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Q7Z5J4 (RAI1_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 97. 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·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Retinoic acid-induced protein 1
Gene names
Name:RAI1
Synonyms:KIAA1820
OrganismHomo sapiens (Human) [Reference proteome]
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo

Protein attributes

Sequence length1906 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Transcriptional regulator of the circadian clock components: CLOCK, ARNTL/BMAL1, ARNTL2/BMAL2, PER1/3, CRY1/2, NR1D1/2 and RORA/C. Positively regulates the transcriptional activity of CLOCK a core component of the circadian clock. Regulates transcription through chromatin remodeling by interacting with other proteins in chromatin as well as proteins in the basic transcriptional machinery. May be important for embryonic and postnatal development. May be involved in neuronal differentiation. Ref.13

Subcellular location

Cytoplasm. Nucleus. Note: In neurons, localized to neurites By similarity.

Tissue specificity

Expressed in all tissues examined with higher expression in the heart and brain. No expression was seen in the corpus callosum of the brain. Ref.2

Polymorphism

The poly-Gln tract is polymorphic and the number of Gln varies from 12 to 14. The size of the poly-Gln region may influence the age at onset of spinocerebellar ataxia type 2 (SCA2).

Involvement in disease

Smith-Magenis syndrome (SMS) [MIM:182290]: Characterized by congenital mental retardation associated with development and growth delays. Affected persons have characteristic behavioral abnormalities, including self-injurious behaviors and sleep disturbance, and distinct craniofacial and skeletal anomalies.
Note: The disease is caused by mutations affecting the gene represented in this entry.

Sequence similarities

Contains 1 PHD-type zinc finger.

Sequence caution

The sequence BAB47449.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.

Alternative products

This entry describes 4 isoforms produced by alternative splicing. [Align] [Select]
Isoform 1 (identifier: Q7Z5J4-1)

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: Q7Z5J4-2)

The sequence of this isoform differs from the canonical sequence as follows:
     207-233: THFPQHSQSFPTSSTYSSSVQGGGQGA → WWAGG
     407-434: VDTQAGNCKPLQKDKLPENLLSDLSLQS → PAD
     1415-1479: Missing.
     1803-1821: Missing.
     1856-1906: MCSSCQEAGA...LKCPKHKRLP → HGGTVALAPG...LCWAMPGTWK
Isoform 3 (identifier: Q7Z5J4-3)

The sequence of this isoform differs from the canonical sequence as follows:
     1598-1640: FVRVEKRDAF...ASSSSSSSSF → LEPSLGAQNP...AYSAREQGQR
     1641-1906: Missing.
Note: No experimental confirmation available.
Isoform 4 (identifier: Q7Z5J4-4)

The sequence of this isoform differs from the canonical sequence as follows:
     947-966: SHMKPGEEGPDGERAPGDST → YSVYICIHIHIYNIYEDCKC
     967-1906: Missing.
Note: No experimental confirmation available.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 19061906Retinoic acid-induced protein 1
PRO_0000097159

Regions

Zinc finger1856 – 190348PHD-type
Motif1160 – 117718Nuclear localization signal Potential
Motif1223 – 124018Nuclear localization signal Potential
Compositional bias124 – 13512Poly-Pro
Compositional bias156 – 336181Gln-rich
Compositional bias278 – 29114Poly-Gln
Compositional bias1243 – 12497Poly-Ser
Compositional bias1493 – 14964Poly-Gly
Compositional bias1628 – 164114Ser-rich
Compositional bias1746 – 17516Poly-Ala

Amino acid modifications

Modified residue5681Phosphoserine Ref.12
Modified residue6831Phosphoserine Ref.9 Ref.11 Ref.12
Modified residue6961Phosphothreonine Ref.9
Modified residue8801Phosphoserine Ref.9
Modified residue8921Phosphoserine Ref.9
Modified residue10641Phosphoserine Ref.11
Modified residue10681Phosphothreonine Ref.11
Modified residue11221Phosphoserine Ref.9
Modified residue13521Phosphoserine Ref.9 Ref.12
Modified residue13581Phosphoserine Ref.9 Ref.12
Modified residue13741Phosphoserine Ref.9 Ref.11 Ref.12
Modified residue14311Phosphoserine Ref.9

