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Aliases for RAI1 Gene

Aliases for RAI1 Gene

  • Retinoic Acid Induced 1 2 3 5
  • Smith-Magenis Syndrome Chromosome Region 2 3
  • Retinoic Acid-Induced Protein 1 3
  • KIAA1820 4
  • SMCR 3
  • SMS 3

External Ids for RAI1 Gene

Previous HGNC Symbols for RAI1 Gene

  • SMCR

Previous GeneCards Identifiers for RAI1 Gene

  • GC17P017899
  • GC17P018957
  • GC17P017527
  • GC17P017785
  • GC17P017525
  • GC17P017379

Summaries for RAI1 Gene

Entrez Gene Summary for RAI1 Gene

  • This gene is located within the Smith-Magenis syndrome region on chromosome 17. It is highly similar to its mouse counterpart and is expressed at high levels mainly in neuronal tissues. The protein encoded by this gene includes a polymorphic polyglutamine tract in the N-terminal domain. Expression of the mouse counterpart in neurons is induced by retinoic acid. This gene is associated with both the severity of the phenotype and the response to medication in schizophrenic patients. [provided by RefSeq, Jul 2008]

GeneCards Summary for RAI1 Gene

RAI1 (Retinoic Acid Induced 1) is a Protein Coding gene. Diseases associated with RAI1 include Smith-Magenis Syndrome and Otof-Related Deafness. Among its related pathways are BMAL1-CLOCK,NPAS2 activates circadian gene expression. GO annotations related to this gene include enhancer binding. An important paralog of this gene is TCF20.

UniProtKB/Swiss-Prot for RAI1 Gene

  • 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.

No data available for Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for RAI1 Gene

Genomics for RAI1 Gene

Regulatory Elements for RAI1 Gene

Enhancers for RAI1 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH17F017720 0.5 ENCODE 12.6 +38.9 38948 0.8 SOX13 ZNF792 SUZ12 SAP130 ARID4B ZNF384 ZFHX2 EGR2 ZNF263 SOX5 RAI1 SREBF1 TOM1L2 PIR55057 RAI1-AS1
GH17F017722 0.7 Ensembl ENCODE 12.6 +45.4 45376 9.5 HDGF PKNOX1 ARID4B ZNF2 ZNF143 FOS ZNF202 NFYC SMARCB1 ZNF592 DRG2 FAM106A RAI1 FOXO3B ENSG00000264885 ENSG00000265511 SREBF1 SMCR8 ACTG1P24 LOC100419436
GH17F017708 1.4 FANTOM5 Ensembl ENCODE 12.4 +30.6 30627 7.0 HDGF PKNOX1 MLX ARID4B SIN3A DMAP1 SLC30A9 ZNF143 FOS SP3 ZNF286B ENSG00000264885 LOC100419436 RAI1 UPF3AP1 SREBF1 MIR33B MYO15A TOM1L2 TOP3A
GH17F017809 0.8 ENCODE 12.3 +129.9 129857 3.4 PKNOX1 MLX ARID4B ZNF2 ZNF48 YY1 GLIS2 ZNF143 PAF1 ZNF263 TOM1L2 SREBF1 RAI1 GC17M017811 PIR43249
GH17F017808 0.6 ENCODE 12.3 +127.4 127399 0.3 BCOR HDGF SAP130 CHD4 KLF17 ZMYM3 ZNF121 ZNF169 ADNP ZNF600 RAI1 GC17M017811 PIR43249
- Elite enhancer/Elite enhancer-gene association Download Table
Download GeneHancer data dump

Enhancers around RAI1 on UCSC Golden Path with GeneCards custom track

Promoters for RAI1 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00001534657 727 2401 ATF1 ZFP64 ARID4B SIN3A BRCA1 GLIS2 ZNF143 FOS YY2 REST

Genomic Location for RAI1 Gene

Chromosome:
17
Start:
17,681,473 bp from pter
End:
17,811,453 bp from pter
Size:
129,981 bases
Orientation:
Plus strand

Genomic View for RAI1 Gene

Genes around RAI1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
RAI1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for RAI1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for RAI1 Gene

Proteins for RAI1 Gene

  • Protein details for RAI1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q7Z5J4-RAI1_HUMAN
    Recommended name:
    Retinoic acid-induced protein 1
    Protein Accession:
    Q7Z5J4
    Secondary Accessions:
    • Q8N3B4
    • Q8ND08
    • Q8WU64
    • Q96JK5
    • Q9H1C1
    • Q9H1C2
    • Q9UF69

    Protein attributes for RAI1 Gene

    Size:
    1906 amino acids
    Molecular mass:
    203352 Da
    Quaternary structure:
    No Data Available
    SequenceCaution:
    • Sequence=BAB47449.1; Type=Erroneous initiation; Note=Translation N-terminally shortened.; Evidence={ECO:0000305};

