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

Ligand-dependent nuclear receptor-interacting factor 1

Gene

LRIF1

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Represses the ligand-induced transcriptional activity of retinoic acid receptor alpha (RARA). This repression may occur through direct recruitment of histone deacetylases.1 Publication

GO - Biological processi

Complete GO annotation...

Keywords - Biological processi

Transcription, Transcription regulation

Names & Taxonomyi

Protein namesi
Recommended name:
Ligand-dependent nuclear receptor-interacting factor 1
Alternative name(s):
Receptor-interacting factor 1
Gene namesi
Name:LRIF1
Synonyms:C1orf103, RIF1
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 1

Organism-specific databases

HGNCiHGNC:30299. LRIF1.

Subcellular locationi

  • Nucleus matrix 1 Publication

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi628 – 630KKR → AAA: Slightly reduces nuclear localization. 1 Publication3
Mutagenesisi642 – 644KKR → AAA: Abolishes nuclear localization. 1 Publication3

Organism-specific databases

DisGeNETi55791.
OpenTargetsiENSG00000121931.
PharmGKBiPA142672487.

Polymorphism and mutation databases

BioMutaiLRIF1.
DMDMi74744778.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002506861 – 769Ligand-dependent nuclear receptor-interacting factor 1Add BLAST769

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei402PhosphoserineCombined sources1
Modified residuei430PhosphoserineCombined sources1
Modified residuei436PhosphoserineCombined sources1
Modified residuei502PhosphoserineCombined sources1
Modified residuei599PhosphoserineCombined sources1
Cross-linki702Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources
Modified residuei732PhosphothreonineCombined sources1

Keywords - PTMi

Isopeptide bond, Phosphoprotein, Ubl conjugation

Proteomic databases

EPDiQ5T3J3.
MaxQBiQ5T3J3.
PaxDbiQ5T3J3.
PeptideAtlasiQ5T3J3.
PRIDEiQ5T3J3.

PTM databases

iPTMnetiQ5T3J3.
PhosphoSitePlusiQ5T3J3.

Expressioni

Tissue specificityi

Widely expressed, with the highest expression levels in heart, liver and placenta.1 Publication

Gene expression databases

BgeeiENSG00000121931.
CleanExiHS_C1orf103.
HS_RIF1.
GenevisibleiQ5T3J3. HS.

Organism-specific databases

HPAiHPA044515.

Interactioni

Subunit structurei

Interacts with RARA.1 Publication

Binary interactionsi

WithEntry#Exp.IntActNotes
CBX3Q131854EBI-473196,EBI-78176
CBX5P459733EBI-473196,EBI-78219
GIT1Q9Y2X72EBI-473196,EBI-466061

Protein-protein interaction databases

BioGridi120905. 165 interactors.
IntActiQ5T3J3. 47 interactors.
MINTiMINT-1405302.
STRINGi9606.ENSP00000358778.

Structurei

3D structure databases

ProteinModelPortaliQ5T3J3.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Coiled coil

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Coiled coili740 – 769Sequence analysisAdd BLAST30

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Motifi628 – 631Nuclear localization signal1 Publication4
Motifi642 – 645Nuclear localization signal1 Publication4

Sequence similaritiesi

Belongs to the LRIF1 family.Curated

Keywords - Domaini

Coiled coil

Phylogenomic databases

eggNOGiENOG410IE1C. Eukaryota.
ENOG41129E9. LUCA.
GeneTreeiENSGT00390000017353.
HOVERGENiHBG080960.
InParanoidiQ5T3J3.
OMAiMPIKDNA.
OrthoDBiEOG091G029S.
PhylomeDBiQ5T3J3.
TreeFamiTF336147.

Family and domain databases

InterProiIPR026191. LRIF1.
[Graphical view]
PANTHERiPTHR16131. PTHR16131. 1 hit.
PfamiPF15741. LRIF1. 1 hit.
[Graphical view]

Sequences (2)i

Sequence statusi: Complete.