Natural variations

Alternative sequence207 – 23327THFPQ…GGQGA → WWAGG in isoform 2.
VSP_010995
Alternative sequence407 – 43428VDTQA…LSLQS → PAD in isoform 2.
VSP_010996
Alternative sequence947 – 96620SHMKP…PGDST → YSVYICIHIHIYNIYEDCKC in isoform 4.
VSP_010997
Alternative sequence967 – 1906940Missing in isoform 4.
VSP_010998
Alternative sequence1415 – 147965Missing in isoform 2.
VSP_010999
Alternative sequence1598 – 164043FVRVE…SSSSF → LEPSLGAQNPRSGQNAPPAP ADARPLCTTRDRRAYSAREQ GQR in isoform 3.
VSP_011000
Alternative sequence1641 – 1906266Missing in isoform 3.
VSP_011001
Alternative sequence1803 – 182119Missing in isoform 2.
VSP_011002
Alternative sequence1856 – 190651MCSSC…HKRLP → HGGTVALAPGDFSLPGLRFA SLFQGPSWCDCPVLATSTPS SWSRCVPAAKKPGPPLGAAT KDASTPTTTRVPAMQVRARP GTGGHWSPSKQSRGTLPGHS SPNPGPISLFSFPPLLPQQF FYPSVCLDLCWAMPGTWK in isoform 2.
VSP_011003
Natural variant901G → A.
Corresponds to variant rs3803763 [ dbSNP | Ensembl ].
VAR_051300
Natural variant1651P → T.
Corresponds to variant rs11649804 [ dbSNP | Ensembl ].
VAR_024344
Natural variant9391Q → P.
Corresponds to variant rs1759075 [ dbSNP | Ensembl ].
VAR_051301

Experimental info

Sequence conflict4401S → L in AAO31738. Ref.2
Sequence conflict13021L → F in AAO31738. Ref.2
Sequence conflict15131G → A in AAO31738. Ref.2
Sequence conflict16821T → A in CAD39144. Ref.5

Sequences

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

Last modified July 19, 2004. Version 2.
Checksum: 8D33A56C33BFE888

FASTA1,906203,352
        10         20         30         40         50         60 
MQSFRERCGF HGKQQNYQQT SQETSRLENY RQPSQAGLSC DRQRLLAKDY YNPQPYPSYE 

        70         80         90        100        110        120 
GGAGTPSGTA AAVAADKYHR GSKALPTQQG LQGRPAFPGY GVQDSSPYPG RYAGEESLQA 

       130        140        150        160        170        180 
WGAPQPPPPQ PQPLPAGVAK YDENLMKKTA VPPSRQYAEQ GAQVPFRTHS LHVQQPPPPQ 

       190        200        210        220        230        240 
QPLAYPKLQR QKLQNDIASP LPFPQGTHFP QHSQSFPTSS TYSSSVQGGG QGAHSYKSCT 

       250        260        270        280        290        300 
APTAQPHDRP LTASSSLAPG QRVQNLHAYQ SGRLSYDQQQ QQQQQQQQQQ QALQSRHHAQ 

       310        320        330        340        350        360 
ETLHYQNLAK YQHYGQQGQG YCQPDAAVRT PEQYYQTFSP SSSHSPARSV GRSPSYSSTP 

       370        380        390        400        410        420 
SPLMPNLENF PYSQQPLSTG AFPAGITDHS HFMPLLNPSP TDATSSVDTQ AGNCKPLQKD 

       430        440        450        460        470        480 
KLPENLLSDL SLQSLTALTS QVENISNTVQ QLLLSKAAVP QKKGVKNLVS RTPEQHKSQH 

