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Protein

RNA-binding protein Raly

Gene

Raly

Organism
Mus musculus (Mouse)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

RNA-binding protein that acts as a transcriptional cofactor for cholesterol biosynthetic genes in the liver (PubMed:27251289). Binds the lipid-responsive non-coding RNA LeXis and is required for LeXis-mediated effect on cholesterogenesis (PubMed:27251289). May be a heterogeneous nuclear ribonucleoprotein (hnRNP) (By similarity).By similarity1 Publication

GO - Molecular functioni

  • RNA binding Source: UniProtKB
  • transcription cofactor activity Source: UniProtKB

GO - Biological processi

  • mRNA processing Source: UniProtKB-KW
  • regulation of cholesterol homeostasis Source: UniProtKB
  • regulation of nucleic acid-templated transcription Source: UniProtKB
  • regulation of transcription, DNA-templated Source: UniProtKB-KW
  • RNA splicing Source: UniProtKB-KW
  • transcription, DNA-templated Source: UniProtKB-KW

Keywordsi

Molecular functionRibonucleoprotein, RNA-binding
Biological processmRNA processing, mRNA splicing, Transcription, Transcription regulation

Names & Taxonomyi

Protein namesi
Recommended name:
RNA-binding protein Raly
Alternative name(s):
Maternally-expressed hnRNP C-related protein
hnRNP associated with lethal yellow protein
Gene namesi
Name:Raly
Synonyms:Merc
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaMyomorphaMuroideaMuridaeMurinaeMusMus
Proteomesi
  • UP000000589 Componenti: Chromosome 2

Organism-specific databases

MGIiMGI:97850. Raly.

Subcellular locationi

GO - Cellular componenti

  • catalytic step 2 spliceosome Source: MGI
  • nucleus Source: UniProtKB

Keywords - Cellular componenti

Nucleus, Spliceosome

Pathology & Biotechi

Involvement in diseasei

Defects in Raly are the cause of lethal yellow mutation (A(y)), a dominant allele that cause embryonic lethality when homozygous, and pleiotropic effects when heterozygous, including yellow pelage, obesity, non-insulin dependent diabetes and increased tumor susceptibility. A(y) is due to a 170 kb deletion that removes all but the promoter and non-coding first exon of Raly and links them to the ASIP/Agouti gene.2 Publications

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemovedBy similarity
ChainiPRO_00000817472 – 312RNA-binding protein RalyAdd BLAST311

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei2N-acetylserineBy similarity1
Cross-linki4Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)By similarity
Modified residuei44N6-acetyllysineCombined sources1
Cross-linki94Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)By similarity
Cross-linki99Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)By similarity
Modified residuei135PhosphoserineCombined sources1
Cross-linki159Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)By similarity
Modified residuei165N6-acetyllysine; alternateCombined sources1
Cross-linki165Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2); alternateBy similarity
Cross-linki179Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)By similarity
Cross-linki191Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)By similarity
Modified residuei268PhosphothreonineCombined sources1
Modified residuei270PhosphoserineCombined sources1
Modified residuei274PhosphothreonineCombined sources1
Modified residuei292PhosphothreonineCombined sources1
Modified residuei294PhosphoserineCombined sources1
Modified residuei301PhosphoserineCombined sources1
Modified residuei304PhosphothreonineCombined sources1

Keywords - PTMi

Acetylation, Isopeptide bond, Phosphoprotein, Ubl conjugation

Proteomic databases

PaxDbiQ64012.
PeptideAtlasiQ64012.
PRIDEiQ64012.

PTM databases

iPTMnetiQ64012.
PhosphoSitePlusiQ64012.

Expressioni

Tissue specificityi

Widely expressed. Expressed in brain, testis, lung, spleen and kidney. Weakly expressed in liver.1 Publication

Developmental stagei

Expressed in the unfertilized egg, in the blastocyst, as well as in the developing embryo and fetus. Expressed in developing skin.1 Publication

Gene expression databases

BgeeiENSMUSG00000027593.
CleanExiMM_RALY.
ExpressionAtlasiQ64012. baseline and differential.
GenevisibleiQ64012. MM.

Interactioni

Subunit structurei

Identified in the spliceosome C complex.By similarity

Protein-protein interaction databases

BioGridi202579. 2 interactors.
IntActiQ64012. 4 interactors.
MINTiMINT-1867928.
STRINGi10090.ENSMUSP00000029120.

Structurei

3D structure databases

ProteinModelPortaliQ64012.
SMRiQ64012.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini21 – 92RRMPROSITE-ProRule annotationAdd BLAST72

Coiled coil

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Coiled coili184 – 216Sequence analysisAdd BLAST33

Sequence similaritiesi

Belongs to the RRM HNRPC family. RALY subfamily.Curated

Keywords - Domaini

Coiled coil

Phylogenomic databases

eggNOGiKOG0118. Eukaryota.
COG0724. LUCA.
GeneTreeiENSGT00390000006718.
HOGENOMiHOG000231958.
HOVERGENiHBG002302.
InParanoidiQ64012.
KOiK12895.
OMAiXLFDYRG.
OrthoDBiEOG091G0O1Q.
TreeFamiTF330974.

