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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
  • 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 17P11.2 Microduplication Syndrome. 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 Score Enhancer Sources TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Other Gene Targets for Enhancer

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

ENSRs around RAI1 on UCSC Golden Path with GeneCards custom track

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

Proteomics data for RAI1 Gene at MOPED

Post-translational modifications for RAI1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for RAI1 Gene

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 PHD-type zinc finger.
Similarity:
  • 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.
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

No data available for Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , 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

No data available for Gene Ontology (GO) - Cellular Components for RAI1 Gene

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:0032922 circadian regulation of gene expression IEA,IMP 22578325
GO:0045944 positive regulation of transcription from RNA polymerase II promoter IBA --
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:

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 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, MOPED, and MaxQB for RAI1 Gene



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
cow
(Bos Taurus)
Mammalia RAI1 35
  • 86.96 (n)
  • 87.62 (a)
RAI1 36
  • 87 (a)
OneToOne
dog
(Canis familiaris)
Mammalia RAI1 35
  • 88.15 (n)
  • 90.82 (a)
RAI1 36
  • 90 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Rai1 35
  • 82.74 (n)
  • 83.65 (a)
Rai1 16
Rai1 36
  • 83 (a)
OneToOne
chimpanzee
(Pan troglodytes)
Mammalia RAI1 35
  • 99.3 (n)
  • 99.53 (a)
RAI1 36
  • 99 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Rai1 35
  • 82.29 (n)
  • 84.16 (a)
oppossum
(Monodelphis domestica)
Mammalia RAI1 36
  • 64 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia RAI1 36
  • 66 (a)
OneToOne
chicken
(Gallus gallus)
Aves RAI1 35
  • 66.93 (n)
  • 60.92 (a)
RAI1 36
  • 54 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia RAI1 36
  • 45 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia rai1 35
  • 55.8 (n)
  • 49.08 (a)
zebrafish
(Danio rerio)
Actinopterygii RAI1 36
  • 20 (a)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta CG5098 36
  • 13 (a)
OneToMany
Species with no ortholog for RAI1:
  • 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
rs11649804 - 17,793,441(+) AGGTG(A/C)CCTTT reference, missense
rs3803763 - 17,793,217(+) GCAAG(C/G)CCTGC reference, missense
rs1759075 - 17,795,764(-) AGCGC(G/T)GGACC reference, missense
rs941444 -- 17,790,577(+) TGTCT(C/G)TCTTT intron-variant
rs941447 -- 17,754,760(-) GCCTG(C/G)TGGCA intron-variant

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

Variant ID Type Subtype PubMed ID
nsv155 OTHER Inversion 15895083
nsv499114 OTHER Inversion 21111241
nsv907748 CNV Loss 21882294
nsv833384 CNV Loss 17160897
dgv3072n71 CNV Loss 21882294
nsv907755 CNV Loss 21882294
nsv827910 CNV Gain 20364138
nsv833385 CNV Loss 17160897
nsv827911 CNV Gain 20364138
dgv3073n71 CNV Loss 21882294
nsv522668 CNV Loss 19592680
dgv3074n71 CNV Loss 21882294
nsv9501 CNV Gain 18304495
dgv3075n71 CNV Loss 21882294
dgv3076n71 CNV Loss 21882294
nsv907766 CNV Loss 21882294
nsv526904 CNV Loss 19592680
nsv817753 CNV Loss 17921354
nsv907767 CNV Loss 21882294
nsv907768 CNV Loss 21882294
esv2659754 CNV Deletion 23128226
nsv820244 CNV Loss 19587683

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

Disorders for RAI1 Gene

MalaCards: The human disease database

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

Disorder Aliases PubMed IDs
smith-magenis syndrome
  • smith magenis syndrome
17p11.2 microduplication syndrome
  • potocki-lupski syndrome
moyamoya disease
  • moyamoya disease 3
spinocerebellar ataxia 2
  • amyotrophic lateral sclerosis 13
- 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 67
  2. RAI1 variations in Smith-Magenis syndrome patients without 17p11.2 deletions. (PMID: 15788730) Girirajan S. … Elsea S.H. (J. Med. Genet. 2005) 3 23
  3. Mutations of RAI1, a PHD-containing protein, in nondeletion patients with Smith-Magenis syndrome. (PMID: 15565467) Bi W. … Lupski J.R. (Hum. Genet. 2004) 3 23
  4. Transcription mapping in a medulloblastoma breakpoint interval and Smith-Magenis syndrome candidate region: identification of 53 transcriptional units and new candidate genes. (PMID: 10036180) Seranski P. … Poustka A. (Genomics 1999) 2 3
  5. Expression in the human brain of retinoic acid induced 1, a protein associated with neurobehavioural disorders. (PMID: 24519454) Fragoso Y.D. … McCaffery P. (Brain Struct Funct 2015) 3

Products for RAI1 Gene

Sources for RAI1 Gene

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