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Protein

U3 small nucleolar RNA-associated protein 4 homolog

Gene

UTP4

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

Functioni

Ribosome biogenesis factor. Involved in nucleolar processing of pre-18S ribosomal RNA. Involved in small subunit (SSU) pre-rRNA processing at sites A', A0, 1 and 2b. Required for optimal pre-ribosomal RNA transcription by RNA polymerase (PubMed:17699751, PubMed:19732766). 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 (PubMed:19732766).3 Publications

GO - Molecular functioni

GO - Biological processi

  • maturation of SSU-rRNA Source: UniProtKB
  • maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) Source: GO_Central
  • regulation of transcription, DNA-templated Source: UniProtKB
  • rRNA processing Source: Reactome

Keywordsi

Biological processRibosome biogenesis, 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

EuPathDBiHostDB:ENSG00000141076.17
HGNCiHGNC:1983 UTP4
MIMi607456 gene
neXtProtiNX_Q969X6

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

Chromosome, Nucleus

Pathology & Biotechi

Keywords - Diseasei

Disease mutation

Organism-specific databases

DisGeNETi84916
MalaCardsiUTP4
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

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Cross-linki321Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources

Post-translational modificationi

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

Keywords - PTMi

Isopeptide bond, Phosphoprotein, Ubl conjugation

Proteomic databases

EPDiQ969X6
MaxQBiQ969X6
PaxDbiQ969X6
PeptideAtlasiQ969X6
PRIDEiQ969X6
ProteomicsDBi75873
75874 [Q969X6-2]
75875 [Q969X6-3]

2D gel databases

SWISS-2DPAGEiQ969X6

PTM databases

iPTMnetiQ969X6
PhosphoSitePlusiQ969X6

Expressioni

Gene expression databases

BgeeiENSG00000141076 Expressed in 198 organ(s), highest expression level in kidney epithelium
CleanExiHS_CIRH1A
ExpressionAtlasiQ969X6 baseline and differential
GenevisibleiQ969X6 HS

Organism-specific databases

HPAiHPA041139
HPA043542

Interactioni

Subunit structurei

Interacts with HIVEP1 (PubMed:19732766) Interacts with NOL11 (PubMed:22916032). Interacts directly with UTP15 and WDR43 (PubMed:24219289). May be a component of the proposed t-UTP subcomplex of the ribosomal small subunit (SSU) processome containing at least UTP4, WDR43, HEATR1, UTP15, WDR75 (PubMed:17699751, PubMed:22916032).1 Publication3 Publications

Binary interactionsi

Protein-protein interaction databases

BioGridi124353, 51 interactors
IntActiQ969X6, 23 interactors
MINTiQ969X6
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

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, 3 hits
InterProiView protein in InterPro
IPR015943 WD40/YVTN_repeat-like_dom_sf
IPR001680 WD40_repeat
IPR017986 WD40_repeat_dom
IPR036322 WD40_repeat_dom_sf
PfamiView protein in Pfam
PF00400 WD40, 1 hit
SMARTiView protein in SMART
SM00320 WD40, 10 hits
SUPFAMiSSF50978 SSF50978, 1 hit
PROSITEiView protein in PROSITE
PS50294 WD_REPEATS_REGION, 1 hit

Sequences (3+)i

Sequence statusi: Complete.

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

This entry has 3 described isoforms and 12 potential isoforms that are computationally mapped.Show allAlign All

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

Computationally mapped potential isoform sequencesi

There are 12 potential isoforms mapped to this entry.BLASTAlignShow allAdd to basket
EntryEntry nameProtein names
Gene namesLengthAnnotation
I3L4T9I3L4T9_HUMAN
U3 small nucleolar RNA-associated p...
UTP4
182Annotation score:
H3BSH7H3BSH7_HUMAN
U3 small nucleolar RNA-associated p...
UTP4
700Annotation score:
H3BPD7H3BPD7_HUMAN
U3 small nucleolar RNA-associated p...
UTP4
148Annotation score:
J3KSI1J3KSI1_HUMAN
U3 small nucleolar RNA-associated p...
UTP4
198Annotation score:
J3KTR0J3KTR0_HUMAN
U3 small nucleolar RNA-associated p...
UTP4
142Annotation score:
J3KSE6J3KSE6_HUMAN
U3 small nucleolar RNA-associated p...
UTP4
78Annotation score:
H3BRM8H3BRM8_HUMAN
U3 small nucleolar RNA-associated p...
UTP4
211Annotation score:
A0A0J9YWK2A0A0J9YWK2_HUMAN
U3 small nucleolar RNA-associated p...
UTP4
450Annotation score:
A0A0J9YXV4A0A0J9YXV4_HUMAN
U3 small nucleolar RNA-associated p...
UTP4
396Annotation score:
A0A0J9YX18A0A0J9YX18_HUMAN
U3 small nucleolar RNA-associated p...
UTP4
71Annotation score:
There are more potential isoformsShow all

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 dbSNP:rs8056684Ensembl.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 dbSNP:rs119465999EnsemblClinVar.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

Similar proteinsi

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, 51 interactors
IntActiQ969X6, 23 interactors
MINTiQ969X6
STRINGi9606.ENSP00000327179

PTM databases

iPTMnetiQ969X6
PhosphoSitePlusiQ969X6

Polymorphism and mutation databases

BioMutaiCIRH1A
DMDMi41016916

2D gel databases

SWISS-2DPAGEiQ969X6

Proteomic databases

EPDiQ969X6
MaxQBiQ969X6
PaxDbiQ969X6
PeptideAtlasiQ969X6
PRIDEiQ969X6
ProteomicsDBi75873
75874 [Q969X6-2]
75875 [Q969X6-3]

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
EuPathDBiHostDB:ENSG00000141076.17
GeneCardsiUTP4
HGNCiHGNC:1983 UTP4
HPAiHPA041139
HPA043542
MalaCardsiUTP4
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

ChiTaRSiUTP4 human
GeneWikiiCIRH1A
GenomeRNAii84916
PROiPR:Q969X6
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000141076 Expressed in 198 organ(s), highest expression level in kidney epithelium
CleanExiHS_CIRH1A
ExpressionAtlasiQ969X6 baseline and differential
GenevisibleiQ969X6 HS

Family and domain databases

Gene3Di2.130.10.10, 3 hits
InterProiView protein in InterPro
IPR015943 WD40/YVTN_repeat-like_dom_sf
IPR001680 WD40_repeat
IPR017986 WD40_repeat_dom
IPR036322 WD40_repeat_dom_sf
PfamiView protein in Pfam
PF00400 WD40, 1 hit
SMARTiView protein in SMART
SM00320 WD40, 10 hits
SUPFAMiSSF50978 SSF50978, 1 hit
PROSITEiView protein in PROSITE
PS50294 WD_REPEATS_REGION, 1 hit
ProtoNetiSearch...

Entry informationi

Entry nameiUTP4_HUMAN
AccessioniPrimary (citable) accession number: Q969X6
Secondary accession number(s): Q8NCD9
, Q8TF14, Q96SP0, Q96SR9, Q96SZ9, Q96T13, Q9BWK6
Entry historyiIntegrated into UniProtKB/Swiss-Prot: January 16, 2004
Last sequence update: December 1, 2001
Last modified: November 7, 2018
This is version 161 of the entry and version 1 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

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
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