    Alternative splice isoforms for RAI1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for RAI1 Gene

Post-translational modifications for RAI1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for RAI1 Gene

Domains & Families for RAI1 Gene

Protein Domains for RAI1 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for RAI1 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q7Z5J4

UniProtKB/Swiss-Prot:

RAI1_HUMAN :
  • Contains 1 C2HC pre-PHD-type zinc finger.
Similarity:
  • Contains 1 C2HC pre-PHD-type zinc finger.
  • Contains 1 PHD-type zinc finger.
genes like me logo Genes that share domains with RAI1: view

No data available for Gene Families for RAI1 Gene

Function for RAI1 Gene

Molecular function for RAI1 Gene

GENATLAS Biochemistry:
retinoic acid induced gene 1,homolog of murine gene,expressed in brain,involved in the control of early neural differentiation
UniProtKB/Swiss-Prot 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.

Gene Ontology (GO) - Molecular Function for RAI1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003700 transcription factor activity, sequence-specific DNA binding IBA --
GO:0005515 protein binding IPI 16189514
GO:0008270 zinc ion binding IEA --
GO:0035326 enhancer binding IDA 22578325
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with RAI1: view
genes like me logo Genes that share phenotypes with RAI1: view

Human Phenotype Ontology for RAI1 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for RAI1 Gene

MGI Knock Outs for RAI1:

Animal Model Products

Inhibitory RNA Products

Clone Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for RAI1 Gene

Localization for RAI1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for RAI1 Gene

Cytoplasm. Nucleus. Note=In neurons, localized to neurites. {ECO:0000250}.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for RAI1 Gene COMPARTMENTS Subcellular localization image for RAI1 gene
Compartment Confidence
mitochondrion 5
nucleus 5
cytosol 2

Gene Ontology (GO) - Cellular Components for RAI1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IDA --
GO:0005654 nucleoplasm IDA --
GO:0005737 cytoplasm IEA --
GO:0005739 mitochondrion IDA --
genes like me logo Genes that share ontologies with RAI1: view

Pathways & Interactions for RAI1 Gene

genes like me logo Genes that share pathways with RAI1: view

Pathways by source for RAI1 Gene

1 Reactome pathway for RAI1 Gene

Gene Ontology (GO) - Biological Process for RAI1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001501 skeletal system development IEA --
GO:0006357 regulation of transcription from RNA polymerase II promoter IEA --
GO:0032922 circadian regulation of gene expression IMP 22578325
GO:0040015 negative regulation of multicellular organism growth IEA --
GO:0045893 positive regulation of transcription, DNA-templated IDA 22578325
genes like me logo Genes that share ontologies with RAI1: view

No data available for SIGNOR curated interactions for RAI1 Gene

Drugs & Compounds for RAI1 Gene

(1) Drugs for RAI1 Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials

(1) Additional Compounds for RAI1 Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with RAI1: view

Transcripts for RAI1 Gene

Unigene Clusters for RAI1 Gene

Retinoic acid induced 1:
Representative Sequences:

Inhibitory RNA Products

Clone Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for RAI1 Gene

No ASD Table

Relevant External Links for RAI1 Gene

GeneLoc Exon Structure for
RAI1
ECgene alternative splicing isoforms for
RAI1

Expression for RAI1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for RAI1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for RAI1 Gene

This gene is overexpressed in Cerebrospinal fluid (60.7).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for RAI1 Gene



NURSA nuclear receptor signaling pathways regulating expression of RAI1 Gene:

RAI1

SOURCE GeneReport for Unigene cluster for RAI1 Gene:

Hs.655395

mRNA Expression by UniProt/SwissProt for RAI1 Gene:

Q7Z5J4-RAI1_HUMAN
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.
genes like me logo Genes that share expression patterns with RAI1: view

Primer Products

No data available for mRNA differential expression in normal tissues and Protein tissue co-expression partners for RAI1 Gene

Orthologs for RAI1 Gene

This gene was present in the common ancestor of animals.

Orthologs for RAI1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia RAI1 34 35
  • 99.3 (n)
dog
(Canis familiaris)
Mammalia RAI1 34 35
  • 88.15 (n)
cow
(Bos Taurus)
Mammalia RAI1 34 35
  • 86.96 (n)
mouse
(Mus musculus)
Mammalia Rai1 34 16 35
  • 82.74 (n)
rat
(Rattus norvegicus)
Mammalia Rai1 34
  • 82.29 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia RAI1 35
  • 66 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia RAI1 35
  • 64 (a)
OneToOne
chicken
(Gallus gallus)
Aves RAI1 34 35
  • 66.93 (n)
lizard
(Anolis carolinensis)
Reptilia RAI1 35
  • 45 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia rai1 34
  • 55.8 (n)
zebrafish
(Danio rerio)
Actinopterygii RAI1 35
  • 20 (a)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta CG5098 35
  • 13 (a)
OneToMany
Species where no ortholog for RAI1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for RAI1 Gene

ENSEMBL:
Gene Tree for RAI1 (if available)
TreeFam:
Gene Tree for RAI1 (if available)

Paralogs for RAI1 Gene

Paralogs for RAI1 Gene

genes like me logo Genes that share paralogs with RAI1: view

Variants for RAI1 Gene

Polymorphic Variants from UniProtKB/Swiss-Prot for RAI1 Gene

RAI1_HUMAN-Q7Z5J4
The poly-Gln tract is polymorphic and the number of Gln varies from 12 to 14 (PubMed:11404004). The size of the poly-Gln region may influence the age at onset of spinocerebellar ataxia type 2 (SCA2) (PubMed:10915763).