       490        500        510        520        530        540 
CSPEGSGYSA EPAGTPLSEP PSSTPQSTHA EPQEADYLSG SEDPLERSFL YCNQARGSPA 

       550        560        570        580        590        600 
RVNSNSKAKP ESVSTCSVTS PDDMSTKSDD SFQSLHGSLP LDSFSKFVAG ERDCPRLLLS 

       610        620        630        640        650        660 
ALAQEDLASE ILGLQEAIGE KADKAWAEAP SLVKDSSKPP FSLENHSACL DSVAKSAWPR 

       670        680        690        700        710        720 
PGEPEALPDS LQLDKGGNAK DFSPGLFEDP SVAFATPDPK KTTGPLSFGT KPTLGVPAPD 

       730        740        750        760        770        780 
PTTAAFDCFP DTTAASSADS ANPFAWPEEN LGDACPRWGL HPGELTKGLE QGGKASDGIS 

       790        800        810        820        830        840 
KGDTHEASAC LGFQEEDPPG EKVASLPGDF KQEEVGGVKE EAGGLLQCPE VAKADRWLED 

       850        860        870        880        890        900 
SRHCCSTADF GDLPLLPPTS RKEDLEAEEE YSSLCELLGS PEQRPGMQDP LSPKAPLICT 

       910        920        930        940        950        960 
KEEVEEVLDS KAGWGSPCHL SGESVILLGP TVGTESKVQS WFESSLSHMK PGEEGPDGER 

       970        980        990       1000       1010       1020 
APGDSTTSDA SLAQKPNKPA VPEAPIAKKE PVPRGKSLRS RRVHRGLPEA EDSPCRAPVL 

      1030       1040       1050       1060       1070       1080 
PKDLLLPESC TGPPQGQMEG AGAPGRGASE GLPRMCTRSL TALSEPRTPG PPGLTTTPAP 

      1090       1100       1110       1120       1130       1140 
PDKLGGKQRA AFKSGKRVGK PSPKAASSPS NPAALPVASD SSPMGSKTKE TDSPSTPGKD 

      1150       1160       1170       1180       1190       1200 
QRSMILRSRT KTQEIFHSKR RRPSEGRLPN CRATKKLLDN SHLPATFKVS SSPQKEGRVS 

      1210       1220       1230       1240       1250       1260 
QRARVPKPGA GSKLSDRPLH ALKRKSAFMA PVPTKKRNLV LRSRSSSSSN ASGNGGDGKE 

      1270       1280       1290       1300       1310       1320 
ERPEGSPTLF KRMSSPKKAK PTKGNGEPAT KLPPPETPDA CLKLASRAAF QGAMKTKVLP 

      1330       1340       1350       1360       1370       1380 
PRKGRGLKLE AIVQKITSPS LKKFACKAPG ASPGNPLSPS LSDKDRGLKG AGGSPVGVEE 

      1390       1400       1410       1420       1430       1440 
GLVNVGTGQK LPTSGADPLC RNPTNRSLKG KLMNSKKLSS TDCFKTEAFT SPEALQPGGT 

      1450       1460       1470       1480       1490       1500 
ALAPKKRSRK GRAGAHGLSK GPLEKRPYLG PALLLTPRDR ASGTQGASED NSGGGGKKPK 

      1510       1520       1530       1540       1550       1560 
MEELGLASQP PEGRPCQPQT RAQKQPGHTN YSSYSKRKRL TRGRAKNTTS SPCKGRAKRR 

      1570       1580       1590       1600       1610       1620 
RQQQVLPLDP AEPEIRLKYI SSCKRLRSDS RTPAFSPFVR VEKRDAFTTI CTVVNSPGDA 

      1630       1640       1650       1660       1670       1680 
PKPHRKPSSS ASSSSSSSSF SLDAAGASLA TLPGGSILQP RPSLPLSSTM HLGPVVSKAL 