This entry describes 2 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q5T3J3-1) [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
MSNNLRRVFL KPAEENSGNA SRCVSGCMYQ VVQTIGSDGK NLLQLLPIPK
60 70 80 90 100
SSGNLIPLVQ SSVMSDALKG NTGKPVQVTF QTQISSSSTS ASVQLPIFQP
110 120 130 140 150
ASSSNYFLTR TVDTSEKGRV TSVGTGNFSS SVSKVQSHGV KIDGLTMQTF
160 170 180 190 200
AVPPSTQKDS SFIVVNTQSL PVTVKSPVLP SGHHLQIPAH AEVKSVPASS
210 220 230 240 250
LPPSVQQKIL ATATTSTSGM VEASQMPTVI YVSPVNTVKN VVTKNFQNIY
260 270 280 290 300
PKPVTEIAKP VILNTTQIPK NVATETQLKG GQHSQAAPVK WIFQDNLQPF
310 320 330 340 350
TPSLVPVKSS NNVASKILKT FVDRKNLGDN TINMPPLSTI DPSGTRSKNM
360 370 380 390 400
PIKDNALVMF NGKVYLLAKK GTDVLPSQID QQNSVSPDTP VRKDTLQTVS
410 420 430 440 450
SSPVTEISRE VVNIVLAKSK SSQMETKSLS NTQLASMANL RAEKNKVEKP
460 470 480 490 500
SPSTTNPHMN QSSNYLKQSK TLFTNPIFPV GFSTGHNAPR KVTAVIYARK
510 520 530 540 550
GSVLQSIEKI SSSVDATTVT SQQCVFRDQE PKIHNEMAST SDKGAQGRND
560 570 580 590 600
KKDSQGRSNK ALHLKSDAEF KKIFGLTKDL RVCLTRIPDH LTSGEGFDSF
610 620 630 640 650
SSLVKSGTYK ETEFMVKEGE RKQQNFDKKR KAKTNKKMDH IKKRKTENAY
660 670 680 690 700
NAIINGEANV TGSQLLSSIL PTSDVSQHNI LTSHSKTRQE KRTEMEYYTH
710 720 730 740 750
EKQEKGTLNS NAAYEQSHFF NKNYTEDIFP VTPPELEETI RDEKIRRLKQ
760
VLREKEAALE EMRKKMHQK
Length:769
Mass (Da):84,568
Last modified:December 21, 2004 - v1
Checksum:iD39A2BB494F16AAA
GO
Isoform 2 (identifier: Q5T3J3-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-536: Missing.

Note: No experimental confirmation available.
Show »
Length:233
Mass (Da):26,917
Checksum:iD1E3BE5BCD299BAB
GO

Sequence cautioni

The sequence AAH08115 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.Curated
The sequence AAO43631 differs from that shown. Reason: Frameshift at position 23.Curated
The sequence BAA92097 differs from that shown. Reason: Frameshift at position 667.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti66 – 68DAL → NA in AAO43631 (Ref. 1) Curated3
Sequence conflicti72 – 80TGKPVQVTF → PGNQFSY in AAO43631 (Ref. 1) Curated9
Sequence conflicti108 – 111LTRT → PSRP in AAO43631 (Ref. 1) Curated4
Sequence conflicti666Missing in BAA92097 (PubMed:14702039).Curated1

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_050703438A → T.Corresponds to variant rs2232041dbSNPEnsembl.1
Natural variantiVAR_027599599S → P.Corresponds to variant rs2232045dbSNPEnsembl.1
Natural variantiVAR_027600641I → M.Corresponds to variant rs2232047dbSNPEnsembl.1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_0207211 – 536Missing in isoform 2. 1 PublicationAdd BLAST536

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AY190122 mRNA. Translation: AAO43631.1. Frameshift.
AK001826 mRNA. Translation: BAA91928.1.
AK002131 mRNA. Translation: BAA92097.1. Frameshift.
AL360270 Genomic DNA. Translation: CAI17128.1.
BC008115 mRNA. Translation: AAH08115.1. Different initiation.
AL834466 mRNA. Translation: CAD39125.1.
CCDSiCCDS30800.1. [Q5T3J3-1]
CCDS41366.1. [Q5T3J3-2]
RefSeqiNP_001006946.1. NM_001006945.1. [Q5T3J3-2]
NP_060842.3. NM_018372.3. [Q5T3J3-1]
UniGeneiHs.25245.

