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Q5T3J3 (LRIF1_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 81. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (5) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Interactions·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Ligand-dependent nuclear receptor-interacting factor 1
Alternative name(s):
Receptor-interacting factor 1
Gene names
Name:LRIF1
Synonyms:C1orf103, RIF1
OrganismHomo sapiens (Human) [Reference proteome]
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo

Protein attributes

Sequence length769 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Represses the ligand-induced transcriptional activity of retinoic acid receptor alpha (RARA). This repression may occur through direct recruitment of histone deacetylases. Ref.4

Subunit structure

Interacts with RARA. Ref.4

Subcellular location

Nucleus matrix Ref.4.

Tissue specificity

Widely expressed, with the highest expression levels in heart, liver and placenta. Ref.4

Sequence similarities

Belongs to the LRIF1 family.

Sequence caution

The sequence AAH08115.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.

The sequence AAO43631.1 differs from that shown. Reason: Frameshift at position 23.

The sequence BAA92097.1 differs from that shown. Reason: Frameshift at position 667.

Ontologies

Keywords
   Biological processTranscription
Transcription regulation
   Cellular componentNucleus
   Coding sequence diversityAlternative splicing
Polymorphism
   DomainCoiled coil
   PTMPhosphoprotein
   Technical termComplete proteome
Reference proteome
Gene Ontology (GO)
   Biological_processregulation of transcription, DNA-templated

Inferred from electronic annotation. Source: UniProtKB-KW

transcription, DNA-templated

Inferred from electronic annotation. Source: UniProtKB-KW

   Cellular_componentactin cytoskeleton

Inferred from direct assay. Source: HPA

nuclear matrix

Inferred from electronic annotation. Source: UniProtKB-SubCell

nucleus

Inferred from direct assay. Source: HPA

   Molecular_functionprotein binding

Inferred from physical interaction PubMed 15383276. Source: IntAct

Complete GO annotation...

Binary interactions

With

Entry

#Exp.

IntAct

Notes

GIT1Q9Y2X72EBI-473196,EBI-466061

Alternative products

This entry describes 2 isoforms produced by alternative splicing. [Align] [Select]
Isoform 1 (identifier: Q5T3J3-1)

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.
Isoform 2 (identifier: Q5T3J3-2)

The sequence of this isoform differs from the canonical sequence as follows:
     1-536: Missing.
Note: No experimental confirmation available.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 769769Ligand-dependent nuclear receptor-interacting factor 1
PRO_0000250686

Regions

Coiled coil740 – 76930 Potential
Motif628 – 6314Nuclear localization signal Ref.4
Motif642 – 6454Nuclear localization signal Ref.4

Amino acid modifications

Modified residue4021Phosphoserine Ref.8
Modified residue5991Phosphoserine Ref.8
Modified residue7321Phosphothreonine Ref.8

Natural variations

Alternative sequence1 – 536536Missing in isoform 2.
VSP_020721
Natural variant4381A → T.
Corresponds to variant rs2232041 [ dbSNP | Ensembl ].
VAR_050703
Natural variant5991S → P.
Corresponds to variant rs2232045 [ dbSNP | Ensembl ].
VAR_027599
Natural variant6411I → M.
Corresponds to variant rs2232047 [ dbSNP | Ensembl ].
VAR_027600

Experimental info

Mutagenesis628 – 6303KKR → AAA: Slightly reduces nuclear localization.
Mutagenesis642 – 6443KKR → AAA: Abolishes nuclear localization.
Sequence conflict66 – 683DAL → NA in AAO43631. Ref.1
Sequence conflict72 – 809TGKPVQVTF → PGNQFSY in AAO43631. Ref.1
Sequence conflict108 – 1114LTRT → PSRP in AAO43631. Ref.1
Sequence conflict6661Missing in BAA92097. Ref.2

Sequences

Sequence LengthMass (Da)Tools
Isoform 1 [UniParc].

