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
Homo sapiens (Human)
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. Binds the lipid-responsive non-coding RNA LeXis and is required for LeXis-mediated effect on cholesterogenesis (By similarity). May be a heterogeneous nuclear ribonucleoprotein (hnRNP) (PubMed:9376072).By similarity1 Publication

GO - Molecular functioni

  • nucleotide binding Source: InterPro
  • poly(A) RNA binding Source: UniProtKB
  • RNA binding Source: ProtInc
  • transcription cofactor activity Source: UniProtKB

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Ribonucleoprotein

Keywords - Biological processi

mRNA processing, mRNA splicing, Transcription, Transcription regulation

Keywords - Ligandi

RNA-binding

Enzyme and pathway databases

BioCyciZFISH:ENSG00000125970-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
RNA-binding protein Raly
Alternative name(s):
Autoantigen p542
Heterogeneous nuclear ribonucleoprotein C-like 2
Short name:
hnRNP core protein C-like 2
hnRNP associated with lethal yellow protein homolog
Gene namesi
Name:RALY
Synonyms:HNRPCL2, P542
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 20

Organism-specific databases

HGNCiHGNC:15921. RALY.

Subcellular locationi

  • Nucleus By similarity

GO - Cellular componenti

  • catalytic step 2 spliceosome Source: UniProtKB
  • nucleus Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Nucleus, Spliceosome

Pathology & Biotechi

Organism-specific databases

DisGeNETi22913.
OpenTargetsiENSG00000125970.
PharmGKBiPA34201.

Polymorphism and mutation databases

BioMutaiRALY.
DMDMi25091115.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemovedCombined sources
ChainiPRO_00000817462 – 306RNA-binding protein RalyAdd BLAST305

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei2N-acetylserineCombined sources1
Cross-linki4Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources
Modified residuei44N6-acetyllysineBy similarity1
Modified residuei63PhosphoserineCombined sources1
Modified residuei106PhosphoserineCombined sources1
Modified residuei135PhosphoserineCombined sources1 Publication1
Cross-linki159Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources
Modified residuei165N6-acetyllysine; alternateCombined sources1
Cross-linki165Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2); alternateCombined sources
Modified residuei262PhosphothreonineBy similarity1
Modified residuei264PhosphoserineBy similarity1
Modified residuei286PhosphothreonineCombined sources1
Modified residuei288PhosphoserineCombined sources1
Modified residuei295PhosphoserineCombined sources1
Modified residuei298PhosphothreonineCombined sources1
Isoform 1 (identifier: Q9UKM9-2)
Modified residuei106PhosphoserineCombined sources1

Keywords - PTMi

Acetylation, Isopeptide bond, Phosphoprotein, Ubl conjugation

Proteomic databases

EPDiQ9UKM9.
PaxDbiQ9UKM9.
PeptideAtlasiQ9UKM9.
PRIDEiQ9UKM9.

PTM databases

iPTMnetiQ9UKM9.
PhosphoSitePlusiQ9UKM9.
SwissPalmiQ9UKM9.

Expressioni

Tissue specificityi

Expressed in heart, brain, lung, liver, skeletal muscle, kidney and pancreas. Weakly expressed in placenta.1 Publication

Gene expression databases

BgeeiENSG00000125970.
CleanExiHS_RALY.
ExpressionAtlasiQ9UKM9. baseline and differential.
GenevisibleiQ9UKM9. HS.

Organism-specific databases

HPAiHPA040971.
HPA043614.

Interactioni

Subunit structurei

Identified in the spliceosome C complex.1 Publication

Protein-protein interaction databases

BioGridi116575. 90 interactors.
IntActiQ9UKM9. 42 interactors.
MINTiMINT-2869971.
STRINGi9606.ENSP00000246194.

