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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

GO - Biological processi

  • mRNA splicing, via spliceosome Source: UniProtKB
Complete GO annotation...

Keywords - Molecular functioni

Ribonucleoprotein

Keywords - Biological processi

mRNA processing, mRNA splicing, Transcription, Transcription regulation

Keywords - Ligandi

RNA-binding

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

PharmGKBiPA34201.

Polymorphism and mutation databases

BioMutaiRALY.
DMDMi25091115.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methionineiRemovedCombined sources
Chaini2 – 306305RNA-binding protein RalyPRO_0000081746Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei2 – 21N-acetylserineCombined sources
Cross-linki4 – 4Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources
Modified residuei44 – 441N6-acetyllysineBy similarity
Modified residuei63 – 631PhosphoserineCombined sources
Modified residuei106 – 1061PhosphoserineCombined sources
Modified residuei135 – 1351PhosphoserineCombined sources1 Publication
Cross-linki159 – 159Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources
Modified residuei165 – 1651N6-acetyllysine; alternateCombined sources
Cross-linki165 – 165Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2); alternateCombined sources
Modified residuei262 – 2621PhosphothreonineBy similarity
Modified residuei264 – 2641PhosphoserineBy similarity
Modified residuei286 – 2861PhosphothreonineCombined sources
Modified residuei288 – 2881PhosphoserineCombined sources
Modified residuei295 – 2951PhosphoserineCombined sources
Modified residuei298 – 2981PhosphothreonineCombined sources
Isoform 1 (identifier: Q9UKM9-2)
Modified residuei106 – 1061PhosphoserineCombined sources

Keywords - PTMi

Acetylation, Isopeptide bond, Phosphoprotein, Ubl conjugation

Proteomic databases

EPDiQ9UKM9.
MaxQBiQ9UKM9.
PaxDbiQ9UKM9.
PeptideAtlasiQ9UKM9.
PRIDEiQ9UKM9.

PTM databases

iPTMnetiQ9UKM9.
PhosphoSiteiQ9UKM9.
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 interactions.
IntActiQ9UKM9. 42 interactions.
MINTiMINT-2869971.
STRINGi9606.ENSP00000246194.

Structurei

Secondary structure

1
306
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi20 – 256Combined sources
Helixi35 – 428Combined sources
Helixi43 – 453Combined sources
Beta strandi49 – 546Combined sources
Beta strandi57 – 615Combined sources
Beta strandi63 – 653Combined sources
Helixi66 – 7510Combined sources
Beta strandi87 – 904Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1WF1NMR-A1-97[»]
ProteinModelPortaliQ9UKM9.
SMRiQ9UKM9. Positions 3-97.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ9UKM9.

Family & Domainsi

Domains and Repeats

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

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni227 – 25327Epitope (recognized by BKRF1 antibodies)Add
BLAST

Coiled coil

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Coiled coili183 – 21634Sequence analysisAdd
BLAST

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi225 – 25127Poly-GlyAdd
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.
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)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti214 – 2152EQ → DE in AAC28898 (PubMed:9376072).Curated
Sequence conflicti230 – 2301A → AS in AAC28898 (PubMed:9376072).Curated

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti139 – 1391V → M.
Corresponds to variant rs35191085 [ dbSNP | Ensembl ].
VAR_052215
Natural varianti215 – 2151Q → R.
Corresponds to variant rs3180568 [ dbSNP | Ensembl ].
VAR_015223
Natural varianti251 – 2511G → S.
Corresponds to variant rs2281209 [ dbSNP | Ensembl ].
VAR_015224

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei110 – 12516Missing in isoform 1. 2 PublicationsVSP_005804Add
BLAST

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]
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]
UniGeneiHs.136947.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1WF1NMR-A1-97[»]
ProteinModelPortaliQ9UKM9.
SMRiQ9UKM9. Positions 3-97.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

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

PTM databases

iPTMnetiQ9UKM9.
PhosphoSiteiQ9UKM9.
SwissPalmiQ9UKM9.

Polymorphism and mutation databases

BioMutaiRALY.
DMDMi25091115.

Proteomic databases

EPDiQ9UKM9.
MaxQBiQ9UKM9.
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.
GeneCardsiRALY.
HGNCiHGNC:15921. RALY.
HPAiHPA040971.
HPA043614.
MIMi614663. gene.
neXtProtiNX_Q9UKM9.
PharmGKBiPA34201.
GenAtlasiSearch...

Phylogenomic databases

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

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: September 7, 2016
This is version 153 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.