Last modified December 21, 2004. Version 1.
Checksum: D39A2BB494F16AAA

FASTA76984,568
        10         20         30         40         50         60 
MSNNLRRVFL KPAEENSGNA SRCVSGCMYQ VVQTIGSDGK NLLQLLPIPK SSGNLIPLVQ 

        70         80         90        100        110        120 
SSVMSDALKG NTGKPVQVTF QTQISSSSTS ASVQLPIFQP ASSSNYFLTR TVDTSEKGRV 

       130        140        150        160        170        180 
TSVGTGNFSS SVSKVQSHGV KIDGLTMQTF AVPPSTQKDS SFIVVNTQSL PVTVKSPVLP 

       190        200        210        220        230        240 
SGHHLQIPAH AEVKSVPASS LPPSVQQKIL ATATTSTSGM VEASQMPTVI YVSPVNTVKN 

       250        260        270        280        290        300 
VVTKNFQNIY PKPVTEIAKP VILNTTQIPK NVATETQLKG GQHSQAAPVK WIFQDNLQPF 

       310        320        330        340        350        360 
TPSLVPVKSS NNVASKILKT FVDRKNLGDN TINMPPLSTI DPSGTRSKNM PIKDNALVMF 

       370        380        390        400        410        420 
NGKVYLLAKK GTDVLPSQID QQNSVSPDTP VRKDTLQTVS SSPVTEISRE VVNIVLAKSK 

       430        440        450        460        470        480 
SSQMETKSLS NTQLASMANL RAEKNKVEKP SPSTTNPHMN QSSNYLKQSK TLFTNPIFPV 

       490        500        510        520        530        540 
GFSTGHNAPR KVTAVIYARK GSVLQSIEKI SSSVDATTVT SQQCVFRDQE PKIHNEMAST 

       550        560        570        580        590        600 
SDKGAQGRND KKDSQGRSNK ALHLKSDAEF KKIFGLTKDL RVCLTRIPDH LTSGEGFDSF 

       610        620        630        640        650        660 
SSLVKSGTYK ETEFMVKEGE RKQQNFDKKR KAKTNKKMDH IKKRKTENAY NAIINGEANV 

       670        680        690        700        710        720 
TGSQLLSSIL PTSDVSQHNI LTSHSKTRQE KRTEMEYYTH EKQEKGTLNS NAAYEQSHFF 

       730        740        750        760 
NKNYTEDIFP VTPPELEETI RDEKIRRLKQ VLREKEAALE EMRKKMHQK 

« Hide

Isoform 2 [UniParc].

Checksum: D1E3BE5BCD299BAB
Show »

