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Q5T3J3

- LRIF1_HUMAN

UniProt

Q5T3J3 - LRIF1_HUMAN

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Protein
Ligand-dependent nuclear receptor-interacting factor 1
Gene
LRIF1, C1orf103, RIF1
Organism
Homo sapiens (Human)
Status
Reviewed - 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 - Molecular functioni

  1. protein binding Source: IntAct
Complete GO annotation...

GO - Biological processi

  1. regulation of transcription, DNA-templated Source: UniProtKB-KW
  2. transcription, DNA-templated Source: UniProtKB-KW
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
ProteomesiUP000005640: Chromosome 1

Organism-specific databases

HGNCiHGNC:30299. LRIF1.

Subcellular locationi

Nucleus matrix 1 Publication

GO - Cellular componenti

  1. actin cytoskeleton Source: HPA
  2. nuclear matrix Source: UniProtKB-SubCell
  3. nucleus Source: HPA
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi628 – 6303KKR → AAA: Slightly reduces nuclear localization.
Mutagenesisi642 – 6443KKR → AAA: Abolishes nuclear localization.

Organism-specific databases

PharmGKBiPA142672487.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 769769Ligand-dependent nuclear receptor-interacting factor 1
PRO_0000250686Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei402 – 4021Phosphoserine1 Publication
Modified residuei599 – 5991Phosphoserine1 Publication
Modified residuei732 – 7321Phosphothreonine1 Publication

Keywords - PTMi

Phosphoprotein

Proteomic databases

MaxQBiQ5T3J3.
PaxDbiQ5T3J3.
PeptideAtlasiQ5T3J3.
PRIDEiQ5T3J3.

PTM databases

PhosphoSiteiQ5T3J3.

Expressioni

Tissue specificityi

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

Gene expression databases

BgeeiQ5T3J3.
CleanExiHS_C1orf103.
HS_RIF1.
GenevestigatoriQ5T3J3.

Organism-specific databases

HPAiHPA044515.
HPA053717.

Interactioni

Subunit structurei

Interacts with RARA.1 Publication

Binary interactionsi

WithEntry#Exp.IntActNotes
GIT1Q9Y2X72EBI-473196,EBI-466061

Protein-protein interaction databases

BioGridi120905. 133 interactions.
IntActiQ5T3J3. 33 interactions.
MINTiMINT-1405302.
STRINGi9606.ENSP00000358778.

Structurei

3D structure databases

ProteinModelPortaliQ5T3J3.

Family & Domainsi

Coiled coil

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Coiled coili740 – 76930 Reviewed prediction
Add
BLAST

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi628 – 6314Nuclear localization signal1 Publication
Motifi642 – 6454Nuclear localization signal1 Publication

Sequence similaritiesi

Belongs to the LRIF1 family.

Keywords - Domaini

Coiled coil

Phylogenomic databases

eggNOGiNOG26300.
HOVERGENiHBG080960.
InParanoidiQ5T3J3.
OMAiCVSGCMY.
OrthoDBiEOG7J446C.
PhylomeDBiQ5T3J3.
TreeFamiTF336147.

Family and domain databases

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

Sequences (2)i

Sequence statusi: Complete.

This entry describes 2 isoformsi produced by alternative splicing. Align

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

MSNNLRRVFL KPAEENSGNA SRCVSGCMYQ VVQTIGSDGK NLLQLLPIPK    50
SSGNLIPLVQ SSVMSDALKG NTGKPVQVTF QTQISSSSTS ASVQLPIFQP 100
ASSSNYFLTR TVDTSEKGRV TSVGTGNFSS SVSKVQSHGV KIDGLTMQTF 150
AVPPSTQKDS SFIVVNTQSL PVTVKSPVLP SGHHLQIPAH AEVKSVPASS 200
LPPSVQQKIL ATATTSTSGM VEASQMPTVI YVSPVNTVKN VVTKNFQNIY 250
PKPVTEIAKP VILNTTQIPK NVATETQLKG GQHSQAAPVK WIFQDNLQPF 300
TPSLVPVKSS NNVASKILKT FVDRKNLGDN TINMPPLSTI DPSGTRSKNM 350
PIKDNALVMF NGKVYLLAKK GTDVLPSQID QQNSVSPDTP VRKDTLQTVS 400
SSPVTEISRE VVNIVLAKSK SSQMETKSLS NTQLASMANL RAEKNKVEKP 450
SPSTTNPHMN QSSNYLKQSK TLFTNPIFPV GFSTGHNAPR KVTAVIYARK 500
GSVLQSIEKI SSSVDATTVT SQQCVFRDQE PKIHNEMAST SDKGAQGRND 550
KKDSQGRSNK ALHLKSDAEF KKIFGLTKDL RVCLTRIPDH LTSGEGFDSF 600
SSLVKSGTYK ETEFMVKEGE RKQQNFDKKR KAKTNKKMDH IKKRKTENAY 650
NAIINGEANV TGSQLLSSIL PTSDVSQHNI LTSHSKTRQE KRTEMEYYTH 700
EKQEKGTLNS NAAYEQSHFF NKNYTEDIFP VTPPELEETI RDEKIRRLKQ 750
VLREKEAALE EMRKKMHQK 769
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 AAO43631.1 differs from that shown. Reason: Frameshift at position 23.
The sequence BAA92097.1 differs from that shown. Reason: Frameshift at position 667.
The sequence AAH08115.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti438 – 4381A → T.
Corresponds to variant rs2232041 [ dbSNP | Ensembl ].
VAR_050703
Natural varianti599 – 5991S → P.
Corresponds to variant rs2232045 [ dbSNP | Ensembl ].
VAR_027599
Natural varianti641 – 6411I → M.
Corresponds to variant rs2232047 [ dbSNP | Ensembl ].
VAR_027600

