-UTP complex Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Chromosome, Nucleus

Pathology & Biotechi

Keywords - Diseasei

Disease mutation

Organism-specific databases

DisGeNETi84916.
MalaCardsiCIRH1A.
OpenTargetsiENSG00000141076.
Orphaneti168583. Hereditary North American Indian childhood cirrhosis.
PharmGKBiPA26520.

Polymorphism and mutation databases

BioMutaiCIRH1A.
DMDMi41016916.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000509081 – 686U3 small nucleolar RNA-associated protein 4 homologAdd BLAST686

Post-translational modificationi

May be phosphorylated during mitosis; may control the association of this protein with WRD43 and UTP15.1 Publication

Keywords - PTMi

Phosphoprotein

Proteomic databases

EPDiQ969X6.
MaxQBiQ969X6.
PaxDbiQ969X6.
PeptideAtlasiQ969X6.
PRIDEiQ969X6.

2D gel databases

SWISS-2DPAGEQ969X6.

PTM databases

iPTMnetiQ969X6.
PhosphoSitePlusiQ969X6.

Expressioni

Gene expression databases

BgeeiENSG00000141076.
CleanExiHS_CIRH1A.
ExpressionAtlasiQ969X6. baseline and differential.
GenevisibleiQ969X6. HS.

Organism-specific databases

HPAiHPA041139.

Interactioni

Subunit structurei

Interacts with HIVEP1 (PubMed:19732766). Forms a complex with NOL11, UTP15, WDR43 and WDR75; within this complex, directly interacts with NOL11, UTP15 and WDR43 (PubMed:22916032, PubMed:24219289).3 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
HIVEP1P158223EBI-2602591,EBI-722264

Protein-protein interaction databases

BioGridi124353. 34 interactors.
IntActiQ969X6. 16 interactors.
MINTiMINT-3050326.
STRINGi9606.ENSP00000327179.

Structurei

3D structure databases

ProteinModelPortaliQ969X6.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Repeati7 – 50WD 1Add BLAST44
Repeati51 – 92WD 2Add BLAST42
Repeati93 – 135WD 3Add BLAST43
Repeati136 – 181WD 4Add BLAST46
Repeati182 – 226WD 5Add BLAST45
Repeati227 – 275WD 6Add BLAST49
Repeati276 – 317WD 7Add BLAST42
Repeati318 – 377WD 8Add BLAST60
Repeati378 – 427WD 9Add BLAST50
Repeati428 – 475WD 10Add BLAST48
Repeati476 – 516WD 11Add BLAST41
Repeati517 – 566WD 12Add BLAST50
Repeati567 – 627WD 13Add BLAST61
Repeati628 – 666WD 14Add BLAST39

Sequence similaritiesi

Contains 14 WD repeats.PROSITE-ProRule annotation

Keywords - Domaini

Repeat, WD repeat

Phylogenomic databases

eggNOGiKOG2048. Eukaryota.
ENOG410XQNR. LUCA.
GeneTreeiENSGT00390000008662.
HOVERGENiHBG050963.
InParanoidiQ969X6.
KOiK14548.
OrthoDBiEOG091G06F9.
PhylomeDBiQ969X6.
TreeFamiTF313159.

Family and domain databases

Gene3Di2.130.10.10. 2 hits.
InterProiIPR015943. WD40/YVTN_repeat-like_dom.
IPR001680. WD40_repeat.
IPR017986. WD40_repeat_dom.
[Graphical view]
PfamiPF00400. WD40. 1 hit.
[Graphical view]
SMARTiSM00320. WD40. 10 hits.
[Graphical view]
SUPFAMiSSF50978. SSF50978. 1 hit.
PROSITEiPS50294. WD_REPEATS_REGION. 1 hit.
[Graphical view]

Sequences (3)i

Sequence statusi: Complete.