Structurei

Secondary structure

1306
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi20 – 25Combined sources6
Helixi35 – 42Combined sources8
Helixi43 – 45Combined sources3
Beta strandi49 – 54Combined sources6
Beta strandi57 – 61Combined sources5
Beta strandi63 – 65Combined sources3
Helixi66 – 75Combined sources10
Beta strandi87 – 90Combined sources4

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1WF1NMR-A1-97[»]
ProteinModelPortaliQ9UKM9.
SMRiQ9UKM9.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ9UKM9.

Family & Domainsi

Domains and Repeats

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

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni227 – 253Epitope (recognized by BKRF1 antibodies)Add BLAST27

Coiled coil

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Coiled coili183 – 216Sequence analysisAdd BLAST34

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi225 – 251Poly-GlyAdd BLAST27

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.
HOVERGENiHBG002302.
InParanoidiQ9UKM9.
KOiK12895.
OMAiARDECED.
OrthoDBiEOG091G0O1Q.
PhylomeDBiQ9UKM9.
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: Q9UKM9-1) [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
MSLKLQASNV TNKNDPKSIN SRVFIGNLNT ALVKKSDVET IFSKYGRVAG
60 70 80 90 100
CSVHKGYAFV QYSNERHARA AVLGENGRVL AGQTLDINMA GEPKPDRPKG
110 120 130 140 150
LKRAASAIYS GYIFDYDYYR DDFYDRLFDY RGRLSPVPVP RAVPVKRPRV
160 170 180 190 200
TVPLVRRVKT NVPVKLFARS TAVTTSSAKI KLKSSELQAI KTELTQIKSN
210 220 230 240 250
IDALLSRLEQ IAAEQKANPD GKKKGDGGGA GGGGGGGGSG GGGSGGGGGG
260 270 280 290 300
GSSRPPAPQE NTTSEAGLPQ GEARTRDDGD EEGLLTHSEE ELEHSQDTDA

DDGALQ
Length:306
Mass (Da):32,463
Last modified:May 1, 2000 - v1
Checksum:i7F4376D3BD8E4728
GO
Isoform 1 (identifier: Q9UKM9-2) [UniParc]FASTAAdd to basket

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

Show »
Length:290
Mass (Da):30,364
Checksum:i228F7E277DB066C9
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti214 – 215EQ → DE in AAC28898 (PubMed:9376072).Curated2
Sequence conflicti230A → AS in AAC28898 (PubMed:9376072).Curated1

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_052215139V → M.Corresponds to variant rs35191085dbSNPEnsembl.1
Natural variantiVAR_015223215Q → R.Corresponds to variant rs3180568dbSNPEnsembl.1
Natural variantiVAR_015224251G → S.Corresponds to variant rs2281209dbSNPEnsembl.1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_005804110 – 125Missing in isoform 1. 2 PublicationsAdd BLAST16

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF148457 mRNA. Translation: AAF04487.1.
L38696 mRNA. Translation: AAC28898.1.
AL031668 Genomic DNA. Translation: CAI22150.1.
AL031668 Genomic DNA. Translation: CAB43742.1.
BC105018 mRNA. Translation: AAI05019.1.
CCDSiCCDS13229.1. [Q9UKM9-2]
CCDS13230.1. [Q9UKM9-1]
RefSeqiNP_031393.2. NM_007367.3. [Q9UKM9-2]
NP_057951.1. NM_016732.2. [Q9UKM9-1]
XP_005260391.1. XM_005260334.4. [Q9UKM9-1]
XP_005260393.1. XM_005260336.4. [Q9UKM9-2]
XP_011526996.1. XM_011528694.2. [Q9UKM9-1]
XP_011526997.1. XM_011528695.2. [Q9UKM9-1]
XP_016883220.1. XM_017027731.1. [Q9UKM9-1]
UniGeneiHs.136947.