FASTA23326,917

References

« Hide 'large scale' references
[1]"Identification of a transcriptional inhibitory factor for retinoic acid receptor."
Li H., Leo C., Chen A., Chen J.D.
Submitted (DEC-2002) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1).
[2]"Complete sequencing and characterization of 21,243 full-length human cDNAs."
Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R., Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H., Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S. expand/collapse author list , Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K., Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S., Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O., Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H., Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B., Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H., Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O., Isogai T., Sugano S.
Nat. Genet. 36:40-45(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2), NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 269-769 (ISOFORM 1).
Tissue: Placenta.
[3]"The DNA sequence and biological annotation of human chromosome 1."
Gregory S.G., Barlow K.F., McLay K.E., Kaul R., Swarbreck D., Dunham A., Scott C.E., Howe K.L., Woodfine K., Spencer C.C.A., Jones M.C., Gillson C., Searle S., Zhou Y., Kokocinski F., McDonald L., Evans R., Phillips K. expand/collapse author list , Atkinson A., Cooper R., Jones C., Hall R.E., Andrews T.D., Lloyd C., Ainscough R., Almeida J.P., Ambrose K.D., Anderson F., Andrew R.W., Ashwell R.I.S., Aubin K., Babbage A.K., Bagguley C.L., Bailey J., Beasley H., Bethel G., Bird C.P., Bray-Allen S., Brown J.Y., Brown A.J., Buckley D., Burton J., Bye J., Carder C., Chapman J.C., Clark S.Y., Clarke G., Clee C., Cobley V., Collier R.E., Corby N., Coville G.J., Davies J., Deadman R., Dunn M., Earthrowl M., Ellington A.G., Errington H., Frankish A., Frankland J., French L., Garner P., Garnett J., Gay L., Ghori M.R.J., Gibson R., Gilby L.M., Gillett W., Glithero R.J., Grafham D.V., Griffiths C., Griffiths-Jones S., Grocock R., Hammond S., Harrison E.S.I., Hart E., Haugen E., Heath P.D., Holmes S., Holt K., Howden P.J., Hunt A.R., Hunt S.E., Hunter G., Isherwood J., James R., Johnson C., Johnson D., Joy A., Kay M., Kershaw J.K., Kibukawa M., Kimberley A.M., King A., Knights A.J., Lad H., Laird G., Lawlor S., Leongamornlert D.A., Lloyd D.M., Loveland J., Lovell J., Lush M.J., Lyne R., Martin S., Mashreghi-Mohammadi M., Matthews L., Matthews N.S.W., McLaren S., Milne S., Mistry S., Moore M.J.F., Nickerson T., O'Dell C.N., Oliver K., Palmeiri A., Palmer S.A., Parker A., Patel D., Pearce A.V., Peck A.I., Pelan S., Phelps K., Phillimore B.J., Plumb R., Rajan J., Raymond C., Rouse G., Saenphimmachak C., Sehra H.K., Sheridan E., Shownkeen R., Sims S., Skuce C.D., Smith M., Steward C., Subramanian S., Sycamore N., Tracey A., Tromans A., Van Helmond Z., Wall M., Wallis J.M., White S., Whitehead S.L., Wilkinson J.E., Willey D.L., Williams H., Wilming L., Wray P.W., Wu Z., Coulson A., Vaudin M., Sulston J.E., Durbin R.M., Hubbard T., Wooster R., Dunham I., Carter N.P., McVean G., Ross M.T., Harrow J., Olson M.V., Beck S., Rogers J., Bentley D.R.
Nature 441:315-321(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[4]"RIF-1, a novel nuclear receptor corepressor that associates with the nuclear matrix."
Li H.J., Haque Z.K., Chen A., Mendelsohn M.
J. Cell. Biochem. 102:1021-1035(2007) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA] OF 28-769 (ISOFORM 1), FUNCTION, SUBCELLULAR LOCATION, TISSUE SPECIFICITY, MUTAGENESIS, NUCLEAR LOCALIZATION SIGNAL, INTERACTION WITH RARA.
[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] OF 202-769 (ISOFORM 1).
Tissue: Placenta.
[6]"The full-ORF clone resource of the German cDNA consortium."
Bechtel S., Rosenfelder H., Duda A., Schmidt C.P., Ernst U., Wellenreuther R., Mehrle A., Schuster C., Bahr A., Bloecker H., Heubner D., Hoerlein A., Michel G., Wedler H., Koehrer K., Ottenwaelder B., Poustka A., Wiemann S., Schupp I.
BMC Genomics 8:399-399(2007) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 277-769 (ISOFORM 1).
Tissue: Melanoma.
[7]"Kinase-selective enrichment enables quantitative phosphoproteomics of the kinome across the cell cycle."
Daub H., Olsen J.V., Bairlein M., Gnad F., Oppermann F.S., Korner R., Greff Z., Keri G., Stemmann O., Mann M.
Mol. Cell 31:438-448(2008) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
Tissue: Cervix carcinoma.
[8]"A quantitative atlas of mitotic phosphorylation."
Dephoure N., Zhou C., Villen J., Beausoleil S.A., Bakalarski C.E., Elledge S.J., Gygi S.P.
Proc. Natl. Acad. Sci. U.S.A. 105:10762-10767(2008) [PubMed] [Europe PMC] [Abstract]
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-402; SER-599 AND THR-732, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
Tissue: Cervix carcinoma.
[9]"Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis."
Olsen J.V., Vermeulen M., Santamaria A., Kumar C., Miller M.L., Jensen L.J., Gnad F., Cox J., Jensen T.S., Nigg E.A., Brunak S., Mann M.
Sci. Signal. 3:RA3-RA3(2010) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
Tissue: Cervix carcinoma.
[10]"N-terminal acetylome analyses and functional insights of the N-terminal acetyltransferase NatB."
Van Damme P., Lasa M., Polevoda B., Gazquez C., Elosegui-Artola A., Kim D.S., De Juan-Pardo E., Demeyer K., Hole K., Larrea E., Timmerman E., Prieto J., Arnesen T., Sherman F., Gevaert K., Aldabe R.
Proc. Natl. Acad. Sci. U.S.A. 109:12449-12454(2012) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
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.
CCDSCCDS30800.1. [Q5T3J3-1]
CCDS41366.1. [Q5T3J3-2]
RefSeqNP_001006946.1. NM_001006945.1. [Q5T3J3-2]
NP_060842.3. NM_018372.3. [Q5T3J3-1]
UniGeneHs.25245.