This entry describes 3 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q969X6-1) [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
MGEFKVHRVR FFNYVPSGIR CVAYNNQSNR LAVSRTDGTV EIYNLSANYF
60 70 80 90 100
QEKFFPGHES RATEALCWAE GQRLFSAGLN GEIMEYDLQA LNIKYAMDAF
110 120 130 140 150
GGPIWSMAAS PSGSQLLVGC EDGSVKLFQI TPDKIQFERN FDRQKSRILS
160 170 180 190 200
LSWHPSGTHI AAGSIDYISV FDVKSGSAVH KMIVDRQYMG VSKRKCIVWG
210 220 230 240 250
VAFLSDGTII SVDSAGKVQF WDSATGTLVK SHLIANADVQ SIAVADQEDS
260 270 280 290 300
FVVGTAEGTV FHFQLVPVTS NSSEKQWVRT KPFQHHTHDV RTVAHSPTAL
310 320 330 340 350
ISGGTDTHLV FRPLMEKVEV KNYDAALRKI TFPHRCLISC SKKRQLLLFQ
360 370 380 390 400
FAHHLELWRL GSTVATGKNG DTLPLSKNAD HLLHLKTKGP ENIICSCISP
410 420 430 440 450
CGSWIAYSTV SRFFLYRLNY EHDNISLKRV SKMPAFLRSA LQILFSEDST
460 470 480 490 500
KLFVASNQGA LHIVQLSGGS FKHLHAFQPQ SGTVEAMCLL AVSPDGNWLA
510 520 530 540 550
ASGTSAGVHV YNVKQLKLHC TVPAYNFPVT AMAIAPNTNN LVIAHSDQQV
560 570 580 590 600
FEYSIPDKQY TDWSRTVQKQ GFHHLWLQRD TPITHISFHP KRPMHILLHD
610 620 630 640 650
AYMFCIIDKS LPLPNDKTLL YNPFPPTNES DVIRRRTAHA FKISKIYKPL
660 670 680
LFMDLLDERT LVAVERPLDD IIAQLPPPIK KKKFGT
Length:686
Mass (Da):76,890
Last modified:December 1, 2001 - v1
Checksum:i595D8B2F47C03299
GO
Isoform 2 (identifier: Q969X6-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     368-482: Missing.

Show »
Length:571
Mass (Da):64,119
Checksum:i933667DDFFA4F345
GO
Isoform 3 (identifier: Q969X6-3) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     612-625: PLPNDKTLLYNPFP → VSSSLLPPKSSSES
     626-686: Missing.

Note: May be due to intron retention.
Show »
Length:625
Mass (Da):69,639
Checksum:iC1E06A47C8E5078D
GO

Sequence cautioni

The sequence BAB55100 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.Curated
The sequence BAB55116 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.Curated
The sequence BAB55212 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.Curated
The sequence BAB85574 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti101G → V in BAB55116 (PubMed:14702039).Curated1
Sequence conflicti290V → M in BAB55251 (PubMed:14702039).Curated1
Sequence conflicti378N → S in BAB55100 (PubMed:14702039).Curated1
Sequence conflicti419N → S in BAC11214 (PubMed:14702039).Curated1
Sequence conflicti594M → V in BAB55100 (PubMed:14702039).Curated1
Sequence conflicti624F → L in BAC11214 (PubMed:14702039).Curated1

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_053388438R → H.Corresponds to variant rs8056684dbSNPEnsembl.1
Natural variantiVAR_017445565R → W Found in patients with North American Indian childhood cirrhosis; unknown pathological significance; does not affect nucleolar protein location; decreased interaction with HIVEP1 measured in yeast two-hybrid screening. 3 PublicationsCorresponds to variant rs119465999dbSNPEnsembl.1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_009201368 – 482Missing in isoform 2. 1 PublicationAdd BLAST115
Alternative sequenceiVSP_009202612 – 625PLPND…YNPFP → VSSSLLPPKSSSES in isoform 3. 2 PublicationsAdd BLAST14
Alternative sequenceiVSP_009203626 – 686Missing in isoform 3. 2 PublicationsAdd BLAST61

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB075868 mRNA. Translation: BAB85574.2. Different initiation.
AK027419 mRNA. Translation: BAB55100.1. Different initiation.
AK027445 mRNA. Translation: BAB55116.1. Different initiation.
AK027584 mRNA. Translation: BAB55212.1. Different initiation.
AK027634 mRNA. Translation: BAB55251.1.
AK027675 mRNA. Translation: BAB55287.1.
AK074795 mRNA. Translation: BAC11214.1.
BC000167 mRNA. Translation: AAH00167.1.
BC009348 mRNA. Translation: AAH09348.1.
CCDSiCCDS10872.1. [Q969X6-1]
RefSeqiNP_116219.2. NM_032830.2. [Q969X6-1]
UniGeneiHs.461113.

