Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
Protein

RNA-binding protein Raly

Gene

Raly

Organism
Mus musculus (Mouse)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

Probable-RNA binding protein. Could be a heterogeneous nuclear ribonucleoprotein (hnRNP). May be involved in pre-mRNA splicing (By similarity).By similarity

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Ribonucleoprotein

Keywords - Biological processi

mRNA processing, mRNA splicing

Keywords - Ligandi

RNA-binding

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 lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
Proteomesi
  • UP000000589 Componenti: Chromosome 2

Organism-specific databases

MGIiMGI:97850. Raly.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

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.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methionineiRemovedBy similarity
Chaini2 – 312311RNA-binding protein RalyPRO_0000081747Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei2 – 21N-acetylserineBy similarity
Cross-linki4 – 4Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)By similarity
Modified residuei44 – 441N6-acetyllysineCombined sources
Modified residuei135 – 1351PhosphoserineCombined sources
Cross-linki159 – 159Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)By similarity
Modified residuei165 – 1651N6-acetyllysine; alternateCombined sources
Cross-linki165 – 165Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2); alternateBy similarity
Modified residuei268 – 2681PhosphothreonineCombined sources
Modified residuei270 – 2701PhosphoserineCombined sources
Modified residuei274 – 2741PhosphothreonineCombined sources
Modified residuei292 – 2921PhosphothreonineCombined sources
Modified residuei294 – 2941PhosphoserineCombined sources
Modified residuei301 – 3011PhosphoserineCombined sources
Modified residuei304 – 3041PhosphothreonineCombined sources

Keywords - PTMi

Acetylation, Isopeptide bond, Phosphoprotein, Ubl conjugation

Proteomic databases

EPDiQ64012.
MaxQBiQ64012.
PaxDbiQ64012.
PRIDEiQ64012.

PTM databases

iPTMnetiQ64012.
PhosphoSiteiQ64012.

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

BgeeiQ64012.
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 interactions.
IntActiQ64012. 4 interactions.
MINTiMINT-1867928.
STRINGi10090.ENSMUSP00000029120.

Structurei

3D structure databases

ProteinModelPortaliQ64012.
SMRiQ64012. Positions 3-97.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini21 – 9272RRMPROSITE-ProRule annotationAdd
BLAST

Coiled coil

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Coiled coili184 – 21633Sequence analysisAdd
BLAST

Sequence similaritiesi

Belongs to the RRM HNRPC family. RALY subfamily.Curated
Contains 1 RRM (RNA recognition motif) domain.PROSITE-ProRule annotation

Keywords - Domaini

Coiled coil

Phylogenomic databases

eggNOGiKOG0118. Eukaryota.
COG0724. LUCA.
GeneTreeiENSGT00390000006718.
HOGENOMiHOG000231958.
HOVERGENiHBG002302.
InParanoidiQ64012.
KOiK12895.
OMAiQITEDTH.
OrthoDBiEOG7KWSK9.
TreeFamiTF330974.

Family and domain databases

Gene3Di3.30.70.330. 1 hit.
InterProiIPR017347. hnRNP_C.
IPR012677. Nucleotide-bd_a/b_plait.
IPR000504. RRM_dom.
[Graphical view]
PfamiPF00076. RRM_1. 1 hit.
[Graphical view]
PIRSFiPIRSF037992. hnRNP-C_Raly. 1 hit.
SMARTiSM00360. RRM. 1 hit.
[Graphical view]
SUPFAMiSSF54928. SSF54928. 1 hit.
PROSITEiPS50102. RRM. 1 hit.
[Graphical view]

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)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti249 – 2491S → G in AAC60688 (PubMed:8319910).Curated
Sequence conflicti249 – 2491S → G in AAH04851 (PubMed:15489334).Curated
Sequence conflicti249 – 2491S → G in AAH16587 (PubMed:15489334).Curated
Sequence conflicti281 – 2811T → I in AAC60688 (PubMed:8319910).Curated

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei110 – 12516Missing in isoform 1. 4 PublicationsVSP_005805Add
BLAST

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_006499013.2. [Q64012-1]
XP_006499077.1. XM_006499014.2. [Q64012-1]
XP_006499078.1. XM_006499015.2. [Q64012-1]
XP_006499079.1. XM_006499016.1. [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

Cross-referencesi

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_006499013.2. [Q64012-1]
XP_006499077.1. XM_006499014.2. [Q64012-1]
XP_006499078.1. XM_006499015.2. [Q64012-1]
XP_006499079.1. XM_006499016.1. [Q64012-2]
UniGeneiMm.221440.
Mm.475494.