      1690       1700       1710       1720       1730       1740 
STSCLVCCLC QNPANFKDLG DLCGPYYPEH CLPKKKPKLK EKVRPEGTCE EASLPLERTL 

      1750       1760       1770       1780       1790       1800 
KGPECAAAAT AGKPPRPDGP ADPAKQGPLR TSARGLSRRL QSCYCCDGRE DGGEEAAPAD 

      1810       1820       1830       1840       1850       1860 
KGRKHECSKE APAEPGGEAQ EHWVHEACAV WTGGVYLVAG KLFGLQEAMK VAVDMMCSSC 

      1870       1880       1890       1900 
QEAGATIGCC HKGCLHTYHY PCASDAGCIF IEENFSLKCP KHKRLP 

« Hide

Isoform 2 [UniParc].

Checksum: 9C4D9E4EF917A911
Show »

FASTA1,862198,392
Isoform 3 [UniParc].

Checksum: A178ECCDECEDA431
Show »

FASTA1,640175,343
Isoform 4 [UniParc].

Checksum: EBD2A4453EADBA58
Show »

FASTA966104,319

References

« Hide 'large scale' references
[1]"RAI1 is a novel polyglutamine encoding gene that is deleted in Smith-Magenis syndrome patients."
Seranski P., Hoff C., Radelof U., Henning S., Reinhard R., Schwartz C.E., Heiss N., Poustka A.
Gene 270:69-76(2001) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA / MRNA] (ISOFORM 2), POLYMORPHISM OF POLY-GLN REGION, INVOLVEMENT IN SMITH-MAGENIS SYNDROME.
[2]"Molecular cloning and characterization of human RAI1, a gene associated with schizophrenia."
Toulouse A., Rochefort D., Roussel J., Joober R., Rouleau G.A.
Genomics 82:162-171(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), TISSUE SPECIFICITY.
[3]"Prediction of the coding sequences of unidentified human genes. XX. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro."
Nagase T., Nakayama M., Nakajima D., Kikuno R., Ohara O.
DNA Res. 8:85-95(2001) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 3).
Tissue: Brain.
[4]"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] (ISOFORM 4).
Tissue: Muscle.
[5]"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 622-1906.
Tissue: Melanoma and Testis.
[6]"Mutations in RAI1 associated with Smith-Magenis syndrome."
Slager R.E., Newton T.L., Vlangos C.N., Finucane B., Elsea S.H.
Nat. Genet. 33:466-468(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: INVOLVEMENT IN SMITH-MAGENIS SYNDROME.
[7]"CAG repeat length in RAI1 is associated with age at onset variability in spinocerebellar ataxia type 2 (SCA2)."
Hayes S., Turecki G., Brisebois K., Lopes-Cendes I., Gaspar C., Riess O., Ranum L.P., Pulst S.M., Rouleau G.A.
Hum. Mol. Genet. 9:1753-1758(2000) [PubMed] [Europe PMC] [Abstract]
Cited for: ROLE OF THE POLY-GLN REGION IN SPINOCEREBELLAR ATAXIA TYPE 2.
[8]"Combining protein-based IMAC, peptide-based IMAC, and MudPIT for efficient phosphoproteomic analysis."
Cantin G.T., Yi W., Lu B., Park S.K., Xu T., Lee J.-D., Yates J.R. III
J. Proteome Res. 7:1346-1351(2008) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
Tissue: Cervix carcinoma.
[9]"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-683; THR-696; SER-880; SER-892; SER-1122; SER-1352; SER-1358; SER-1374 AND SER-1431, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
Tissue: Cervix carcinoma.
[10]"Lys-N and trypsin cover complementary parts of the phosphoproteome in a refined SCX-based approach."
Gauci S., Helbig A.O., Slijper M., Krijgsveld J., Heck A.J., Mohammed S.
Anal. Chem. 81:4493-4501(2009) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[11]"Quantitative phosphoproteomic analysis of T cell receptor signaling reveals system-wide modulation of protein-protein interactions."
Mayya V., Lundgren D.H., Hwang S.-I., Rezaul K., Wu L., Eng J.K., Rodionov V., Han D.K.
Sci. Signal. 2:RA46-RA46(2009) [PubMed] [Europe PMC] [Abstract]
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-683; SER-1064; THR-1068 AND SER-1374, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
Tissue: Leukemic T-cell.
[12]"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: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-568; SER-683; SER-1352; SER-1358 AND SER-1374, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
Tissue: Cervix carcinoma.
[13]"Smith-Magenis syndrome results in disruption of CLOCK gene transcription and reveals an integral role for RAI1 in the maintenance of circadian rhythmicity."
Williams S.R., Zies D., Mullegama S.V., Grotewiel M.S., Elsea S.H.
Am. J. Hum. Genet. 90:941-949(2012) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
AJ271790 mRNA. Translation: CAC20423.1.
AJ271791 Genomic DNA. Translation: CAC20424.1.
AY172136 mRNA. Translation: AAO31738.1.
AB058723 mRNA. Translation: BAB47449.1. Different initiation.
BC021209 mRNA. Translation: AAH21209.1.
AL133649 mRNA. Translation: CAB63768.1.
AL834468 mRNA. Translation: CAD39127.1.
AL834486 mRNA. Translation: CAD39144.1.
CCDSCCDS11188.1. [Q7Z5J4-1]
PIRT43490.
RefSeqNP_109590.3. NM_030665.3. [Q7Z5J4-1]
UniGeneHs.655395.
Hs.727059.