Genome annotation databases

EnsembliENST00000246194; ENSP00000246194; ENSG00000125970. [Q9UKM9-1]
ENST00000375114; ENSP00000364255; ENSG00000125970. [Q9UKM9-2]
GeneIDi22913.
KEGGihsa:22913.
UCSCiuc002xab.4. human. [Q9UKM9-1]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF148457 mRNA. Translation: AAF04487.1.
L38696 mRNA. Translation: AAC28898.1.
AL031668 Genomic DNA. Translation: CAI22150.1.
AL031668 Genomic DNA. Translation: CAB43742.1.
BC105018 mRNA. Translation: AAI05019.1.
CCDSiCCDS13229.1. [Q9UKM9-2]
CCDS13230.1. [Q9UKM9-1]
RefSeqiNP_031393.2. NM_007367.3. [Q9UKM9-2]
NP_057951.1. NM_016732.2. [Q9UKM9-1]
XP_005260391.1. XM_005260334.4. [Q9UKM9-1]
XP_005260393.1. XM_005260336.4. [Q9UKM9-2]
XP_011526996.1. XM_011528694.2. [Q9UKM9-1]
XP_011526997.1. XM_011528695.2. [Q9UKM9-1]
XP_016883220.1. XM_017027731.1. [Q9UKM9-1]
UniGeneiHs.136947.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1WF1NMR-A1-97[»]
ProteinModelPortaliQ9UKM9.
SMRiQ9UKM9.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi116575. 90 interactors.
IntActiQ9UKM9. 42 interactors.
MINTiMINT-2869971.
STRINGi9606.ENSP00000246194.

PTM databases

iPTMnetiQ9UKM9.
PhosphoSitePlusiQ9UKM9.
SwissPalmiQ9UKM9.

Polymorphism and mutation databases

BioMutaiRALY.
DMDMi25091115.

Proteomic databases

EPDiQ9UKM9.
PaxDbiQ9UKM9.
PeptideAtlasiQ9UKM9.
PRIDEiQ9UKM9.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000246194; ENSP00000246194; ENSG00000125970. [Q9UKM9-1]
ENST00000375114; ENSP00000364255; ENSG00000125970. [Q9UKM9-2]
GeneIDi22913.
KEGGihsa:22913.
UCSCiuc002xab.4. human. [Q9UKM9-1]

Organism-specific databases

CTDi22913.
DisGeNETi22913.
GeneCardsiRALY.
HGNCiHGNC:15921. RALY.
HPAiHPA040971.
HPA043614.
MIMi614663. gene.
neXtProtiNX_Q9UKM9.
OpenTargetsiENSG00000125970.
PharmGKBiPA34201.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG0118. Eukaryota.
COG0724. LUCA.
GeneTreeiENSGT00390000006718.
HOVERGENiHBG002302.
InParanoidiQ9UKM9.
KOiK12895.
OMAiARDECED.
OrthoDBiEOG091G0O1Q.
PhylomeDBiQ9UKM9.
TreeFamiTF330974.

Enzyme and pathway databases

BioCyciZFISH:ENSG00000125970-MONOMER.

Miscellaneous databases

ChiTaRSiRALY. human.
EvolutionaryTraceiQ9UKM9.
GeneWikiiRALY.
GenomeRNAii22913.
PROiQ9UKM9.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000125970.
CleanExiHS_RALY.
ExpressionAtlasiQ9UKM9. baseline and differential.
GenevisibleiQ9UKM9. HS.

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...

Entry informationi

Entry nameiRALY_HUMAN
AccessioniPrimary (citable) accession number: Q9UKM9
Secondary accession number(s): Q14621
, Q2M365, Q5QPL8, Q9BQX6, Q9UJE3
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 15, 2002
Last sequence update: May 1, 2000
Last modified: November 2, 2016
This is version 155 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

Miscellaneous

Autoantigen found in infectious mononucleosis caused by Epstein-Barr virus. An epitope recognized by B-cells, which cross-react with the BKRF1 protein (EBNA-1 nuclear protein) of Epstein-Barr virus has been identified.1 Publication

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. Human chromosome 20
    Human chromosome 20: 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. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  6. 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.