Sequence variations from dbSNP and Humsavar for RAI1 Gene

SNP ID Clin Chr 17 pos Sequence Context AA Info Type
rs104894633 Pathogenic 17,798,371(+) GTGCA(A/G)CAAGG reference, missense
rs104894634 Pathogenic 17,797,633(+) ACGAC(A/C)GCAGC reference, missense
rs376044849 Pathogenic 17,796,229(+) CAAGT(C/T)GGGCA reference, missense
rs398124419 Pathogenic 17,793,360(+) CAGGG(-/G)TGGCC reference, frameshift-variant
rs527236033 Pathogenic 17,795,221(+) CAGGT(A/G)GGGAT reference, stop-gained

Structural Variations from Database of Genomic Variants (DGV) for RAI1 Gene

Variant ID Type Subtype PubMed ID
dgv894e212 CNV loss 25503493
esv2659754 CNV deletion 23128226
esv3640136 CNV loss 21293372
nsv1072723 CNV deletion 25765185
nsv1118747 CNV deletion 24896259
nsv1131132 CNV deletion 24896259
nsv1146061 CNV insertion 26484159
nsv155 OTHER inversion 15895083
nsv499114 OTHER inversion 21111241
nsv522668 CNV loss 19592680
nsv526904 CNV loss 19592680
nsv817753 CNV loss 17921354
nsv820244 CNV loss 19587683
nsv827910 CNV gain 20364138
nsv827911 CNV gain 20364138
nsv833384 CNV loss 17160897
nsv833385 CNV loss 17160897
nsv9501 CNV gain 18304495
nsv953838 CNV deletion 24416366

Variation tolerance for RAI1 Gene

Residual Variation Intolerance Score: 1.58% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.23; 52.51% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for RAI1 Gene

Human Gene Mutation Database (HGMD)
RAI1
SNPedia medical, phenotypic, and genealogical associations of SNPs for
RAI1

Disorders for RAI1 Gene

MalaCards: The human disease database

(6) MalaCards diseases for RAI1 Gene - From: OMIM, ClinVar, GeneTests, Orphanet, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
smith-magenis syndrome
  • 17p11.2 microdeletion syndrome
otof-related deafness
  • deafness, autosomal recessive 9
deafness, autosomal recessive 9
  • auditory neuropathy, autosomal recessive, 1
potocki-lupski syndrome
  • duplication 17p11.2 syndrome
moyamoya disease
  • moyamoya disease 3
- elite association - COSMIC cancer census association via MalaCards
Search RAI1 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

RAI1_HUMAN
  • 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. {ECO:0000269 PubMed:11404004, ECO:0000269 PubMed:12652298}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for RAI1

Genetic Association Database (GAD)
RAI1
Human Genome Epidemiology (HuGE) Navigator
RAI1
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
RAI1
genes like me logo Genes that share disorders with RAI1: view

No data available for Genatlas for RAI1 Gene

Publications for RAI1 Gene

  1. Smith-Magenis syndrome results in disruption of CLOCK gene transcription and reveals an integral role for RAI1 in the maintenance of circadian rhythmicity. (PMID: 22578325) Williams S.R. … Elsea S.H. (Am. J. Hum. Genet. 2012) 3 4 64
  2. Web-based genome-wide association study identifies two novel loci and a substantial genetic component for Parkinson's disease. (PMID: 21738487) Do C.B. … Eriksson N. (PLoS Genet. 2011) 3 46 64
  3. Maternal genes and facial clefts in offspring: a comprehensive search for genetic associations in two population-based cleft studies from Scandinavia. (PMID: 20634891) Jugessur A. … Murray J.C. (PLoS ONE 2010) 3 46 64
  4. Polymorphisms in RAI and in genes of nucleotide and base excision repair are not associated with risk of testicular cancer. (PMID: 15885892) Laska M.J. … Vogel U. (Cancer Lett. 2005) 3 46 64
  5. RAI1 variations in Smith-Magenis syndrome patients without 17p11.2 deletions. (PMID: 15788730) Girirajan S. … Elsea S.H. (J. Med. Genet. 2005) 3 22 64

Products for RAI1 Gene

Sources for RAI1 Gene

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