Family and domain databases

CDDicd12604. RRM_RALY. 1 hit.
InterProiView protein in InterPro
IPR017347. hnRNP_C.
IPR034502. RALY_RRM.
IPR000504. RRM_dom.
PfamiView protein in Pfam
PF00076. RRM_1. 1 hit.
PIRSFiPIRSF037992. hnRNP-C_Raly. 1 hit.
SMARTiView protein in SMART
SM00360. RRM. 1 hit.
SUPFAMiSSF54928. SSF54928. 1 hit.
PROSITEiView protein in PROSITE
PS50102. RRM. 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 2 (identifier: Q64012-1) [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
MSLKIQTSNV TNKNDPKSIN SRVFIGNLNT AVVKKSDVET IFSKYGRVAG
60 70 80 90 100
CSVHKGYAFV QYANERHARA AVLGENGRVL AGQTLDINMA GEPKPNRPKG
110 120 130 140 150
LKRAATAIYS GYSFDYDYYQ DYFCARLFDY RGRLSPVPVP RAVPVKRPRV
160 170 180 190 200
TVPLVRRVKT TIPVKLFARS TAVTTGSAKI KLKSSELQTI KTELTQIKSN
210 220 230 240 250
IDALLGRLEQ IAEEQKANPD GKKKGDSSSG GGGGSSGGGG SSNVGGGSSG
260 270 280 290 300
GSGSCSSSSR LPAPQEDTAS EAGTPQGEVQ TRDDGDEEGL LTHSEEELEH
310
SQDTDAEDGA LQ
Length:312
Mass (Da):33,188
Last modified:July 27, 2011 - v3
Checksum:iA2A8FD35476BFC44
GO
Isoform 1 (identifier: Q64012-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     110-125: Missing.

Show »
Length:296
Mass (Da):31,199
Checksum:iDF195C31A7964017
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti249S → G in AAC60688 (PubMed:8319910).Curated1
Sequence conflicti249S → G in AAH04851 (PubMed:15489334).Curated1
Sequence conflicti249S → G in AAH16587 (PubMed:15489334).Curated1
Sequence conflicti281T → I in AAC60688 (PubMed:8319910).Curated1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_005805110 – 125Missing in isoform 1. 4 PublicationsAdd BLAST16

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
S72641 mRNA. Translation: AAC60688.1.
L17076 mRNA. No translation available.
AK014356 mRNA. Translation: BAB29294.1.
AL929024 Genomic DNA. Translation: CAM25655.1.
BC004851 mRNA. Translation: AAH04851.1.
BC016587 mRNA. Translation: AAH16587.1.
AF148458 mRNA. Translation: AAF04488.1.
CCDSiCCDS16939.1. [Q64012-2]
CCDS50767.1. [Q64012-1]
PIRiI53142.
RefSeqiNP_001132983.1. NM_001139511.1. [Q64012-2]
NP_001132984.1. NM_001139512.1. [Q64012-2]
NP_001132985.1. NM_001139513.1. [Q64012-1]
NP_075619.2. NM_023130.3. [Q64012-2]
XP_006499076.1. XM_006499013.3. [Q64012-1]
XP_006499077.1. XM_006499014.3. [Q64012-1]
XP_006499078.1. XM_006499015.2. [Q64012-1]
XP_006499079.1. XM_006499016.2. [Q64012-2]
XP_017172120.1. XM_017316631.1. [Q64012-2]
UniGeneiMm.221440.
Mm.475494.

Genome annotation databases

EnsembliENSMUST00000029120; ENSMUSP00000029120; ENSMUSG00000027593. [Q64012-1]
ENSMUST00000058089; ENSMUSP00000058105; ENSMUSG00000027593. [Q64012-2]
ENSMUST00000109701; ENSMUSP00000105323; ENSMUSG00000027593. [Q64012-2]
ENSMUST00000116389; ENSMUSP00000112090; ENSMUSG00000027593. [Q64012-1]
GeneIDi19383.
KEGGimmu:19383.
UCSCiuc008njv.2. mouse. [Q64012-1]

Keywords - Coding sequence diversityi

Alternative splicing

Similar proteinsi

Entry informationi

Entry nameiRALY_MOUSE
AccessioniPrimary (citable) accession number: Q64012
Secondary accession number(s): A2AU63
, Q99K76, Q9CXH8, Q9QZX6
Entry historyiIntegrated into UniProtKB/Swiss-Prot: November 15, 2002
Last sequence update: July 27, 2011
Last modified: August 30, 2017
This is version 151 of the entry and version 3 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. MGD cross-references
    Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot
  2. SIMILARITY comments
    Index of protein domains and families