3D structure databases

ProteinModelPortalQ7Z5J4.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid115966. 21 interactions.
IntActQ7Z5J4. 10 interactions.
MINTMINT-1477867.
STRING9606.ENSP00000323074.

PTM databases

PhosphoSiteQ7Z5J4.

Polymorphism databases

DMDM50400978.

Proteomic databases

MaxQBQ7Z5J4.
PaxDbQ7Z5J4.
PRIDEQ7Z5J4.

Protocols and materials databases

DNASU10743.
StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENST00000353383; ENSP00000323074; ENSG00000108557. [Q7Z5J4-1]
GeneID10743.
KEGGhsa:10743.
UCSCuc002grm.3. human. [Q7Z5J4-1]

Organism-specific databases

CTD10743.
GeneCardsGC17P017525.
GeneReviewsRAI1.
H-InvDBHIX0013588.
HGNCHGNC:9834. RAI1.
HPAHPA023898.
HPA054906.
MIM182290. phenotype.
607642. gene.
neXtProtNX_Q7Z5J4.
Orphanet1713. 17p11.2 microduplication syndrome.
819. Smith-Magenis syndrome.
PharmGKBPA34188.
HUGESearch...
GenAtlasSearch...

Phylogenomic databases

eggNOGNOG146768.
HOVERGENHBG056862.
OMAPRMCTRS.
OrthoDBEOG7G4QDB.
PhylomeDBQ7Z5J4.
TreeFamTF331317.

Gene expression databases

ArrayExpressQ7Z5J4.
BgeeQ7Z5J4.
CleanExHS_RAI1.
GenevestigatorQ7Z5J4.

Family and domain databases

InterProIPR001965. Znf_PHD.
[Graphical view]
SMARTSM00249. PHD. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

ChiTaRSRAI1. human.
GenomeRNAi10743.
NextBio40793.
PROQ7Z5J4.
SOURCESearch...

Entry information

Entry nameRAI1_HUMAN
AccessionPrimary (citable) accession number: Q7Z5J4
Secondary accession number(s): Q8N3B4 expand/collapse secondary AC list , Q8ND08, Q8WU64, Q96JK5, Q9H1C1, Q9H1C2, Q9UF69
Entry history
Integrated into UniProtKB/Swiss-Prot: July 19, 2004
Last sequence update: July 19, 2004
Last modified: July 9, 2014
This is version 97 of the entry and version 2 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 17

Human chromosome 17: entries, gene names and cross-references to MIM