3D structure databases

ProteinModelPortaliQ64012.
SMRiQ64012. Positions 3-97.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

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

PTM databases

iPTMnetiQ64012.
PhosphoSiteiQ64012.

Proteomic databases

EPDiQ64012.
MaxQBiQ64012.
PaxDbiQ64012.
PRIDEiQ64012.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

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]

Organism-specific databases

CTDi22913.
MGIiMGI:97850. Raly.

Phylogenomic databases

eggNOGiKOG0118. Eukaryota.
COG0724. LUCA.
GeneTreeiENSGT00390000006718.
HOGENOMiHOG000231958.
HOVERGENiHBG002302.
InParanoidiQ64012.
KOiK12895.
OMAiQITEDTH.
OrthoDBiEOG7KWSK9.
TreeFamiTF330974.

Miscellaneous databases

ChiTaRSiRaly. mouse.
NextBioi296485.
PROiQ64012.
SOURCEiSearch...

Gene expression databases

BgeeiQ64012.
CleanExiMM_RALY.
ExpressionAtlasiQ64012. baseline and differential.
GenevisibleiQ64012. MM.

Family and domain databases

Gene3Di3.30.70.330. 1 hit.
InterProiIPR017347. hnRNP_C.
IPR012677. Nucleotide-bd_a/b_plait.
IPR000504. RRM_dom.
[Graphical view]
PfamiPF00076. RRM_1. 1 hit.
[Graphical view]
PIRSFiPIRSF037992. hnRNP-C_Raly. 1 hit.
SMARTiSM00360. RRM. 1 hit.
[Graphical view]
SUPFAMiSSF54928. SSF54928. 1 hit.
PROSITEiPS50102. RRM. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "The embryonic lethality of homozygous lethal yellow mice (Ay/Ay) is associated with the disruption of a novel RNA-binding protein."
    Michaud E.J., Bultman S.J., Stubbs L.J., Woychik R.P.
    Genes Dev. 7:1203-1213(1993) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), TISSUE SPECIFICITY, DEVELOPMENTAL STAGE, INVOLVEMENT IN A(Y).
    Tissue: Embryo.
  2. "Pleiotropic effects of the mouse lethal yellow (Ay) mutation explained by deletion of a maternally expressed gene and the simultaneous production of agouti fusion RNAs."
    Duhl D.M., Stevens M.E., Vrieling H., Saxon P.J., Miller M.W., Epstein C.J., Barsh G.S.
    Development 120:1695-1708(1994) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), INVOLVEMENT IN A(Y).
  3. "The transcriptional landscape of the mammalian genome."
    Carninci P., Kasukawa T., Katayama S., Gough J., Frith M.C., Maeda N., Oyama R., Ravasi T., Lenhard B., Wells C., Kodzius R., Shimokawa K., Bajic V.B., Brenner S.E., Batalov S., Forrest A.R., Zavolan M., Davis M.J.
    , Wilming L.G., Aidinis V., Allen J.E., Ambesi-Impiombato A., Apweiler R., Aturaliya R.N., Bailey T.L., Bansal M., Baxter L., Beisel K.W., Bersano T., Bono H., Chalk A.M., Chiu K.P., Choudhary V., Christoffels A., Clutterbuck D.R., Crowe M.L., Dalla E., Dalrymple B.P., de Bono B., Della Gatta G., di Bernardo D., Down T., Engstrom P., Fagiolini M., Faulkner G., Fletcher C.F., Fukushima T., Furuno M., Futaki S., Gariboldi M., Georgii-Hemming P., Gingeras T.R., Gojobori T., Green R.E., Gustincich S., Harbers M., Hayashi Y., Hensch T.K., Hirokawa N., Hill D., Huminiecki L., Iacono M., Ikeo K., Iwama A., Ishikawa T., Jakt M., Kanapin A., Katoh M., Kawasawa Y., Kelso J., Kitamura H., Kitano H., Kollias G., Krishnan S.P., Kruger A., Kummerfeld S.K., Kurochkin I.V., Lareau L.F., Lazarevic D., Lipovich L., Liu J., Liuni S., McWilliam S., Madan Babu M., Madera M., Marchionni L., Matsuda H., Matsuzawa S., Miki H., Mignone F., Miyake S., Morris K., Mottagui-Tabar S., Mulder N., Nakano N., Nakauchi H., Ng P., Nilsson R., Nishiguchi S., Nishikawa S., Nori F., Ohara O., Okazaki Y., Orlando V., Pang