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Protein

Cell growth-regulating nucleolar protein

Gene

Lyar

Organism
Mus musculus (Mouse)
Status
Reviewed-Annotation score: -Experimental evidence at protein leveli

Functioni

Plays a role in the maintenance of the appropriate processing of 47S/45S pre-rRNA to 32S/30S pre-rRNAs and their subsequent processing to produce 18S and 28S rRNAs (By similarity). Also acts at the level of transcription regulation. Along with PRMT5, binds embryonic globin promoter (By similarity). Represses the expression of embryonic globin Hbb-y gene (PubMed:25092918). In neuroblastoma cells, may also repress the expression of oxidative stress genes, including CHAC1, HMOX1, SLC7A11, ULBP1 and that encoding the small nucleolar RNA SNORD41 (By similarity). Preferentially binds to a DNA motif containing 5'-GGTTAT-3' (By similarity). Stimulates phagocytosis of photoreceptor outer segments by retinal pigment epithelial cells (PubMed:25735755). Prevents NCL self-cleavage, maintaining a normal steady-state level of NCL protein in undifferentiated embryonic stem cells (ESCs), which in turn is essential for ESC self-renewal (PubMed:19489080).By similarity3 Publications

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi6Zinc 11
Metal bindingi9Zinc 11
Metal bindingi21Zinc 11
Metal bindingi25Zinc 11
Metal bindingi33Zinc 21
Metal bindingi36Zinc 21
Metal bindingi48Zinc 21
Metal bindingi51Zinc 21

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri1 – 26C2HC LYAR-type 1PROSITE-ProRule annotationAdd BLAST26
Zinc fingeri28 – 52C2HC LYAR-type 2PROSITE-ProRule annotationAdd BLAST25

GO - Molecular functioni

GO - Biological processi

  • erythrocyte development Source: UniProtKB
  • negative regulation of transcription by RNA polymerase II Source: UniProtKB
  • positive regulation of phagocytosis Source: UniProtKB
  • rRNA processing Source: UniProtKB

Keywordsi

Molecular functionDNA-binding, Repressor
Biological processTranscription, Transcription regulation
LigandMetal-binding, Zinc

Names & Taxonomyi

Protein namesi
Recommended name:
Cell growth-regulating nucleolar protein
Alternative name(s):
Ly1 antibody-reactive protein1 Publication
Protein expressed in male leptotene and zygotene spermatocytes 264
Short name:
MLZ-264
Gene namesi
Name:Lyar
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaMyomorphaMuroideaMuridaeMurinaeMusMus
Proteomesi
  • UP000000589 Componenti: Chromosome 5

Organism-specific databases

MGIiMGI:107470 Lyar

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

Cell projection, Cytoplasm, Nucleus

Pathology & Biotechi

Disruption phenotypei

No visible phenotype. Mutant mice are fully fertile and show intact spermatogenesis.1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000845291 – 388Cell growth-regulating nucleolar proteinAdd BLAST388

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Cross-linki14Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)By similarity
Cross-linki204Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)By similarity

Keywords - PTMi

Isopeptide bond, Ubl conjugation

Proteomic databases

EPDiQ08288
MaxQBiQ08288
PaxDbiQ08288
PeptideAtlasiQ08288
PRIDEiQ08288

PTM databases

iPTMnetiQ08288
PhosphoSitePlusiQ08288

Expressioni

Tissue specificityi

Predominantly expressed in testis, in germ cells, and at a moderate level in spleen, liver and lung (at protein level) (PubMed:19489080, PubMed:23212345, PubMed:24990247). Very high levels in spermatogonia, spermatocytes and round spermatids, but not in testicular sperm and mature sperm (at protein level) (PubMed:20339383, PubMed:23212345, PubMed:24990247). Expressed in ovary (PubMed:20339383). Expressed in the retina, including in photoreceptor outer segments (at protein level) (PubMed:25735755). Expressed in undifferentiated embryonic stem cells (PubMed:19489080, PubMed:23212345).5 Publications

Developmental stagei

Expressed in testis and ovary at 15.5 dpc (PubMed:20339383). May be differentially expressed during spermatogenesis. Detected first at P12, the early stage of spermatogenesis. Levels considerably increase at P16, corresponding to the development of pachytene spermatocytes (PubMed:23212345).2 Publications

Gene expression databases

BgeeiENSMUSG00000067367 Expressed in 280 organ(s), highest expression level in testis
CleanExiMM_LYAR
ExpressionAtlasiQ08288 baseline and differential
GenevisibleiQ08288 MM

