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Q5T3J3

- LRIF1_HUMAN

UniProt

Q5T3J3 - LRIF1_HUMAN

Protein

Ligand-dependent nuclear receptor-interacting factor 1

Gene

LRIF1

Organism
Homo sapiens (Human)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 82 (01 Oct 2014)
      Sequence version 1 (21 Dec 2004)
      Previous versions | rss
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    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

    GO - Biological processi

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

    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

    Keywords - Cellular componenti

    Nucleus

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi628 – 6303KKR → AAA: Slightly reduces nuclear localization. 1 Publication
    Mutagenesisi642 – 6443KKR → AAA: Abolishes nuclear localization. 1 Publication

    Organism-specific databases

    PharmGKBiPA142672487.

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 769769Ligand-dependent nuclear receptor-interacting factor 1PRO_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.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Coiled coil

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Coiled coili740 – 76930Sequence AnalysisAdd
    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.Curated

    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.

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti66 – 683DAL → NA in AAO43631. 1 PublicationCurated
    Sequence conflicti72 – 809TGKPVQVTF → PGNQFSY in AAO43631. 1 PublicationCurated
    Sequence conflicti108 – 1114LTRT → PSRP in AAO43631. 1 PublicationCurated
    Sequence conflicti666 – 6661Missing in BAA92097. (PubMed:14702039)Curated

    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. 1 PublicationVSP_020721Add
    BLAST

    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...
    MobiDBi 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

    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: October 1, 2014
    This is version 82 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