K.C., Pavan W.J., Pavesi G., Pesole G., Petrovsky N., Piazza S., Reed J., Reid J.F., Ring B.Z., Ringwald M., Rost B., Ruan Y., Salzberg S.L., Sandelin A., Schneider C., Schoenbach C., Sekiguchi K., Semple C.A., Seno S., Sessa L., Sheng Y., Shibata Y., Shimada H., Shimada K., Silva D., Sinclair B., Sperling S., Stupka E., Sugiura K., Sultana R., Takenaka Y., Taki K., Tammoja K., Tan S.L., Tang S., Taylor M.S., Tegner J., Teichmann S.A., Ueda H.R., van Nimwegen E., Verardo R., Wei C.L., Yagi K., Yamanishi H., Zabarovsky E., Zhu S., Zimmer A., Hide W., Bult C., Grimmond S.M., Teasdale R.D., Liu E.T., Brusic V., Quackenbush J., Wahlestedt C., Mattick J.S., Hume D.A., Kai C., Sasaki D., Tomaru Y., Fukuda S., Kanamori-Katayama M., Suzuki M., Aoki J., Arakawa T., Iida J., Imamura K., Itoh M., Kato T., Kawaji H., Kawagashira N., Kawashima T., Kojima M., Kondo S., Konno H., Nakano K., Ninomiya N., Nishio T., Okada M., Plessy C., Shibata K., Shiraki T., Suzuki S., Tagami M., Waki K., Watahiki A., Okamura-Oho Y., Suzuki H., Kawai J., Hayashizaki Y.
    Science 309:1559-1563(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
    Strain: C57BL/6J.
    Tissue: Embryonic head.
  4. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: C57BL/6J.
  5. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
    The MGC Project Team
    Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
    Tissue: Mammary gland.
  6. Cited for: NUCLEOTIDE SEQUENCE [MRNA] OF 100-135 (ISOFORM 2).
  7. Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-268; SER-270; THR-274; THR-292 AND THR-304, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Liver.
  8. "Specific phosphopeptide enrichment with immobilized titanium ion affinity chromatography adsorbent for phosphoproteome analysis."
    Zhou H., Ye M., Dong J., Han G., Jiang X., Wu R., Zou H.
    J. Proteome Res. 7:3957-3967(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-274, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Liver.
  9. "The phagosomal proteome in interferon-gamma-activated macrophages."
    Trost M., English L., Lemieux S., Courcelles M., Desjardins M., Thibault P.
    Immunity 30:143-154(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-135; THR-268; SER-270 AND THR-274, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  10. Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-268; SER-270; THR-274; THR-292; SER-294; SER-301 AND THR-304, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Brain, Brown adipose tissue, Heart, Kidney, Liver, Lung, Pancreas, Spleen and Testis.
  11. "SIRT5-mediated lysine desuccinylation impacts diverse metabolic pathways."
    Park J., Chen Y., Tishkoff D.X., Peng C., Tan M., Dai L., Xie Z., Zhang Y., Zwaans B.M., Skinner M.E., Lombard D.B., Zhao Y.
    Mol. Cell 50:919-930(2013) [PubMed] [Europe PMC] [Abstract]
    Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT LYS-44 AND LYS-165, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Embryonic fibroblast.

Entry informationi

Entry nameiRALY_MOUSE
AccessioniPrimary (citable) accession number: Q64012
Secondary accession number(s): A2AU63
, Q99K76, Q9CXH8, Q9QZX6
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 15, 2002
Last sequence update: July 27, 2011
Last modified: March 16, 2016
This is version 140 of the entry and version 3 of the sequence. [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

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.