Genome annotation databases

EnsembliENST00000369763; ENSP00000358778; ENSG00000121931. [Q5T3J3-1]
ENST00000485275; ENSP00000432290; ENSG00000121931. [Q5T3J3-2]
ENST00000494675; ENSP00000435259; ENSG00000121931. [Q5T3J3-2]
GeneIDi55791.
KEGGihsa:55791.
UCSCiuc001dzz.4. human. [Q5T3J3-1]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AY190122 mRNA. Translation: AAO43631.1. Frameshift.
AK001826 mRNA. Translation: BAA91928.1.
AK002131 mRNA. Translation: BAA92097.1. Frameshift.
AL360270 Genomic DNA. Translation: CAI17128.1.
BC008115 mRNA. Translation: AAH08115.1. Different initiation.
AL834466 mRNA. Translation: CAD39125.1.
CCDSiCCDS30800.1. [Q5T3J3-1]
CCDS41366.1. [Q5T3J3-2]
RefSeqiNP_001006946.1. NM_001006945.1. [Q5T3J3-2]
NP_060842.3. NM_018372.3. [Q5T3J3-1]
UniGeneiHs.25245.

3D structure databases

ProteinModelPortaliQ5T3J3.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi120905. 165 interactors.
IntActiQ5T3J3. 47 interactors.
MINTiMINT-1405302.
STRINGi9606.ENSP00000358778.

PTM databases

iPTMnetiQ5T3J3.
PhosphoSitePlusiQ5T3J3.

Polymorphism and mutation databases

BioMutaiLRIF1.
DMDMi74744778.

Proteomic databases

EPDiQ5T3J3.
MaxQBiQ5T3J3.
PaxDbiQ5T3J3.
PeptideAtlasiQ5T3J3.
PRIDEiQ5T3J3.

Protocols and materials databases

DNASUi55791.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000369763; ENSP00000358778; ENSG00000121931. [Q5T3J3-1]
ENST00000485275; ENSP00000432290; ENSG00000121931. [Q5T3J3-2]
ENST00000494675; ENSP00000435259; ENSG00000121931. [Q5T3J3-2]
GeneIDi55791.
KEGGihsa:55791.
UCSCiuc001dzz.4. human. [Q5T3J3-1]

Organism-specific databases

CTDi55791.
DisGeNETi55791.
GeneCardsiLRIF1.
HGNCiHGNC:30299. LRIF1.
HPAiHPA044515.
MIMi615354. gene.
neXtProtiNX_Q5T3J3.
OpenTargetsiENSG00000121931.
PharmGKBiPA142672487.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiENOG410IE1C. Eukaryota.
ENOG41129E9. LUCA.
GeneTreeiENSGT00390000017353.
HOVERGENiHBG080960.
InParanoidiQ5T3J3.
OMAiMPIKDNA.
OrthoDBiEOG091G029S.
PhylomeDBiQ5T3J3.
TreeFamiTF336147.

Miscellaneous databases

ChiTaRSiLRIF1. human.
GeneWikiiC1orf103.
GenomeRNAii55791.
PROiQ5T3J3.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000121931.
CleanExiHS_C1orf103.
HS_RIF1.
GenevisibleiQ5T3J3. HS.

Family and domain databases

InterProiIPR026191. LRIF1.
[Graphical view]
PANTHERiPTHR16131. PTHR16131. 1 hit.
PfamiPF15741. LRIF1. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiLRIF1_HUMAN
AccessioniPrimary (citable) accession number: Q5T3J3
Secondary accession number(s): Q86XS4
, Q8N3B6, Q96HT4, Q9NUM5, Q9NV32
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 3, 2006
Last sequence update: December 21, 2004
Last modified: November 30, 2016
This is version 103 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

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Human chromosome 1
    Human chromosome 1: 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. 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.