Genome annotation databases

EnsembliENST00000314423; ENSP00000327179; ENSG00000141076. [Q969X6-1]
ENST00000352319; ENSP00000339164; ENSG00000141076. [Q969X6-2]
ENST00000563094; ENSP00000456622; ENSG00000141076. [Q969X6-3]
ENST00000575702; ENSP00000458843; ENSG00000262788.
GeneIDi84916.
KEGGihsa:84916.
UCSCiuc002ewr.3. human. [Q969X6-1]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB075868 mRNA. Translation: BAB85574.2. Different initiation.
AK027419 mRNA. Translation: BAB55100.1. Different initiation.
AK027445 mRNA. Translation: BAB55116.1. Different initiation.
AK027584 mRNA. Translation: BAB55212.1. Different initiation.
AK027634 mRNA. Translation: BAB55251.1.
AK027675 mRNA. Translation: BAB55287.1.
AK074795 mRNA. Translation: BAC11214.1.
BC000167 mRNA. Translation: AAH00167.1.
BC009348 mRNA. Translation: AAH09348.1.
CCDSiCCDS10872.1. [Q969X6-1]
RefSeqiNP_116219.2. NM_032830.2. [Q969X6-1]
UniGeneiHs.461113.

3D structure databases

ProteinModelPortaliQ969X6.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi124353. 34 interactors.
IntActiQ969X6. 16 interactors.
MINTiMINT-3050326.
STRINGi9606.ENSP00000327179.

PTM databases

iPTMnetiQ969X6.
PhosphoSitePlusiQ969X6.

Polymorphism and mutation databases

BioMutaiCIRH1A.
DMDMi41016916.

2D gel databases

SWISS-2DPAGEQ969X6.

Proteomic databases

EPDiQ969X6.
MaxQBiQ969X6.
PaxDbiQ969X6.
PeptideAtlasiQ969X6.
PRIDEiQ969X6.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000314423; ENSP00000327179; ENSG00000141076. [Q969X6-1]
ENST00000352319; ENSP00000339164; ENSG00000141076. [Q969X6-2]
ENST00000563094; ENSP00000456622; ENSG00000141076. [Q969X6-3]
ENST00000575702; ENSP00000458843; ENSG00000262788.
GeneIDi84916.
KEGGihsa:84916.
UCSCiuc002ewr.3. human. [Q969X6-1]

Organism-specific databases

CTDi84916.
DisGeNETi84916.
GeneCardsiCIRH1A.
HGNCiHGNC:1983. UTP4.
HPAiHPA041139.
MalaCardsiCIRH1A.
MIMi607456. gene.
neXtProtiNX_Q969X6.
OpenTargetsiENSG00000141076.
Orphaneti168583. Hereditary North American Indian childhood cirrhosis.
PharmGKBiPA26520.
HUGEiSearch...
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG2048. Eukaryota.
ENOG410XQNR. LUCA.
GeneTreeiENSGT00390000008662.
HOVERGENiHBG050963.
InParanoidiQ969X6.
KOiK14548.
OrthoDBiEOG091G06F9.
PhylomeDBiQ969X6.
TreeFamiTF313159.

Enzyme and pathway databases

ReactomeiR-HSA-6790901. rRNA modification in the nucleus and cytosol.
R-HSA-6791226. Major pathway of rRNA processing in the nucleolus and cytosol.
SignaLinkiQ969X6.

Miscellaneous databases

ChiTaRSiCIRH1A. human.
GeneWikiiCIRH1A.
GenomeRNAii84916.
PROiQ969X6.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000141076.
CleanExiHS_CIRH1A.
ExpressionAtlasiQ969X6. baseline and differential.
GenevisibleiQ969X6. HS.

Family and domain databases

Gene3Di2.130.10.10. 2 hits.
InterProiIPR015943. WD40/YVTN_repeat-like_dom.
IPR001680. WD40_repeat.
IPR017986. WD40_repeat_dom.
[Graphical view]
PfamiPF00400. WD40. 1 hit.
[Graphical view]
SMARTiSM00320. WD40. 10 hits.
[Graphical view]
SUPFAMiSSF50978. SSF50978. 1 hit.
PROSITEiPS50294. WD_REPEATS_REGION. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiUTP4_HUMAN
AccessioniPrimary (citable) accession number: Q969X6
Secondary accession number(s): Q8NCD9
, Q8TF14, Q96SP0, Q96SR9, Q96SZ9, Q96T13, Q9BWK6
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 16, 2004
Last sequence update: December 1, 2001
Last modified: November 30, 2016
This is version 144 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

Complete proteome, Reference proteome

Documents

  1. Human chromosome 16
    Human chromosome 16: 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. 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.