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei1 – 536536Missing in isoform 2.
VSP_020721Add
BLAST

Sequence conflict

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti66 – 683DAL → NA in AAO43631. 1 Publication
Sequence conflicti72 – 809TGKPVQVTF → PGNQFSY in AAO43631. 1 Publication
Sequence conflicti108 – 1114LTRT → PSRP in AAO43631. 1 Publication
Sequence conflicti666 – 6661Missing in BAA92097. 1 Publication

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
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.3. human. [Q5T3J3-2]
uc001eaa.3. human. [Q5T3J3-1]

Polymorphism databases

DMDMi74744778.

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
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 .
CCDSi CCDS30800.1. [Q5T3J3-1 ]
CCDS41366.1. [Q5T3J3-2 ]
RefSeqi NP_001006946.1. NM_001006945.1. [Q5T3J3-2 ]
NP_060842.3. NM_018372.3. [Q5T3J3-1 ]
UniGenei Hs.25245.

3D structure databases

ProteinModelPortali Q5T3J3.
ModBasei Search...

Protein-protein interaction databases

BioGridi 120905. 133 interactions.
IntActi Q5T3J3. 33 interactions.
MINTi MINT-1405302.
STRINGi 9606.ENSP00000358778.

PTM databases

PhosphoSitei Q5T3J3.

Polymorphism databases

DMDMi 74744778.

Proteomic databases

MaxQBi Q5T3J3.
PaxDbi Q5T3J3.
PeptideAtlasi Q5T3J3.
PRIDEi Q5T3J3.

Protocols and materials databases

DNASUi 55791.
Structural Biology Knowledgebase Search...

Genome annotation databases

Ensembli ENST00000369763 ; ENSP00000358778 ; ENSG00000121931 . [Q5T3J3-1 ]
ENST00000485275 ; ENSP00000432290 ; ENSG00000121931 . [Q5T3J3-2 ]
ENST00000494675 ; ENSP00000435259 ; ENSG00000121931 . [Q5T3J3-2 ]
GeneIDi 55791.
KEGGi hsa:55791.
UCSCi uc001dzz.3. human. [Q5T3J3-2 ]
uc001eaa.3. human. [Q5T3J3-1 ]

Organism-specific databases

CTDi 55791.
GeneCardsi GC01M111491.
HGNCi HGNC:30299. LRIF1.
HPAi HPA044515.
HPA053717.
MIMi 615354. gene.
neXtProti NX_Q5T3J3.
PharmGKBi PA142672487.
GenAtlasi Search...

Phylogenomic databases

eggNOGi NOG26300.
HOVERGENi HBG080960.
InParanoidi Q5T3J3.
OMAi CVSGCMY.
OrthoDBi EOG7J446C.
PhylomeDBi Q5T3J3.
TreeFami TF336147.

Miscellaneous databases

GeneWikii C1orf103.
GenomeRNAii 55791.
NextBioi 60903.
PROi Q5T3J3.
SOURCEi Search...

Gene expression databases

Bgeei Q5T3J3.
CleanExi HS_C1orf103.
HS_RIF1.
Genevestigatori Q5T3J3.

Family and domain databases

InterProi IPR026191. LRIF1.
[Graphical view ]
PANTHERi PTHR16131. PTHR16131. 1 hit.
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  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.
    , 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.
    , 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. 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. 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. Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].

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: July 9, 2014
This is version 81 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

External Data

Dasty 3

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