Interactioni

Subunit structurei

Interacts with PRMT5; this interaction is direct (By similarity). Interacts with GNL2 and RPL23A (By similarity). Interacts with nucleolin/NCL; this interaction is direct (PubMed:19489080, PubMed:23212345).By similarity2 Publications

Protein-protein interaction databases

BioGridi201254, 2 interactors
IntActiQ08288, 3 interactors
MINTiQ08288
STRINGi10090.ENSMUSP00000084791

Structurei

Secondary structure

1388
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

ProteinModelPortaliQ08288
SMRiQ08288
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ08288

Family & Domainsi

Coiled coil

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Coiled coili174 – 216Sequence analysisAdd BLAST43

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi182 – 344Lys-richAdd BLAST163

Domaini

The N-terminal zinc-finger domains are required for the appropriate production of 28S rRNA and the formation of pre-60S particles.By similarity

Zinc finger

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri1 – 26C2HC LYAR-type 1PROSITE-ProRule annotationAdd BLAST26
Zinc fingeri28 – 52C2HC LYAR-type 2PROSITE-ProRule annotationAdd BLAST25

Keywords - Domaini

Coiled coil, Repeat, Zinc-finger

Phylogenomic databases

eggNOGiKOG2186 Eukaryota
ENOG411081U LUCA
GeneTreeiENSGT00390000003477
HOGENOMiHOG000006633
HOVERGENiHBG006298
InParanoidiQ08288
KOiK15263
OMAiNEHHKSE
OrthoDBiEOG091G0L4Z
PhylomeDBiQ08288
TreeFamiTF314925

Family and domain databases

InterProiView protein in InterPro
IPR039999 LYAR
IPR014898 Znf_C2H2_LYAR
IPR036236 Znf_C2H2_sf
PANTHERiPTHR13100 PTHR13100, 1 hit
PfamiView protein in Pfam
PF08790 zf-LYAR, 1 hit
SUPFAMiSSF57667 SSF57667, 2 hits
PROSITEiView protein in PROSITE
PS51804 ZF_C2HC_LYAR, 2 hits

Sequence (1+)i

Sequence statusi: Complete.

This entry has 1 described isoform and 7 potential isoforms that are computationally mapped.Show allAlign All

Q08288-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MVFFTCNACG ESVKKIQVEK HVSNCRNCEC LSCIDCGKDF WGDDYKSHVK
60 70 80 90 100
CISEGQKYGG KGYEAKTHKG DAKQQAWIQK INELIKKPNV SPKVRELLQQ
110 120 130 140 150
ISAFDNVPRK KAKFQNWMKN SLKVHSDSVL EQVWDIFSEA SSSEQDQQQP
160 170 180 190 200
PSHTAKPHAE MPITKVPSAK TNGTTEEQTE AKKNKRERKE ERQKNRKKEK
210 220 230 240 250
KELKLENHQE NLRGQKPKKR KKNQEAGHEA AGEEAAEASG PPEKKKAQGG
260 270 280 290 300
QASEEGADRN GGPGEDAAEG QTKTAAGKRK RPKHSGAESG YKKKKMKLPE
310 320 330 340 350
QPEEGEAKDH EAPSKGKFNW KGTIKAVLKQ APDNEISVKK LKKKVIAQYH
360 370 380
AVMNDHHTSE EELLAIFNRK ISRNPTFKVL KDRVKLLK
Length:388
Mass (Da):43,736
Last modified:July 19, 2005 - v2
Checksum:iD39A0CDC2257BE8C
GO

Computationally mapped potential isoform sequencesi

There are 7 potential isoforms mapped to this entry.BLASTAlignShow allAdd to basket
EntryEntry nameProtein names
Gene namesLengthAnnotation
D3Z5X8D3Z5X8_MOUSE
Cell growth-regulating nucleolar pr...
Lyar
131Annotation score:
D3YU83D3YU83_MOUSE
Cell growth-regulating nucleolar pr...
Lyar
99Annotation score:
D3Z345D3Z345_MOUSE
Cell growth-regulating nucleolar pr...
Lyar
191Annotation score:
D3Z7N3D3Z7N3_MOUSE
Cell growth-regulating nucleolar pr...
Lyar
190Annotation score:
D3Z009D3Z009_MOUSE
Cell growth-regulating nucleolar pr...
Lyar
49Annotation score:
D6RDT2D6RDT2_MOUSE
Cell growth-regulating nucleolar pr...
Lyar mCG_3754
40Annotation score:
A0A0J9YVD4A0A0J9YVD4_MOUSE
Cell growth-regulating nucleolar pr...
Lyar
45Annotation score:

