Q5T3J3 (LRIF1_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Ligand-dependent nuclear receptor-interacting factor 1

Alternative name(s):
Receptor-interacting factor 1

Gene names

Name:	LRIF1
Synonyms:	C1orf103, RIF1

Organism

Homo sapiens (Human) [Reference proteome]

Taxonomic identifier

9606 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Metazoa › Eumetazoa › Bilateria › Deuterostomia › Chordata › Craniata › Vertebrata › Gnathostomata › Teleostomi › Euteleostomi › Sarcopterygii › Tetrapoda › Amniota › Mammalia › Theria › Eutheria › Euarchontoglires › Primates › Haplorrhini › Simiiformes › Catarrhini › Hominoidea › Hominidae › Homininae › Homo

Protein attributes

Sequence length	769 AA.
Sequence status	Complete.
Protein existence	Evidence 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 process	Transcription Transcription regulation
Cellular component	Nucleus
Coding sequence diversity	Alternative splicing Polymorphism
Domain	Coiled coil
PTM	Phosphoprotein
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	regulation of transcription, DNA-dependent Inferred from electronic annotation. Source: UniProtKB-KW transcription, DNA-dependent Inferred from electronic annotation. Source: UniProtKB-KW
Cellular_component	nuclear matrix Inferred from electronic annotation. Source: UniProtKB-SubCell nucleus Inferred from direct assay. Source: HPA
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
GIT1	Q9Y2X7	2	EBI-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 key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 769	769	Ligand-dependent nuclear receptor-interacting factor 1		PRO_0000250686
Regions
	Coiled coil	740 – 769	30	Potential
	Motif	628 – 631	4	Nuclear localization signal Ref.4
	Motif	642 – 645	4	Nuclear localization signal Ref.4
Amino acid modifications
	Modified residue	402	1	Phosphoserine Ref.8
	Modified residue	599	1	Phosphoserine Ref.8
	Modified residue	732	1	Phosphothreonine Ref.8
Natural variations
	Alternative sequence	1 – 536	536	Missing in isoform 2.		VSP_020721
	Natural variant	438	1	A → T. Corresponds to variant rs2232041 [ dbSNP | Ensembl ].		VAR_050703
	Natural variant	599	1	S → P. Corresponds to variant rs2232045 [ dbSNP | Ensembl ].		VAR_027599
	Natural variant	641	1	I → M. Corresponds to variant rs2232047 [ dbSNP | Ensembl ].		VAR_027600
Experimental info
	Mutagenesis	628 – 630	3	KKR → AAA: Slightly reduces nuclear localization.
	Mutagenesis	642 – 644	3	KKR → AAA: Abolishes nuclear localization.
	Sequence conflict	66 – 68	3	DAL → NA in AAO43631. Ref.1
	Sequence conflict	72 – 80	9	TGKPVQVTF → PGNQFSY in AAO43631. Ref.1
	Sequence conflict	108 – 111	4	LTRT → PSRP in AAO43631. Ref.1
	Sequence conflict	666	1	Missing in BAA92097. Ref.2

Sequences

	Sequence		Length	Mass (Da)
	Isoform 1 [UniParc]. Last modified December 21, 2004. Version 1. Checksum: D39A2BB494F16AAA	FASTA	769	84,568
	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
	Isoform 2 [UniParc]. Checksum: D1E3BE5BCD299BAB	FASTA	233	26,917
	10 20 30 40 50 60 MASTSDKGAQ GRNDKKDSQG RSNKALHLKS DAEFKKIFGL TKDLRVCLTR IPDHLTSGEG 70 80 90 100 110 120 FDSFSSLVKS GTYKETEFMV KEGERKQQNF DKKRKAKTNK KMDHIKKRKT ENAYNAIING 130 140 150 160 170 180 EANVTGSQLL SSILPTSDVS QHNILTSHSK TRQEKRTEME YYTHEKQEKG TLNSNAAYEQ 190 200 210 220 230 SHFFNKNYTE DIFPVTPPEL EETIRDEKIR RLKQVLREKE AALEEMRKKM HQK

References

	« Hide 'large scale' referencesShow '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. , 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]	"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, MASS SPECTROMETRY. 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.
+	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.
IPI	IPI00296858. IPI00479789.
RefSeq	NP_001006946.1. NM_001006945.1. NP_060842.3. NM_018372.3.
UniGene	Hs.25245.
3D structure databases
ProteinModelPortal	Q5T3J3.
ModBase	Search...
Protein-protein interaction databases
IntAct	Q5T3J3. 19 interactions.
MINT	MINT-1405302.
STRING	9606.ENSP00000358778.
PTM databases
PhosphoSite	Q5T3J3.
Polymorphism databases
DMDM	74744778.
Proteomic databases
PaxDb	Q5T3J3.
PeptideAtlas	Q5T3J3.
PRIDE	Q5T3J3.
Protocols and materials databases
DNASU	55791.
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
Ensembl	ENST00000369763; ENSP00000358778; ENSG00000121931. ENST00000485275; ENSP00000432290; ENSG00000121931. ENST00000494675; ENSP00000435259; ENSG00000121931.
GeneID	55791.
KEGG	hsa:55791.
UCSC	uc001dzz.3. human. uc001eaa.3. human.
Organism-specific databases
CTD	55791.
GeneCards	GC01M111491.
HGNC	HGNC:30299. LRIF1.
HPA	HPA044515.
neXtProt	NX_Q5T3J3.
PharmGKB	PA142672487.
GenAtlas	Search...
Phylogenomic databases
eggNOG	NOG26300.
HOVERGEN	HBG080960.
InParanoid	Q5T3J3.
OMA	CVSGCMY.
OrthoDB	EOG4RV2QX.
Gene expression databases
Bgee	Q5T3J3.
CleanEx	HS_C1orf103. HS_RIF1.
Genevestigator	Q5T3J3.
GermOnline	ENSG00000121931. Homo sapiens.
Family and domain databases
InterPro	IPR026191. LRIF1. [Graphical view]
PANTHER	PTHR16131. PTHR16131. 1 hit.
ProtoNet	Search...
Other
GenomeRNAi	55791.
NextBio	60903.

Entry information

Entry name

LRIF1_HUMAN

Accession

Primary (citable) accession number: Q5T3J3
Secondary accession number(s): Q86XS4 , Q8N3B6, Q96HT4, Q9NUM5, Q9NV32

Entry history

Integrated into UniProtKB/Swiss-Prot:	October 3, 2006
Last sequence update:	December 21, 2004
Last modified:	April 3, 2013
This is version 71 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Chordata Protein Annotation Program

Disclaimer

Any 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.