3D structure databases

ProteinModelPortalQ5T3J3.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid120905. 133 interactions.
IntActQ5T3J3. 33 interactions.
MINTMINT-1405302.
STRING9606.ENSP00000358778.

PTM databases

PhosphoSiteQ5T3J3.

Polymorphism databases

DMDM74744778.

Proteomic databases

MaxQBQ5T3J3.
PaxDbQ5T3J3.
PeptideAtlasQ5T3J3.
PRIDEQ5T3J3.

Protocols and materials databases

DNASU55791.
StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENST00000369763; ENSP00000358778; ENSG00000121931. [Q5T3J3-1]
ENST00000485275; ENSP00000432290; ENSG00000121931. [Q5T3J3-2]
ENST00000494675; ENSP00000435259; ENSG00000121931. [Q5T3J3-2]
GeneID55791.
KEGGhsa:55791.
UCSCuc001dzz.3. human. [Q5T3J3-2]
uc001eaa.3. human. [Q5T3J3-1]

Organism-specific databases

CTD55791.
GeneCardsGC01M111491.
HGNCHGNC:30299. LRIF1.
HPAHPA044515.
HPA053717.
MIM615354. gene.
neXtProtNX_Q5T3J3.
PharmGKBPA142672487.
GenAtlasSearch...

Phylogenomic databases

eggNOGNOG26300.
HOVERGENHBG080960.
InParanoidQ5T3J3.
OMACVSGCMY.
OrthoDBEOG7J446C.
PhylomeDBQ5T3J3.
TreeFamTF336147.

Gene expression databases

BgeeQ5T3J3.
CleanExHS_C1orf103.
HS_RIF1.
GenevestigatorQ5T3J3.

Family and domain databases

InterProIPR026191. LRIF1.
[Graphical view]
PANTHERPTHR16131. PTHR16131. 1 hit.
ProtoNetSearch...

Other

GeneWikiC1orf103.
GenomeRNAi55791.
NextBio60903.
PROQ5T3J3.
SOURCESearch...

Entry information

Entry nameLRIF1_HUMAN
AccessionPrimary (citable) accession number: Q5T3J3
Secondary accession number(s): Q86XS4 expand/collapse secondary AC list , Q8N3B6, Q96HT4, Q9NUM5, Q9NV32
Entry history
Integrated into UniProtKB/Swiss-Prot: October 3, 2006
Last sequence update: December 21, 2004
Last modified: July 9, 2014
This is version 81 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (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.

Relevant documents

SIMILARITY comments

Index of protein domains and families

MIM cross-references

Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot

Human polymorphisms and disease mutations

Index of human polymorphisms and disease mutations

Human entries with polymorphisms or disease mutations

List of human entries with polymorphisms or disease mutations

Human chromosome 1

Human chromosome 1: entries, gene names and cross-references to MIM