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti21H → Q in AAB26644 (PubMed:8491376).Curated1
Sequence conflicti109R → I in AAB26644 (PubMed:8491376).Curated1
Sequence conflicti234 – 238EAAEA → DGADG in AAB26644 (PubMed:8491376).Curated5
Sequence conflicti267A → R in AAB26644 (PubMed:8491376).Curated1
Sequence conflicti354N → K in BAB24554 (PubMed:16141072).Curated1
Sequence conflicti356 – 359HHTS → TSHH in AAB26644 (PubMed:8491376).Curated4

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
S60885 mRNA Translation: AAB26644.1
AK006373 mRNA Translation: BAB24554.1
CCDSiCCDS19253.1
PIRiA40683
RefSeqiNP_079557.2, NM_025281.3
XP_006503822.1, XM_006503759.1
XP_006503823.1, XM_006503760.1
XP_006503824.1, XM_006503761.1
XP_006503825.1, XM_006503762.1
XP_006503826.1, XM_006503763.1
XP_006503827.1, XM_006503764.1
UniGeneiMm.28560

Genome annotation databases

EnsembliENSMUST00000087514; ENSMUSP00000084791; ENSMUSG00000067367
ENSMUST00000114106; ENSMUSP00000109741; ENSMUSG00000067367
GeneIDi17089
KEGGimmu:17089
UCSCiuc008xgh.2 mouse

Similar proteinsi

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
S60885 mRNA Translation: AAB26644.1
AK006373 mRNA Translation: BAB24554.1
CCDSiCCDS19253.1
PIRiA40683
RefSeqiNP_079557.2, NM_025281.3
XP_006503822.1, XM_006503759.1
XP_006503823.1, XM_006503760.1
XP_006503824.1, XM_006503761.1
XP_006503825.1, XM_006503762.1
XP_006503826.1, XM_006503763.1
XP_006503827.1, XM_006503764.1
UniGeneiMm.28560

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1WJVNMR-A1-66[»]
ProteinModelPortaliQ08288
SMRiQ08288
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi201254, 2 interactors
IntActiQ08288, 3 interactors
MINTiQ08288
STRINGi10090.ENSMUSP00000084791

PTM databases

iPTMnetiQ08288
PhosphoSitePlusiQ08288

Proteomic databases

EPDiQ08288
MaxQBiQ08288
PaxDbiQ08288
PeptideAtlasiQ08288
PRIDEiQ08288

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSMUST00000087514; ENSMUSP00000084791; ENSMUSG00000067367
ENSMUST00000114106; ENSMUSP00000109741; ENSMUSG00000067367
GeneIDi17089
KEGGimmu:17089
UCSCiuc008xgh.2 mouse

Organism-specific databases

CTDi55646
MGIiMGI:107470 Lyar

Phylogenomic databases

eggNOGiKOG2186 Eukaryota
ENOG411081U LUCA
GeneTreeiENSGT00390000003477
HOGENOMiHOG000006633
HOVERGENiHBG006298
InParanoidiQ08288
KOiK15263
OMAiNEHHKSE
OrthoDBiEOG091G0L4Z
PhylomeDBiQ08288
TreeFamiTF314925

Miscellaneous databases

ChiTaRSiLyar mouse
EvolutionaryTraceiQ08288
PROiPR:Q08288
SOURCEiSearch...

Gene expression databases

BgeeiENSMUSG00000067367 Expressed in 280 organ(s), highest expression level in testis
CleanExiMM_LYAR
ExpressionAtlasiQ08288 baseline and differential
GenevisibleiQ08288 MM

Family and domain databases

InterProiView protein in InterPro
IPR039999 LYAR
IPR014898 Znf_C2H2_LYAR
IPR036236 Znf_C2H2_sf
PANTHERiPTHR13100 PTHR13100, 1 hit
PfamiView protein in Pfam
PF08790 zf-LYAR, 1 hit
SUPFAMiSSF57667 SSF57667, 2 hits
PROSITEiView protein in PROSITE
PS51804 ZF_C2HC_LYAR, 2 hits
ProtoNetiSearch...

Entry informationi

Entry nameiLYAR_MOUSE
AccessioniPrimary (citable) accession number: Q08288
Secondary accession number(s): Q9D9X2
Entry historyiIntegrated into UniProtKB/Swiss-Prot: November 1, 1997
Last sequence update: July 19, 2005
Last modified: November 7, 2018
This is version 131 of the entry and version 2 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. MGD cross-references
    Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
UniProt is an ELIXIR core data resource
Main funding by: National Institutes of Health

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