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Aliases for RAI1 Gene

Aliases for RAI1 Gene

  • Retinoic Acid Induced 1 2 3
  • Smith-Magenis Syndrome Chromosome Region 2 3
  • SMCR 3 6
  • SMS 3 6
  • Retinoic Acid-Induced Protein 1 3
  • KIAA1820 4

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 potocki-lupski syndrome. Among its related pathways are Metabolism and Arginine and proline metabolism. 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

Genomic Location for RAI1 Gene

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

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
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 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 :
  • Q7Z5J4
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.

Gene Ontology (GO) - Molecular Function for RAI1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 16189514
GO:0008270 zinc ion binding IEA --
GO:0035326 enhancer binding IDA 22578325
genes like me logo Genes that share ontologies with RAI1: view
genes like me logo Genes that share phenotypes with RAI1: view

Animal Models for RAI1 Gene

MGI Knock Outs for RAI1:

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for RAI1

In Situ Assay Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targeting 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
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 --
GO:0005739 mitochondrion IDA --
genes like me logo Genes that share ontologies with RAI1: view

Pathways for RAI1 Gene

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

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

Compounds for RAI1 Gene

(2) Novoseek inferred chemical compound relationships for RAI1 Gene

Compound -log(P) Hits PubMed IDs
retinoic acid 67.8 10
zinc 15.4 2
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:

CRISPR Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for RAI1

Primer Products

  • OriGene qSTAR qPCR primer pairs in human,mouse,rat for RAI1

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 for RAI1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Integrated Proteomics: protein expression 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 expressions with RAI1: view

In Situ Assay Products

No data available for mRNA differential expression in normal tissues 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 35
  • 99.3 (n)
  • 99.53 (a)
RAI1 36
  • 99 (a)
OneToOne
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
oppossum
(Monodelphis domestica)
Mammalia RAI1 36
  • 64 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia RAI1 36
  • 66 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Rai1 35
  • 82.29 (n)
  • 84.16 (a)
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

Q7Z5J4-RAI1_HUMAN
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)

Sequence variations from dbSNP and Humsavar for RAI1 Gene

SNP ID Clin Chr 17 pos Sequence Context AA Info Type MAF
rs720856 -- 17,742,637(+) AGAGA(C/G)AGAAG intron-variant
rs752579 -- 17,757,033(-) ACCCC(A/G)CGGAG intron-variant
rs941444 -- 17,790,577(+) TGTCT(C/G)TCTTT intron-variant
rs941447 -- 17,754,760(-) GCCTG(C/G)TGGCA intron-variant
rs941448 -- 17,751,228(-) GAAGC(C/G)TGGGC 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

Relevant External Links for RAI1 Gene

HapMap Linkage Disequilibrium report
RAI1
Human Gene Mutation Database (HGMD)
RAI1

PCR Panel Products

  • Copy Number PCR Panels: for RAI1

Disorders for RAI1 Gene

MalaCards: The human disease database

MalaCards: The human disease database. (2) Diseases for RAI1 Gene including...

Search for RAI1 Gene in MalaCards »

(1) OMIM Diseases for RAI1 Gene (607642)

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.

(2) University of Copenhagen DISEASES for RAI1 Gene

(4) Novoseek inferred disease relationships for RAI1 Gene

Disease -log(P) Hits PubMed IDs
smith-magenis syndrome 97 9
anomaly congenital multiple 79.3 1
mental retardation 73.1 3
short stature 44.8 1

Relevant External Links for RAI1

GeneTests
RAI1
GeneReviews
RAI1
Genetic Association Database (GAD)
RAI1
Human Genome Epidemiology (HuGE) Navigator
RAI1
genes like me logo Genes that share disorders with RAI1: view

Publications for RAI1 Gene

  1. RAI1 variations in Smith-Magenis syndrome patients without 17p11.2 deletions. (PMID: 15788730) Girirajan S. … Elsea S.H. (J. Med. Genet. 2005) 3 23
  2. Mutations in RAI1 associated with Smith-Magenis syndrome. (PMID: 12652298) Slager R.E. … Elsea S.H. (Nat. Genet. 2003) 3 4
  3. Molecular cloning and characterization of human RAI1, a gene associated with schizophrenia. (PMID: 12837267) Toulouse A. … Rouleau G.A. (Genomics 2003) 3 4
  4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard D.S. … Malek J. (Genome Res. 2004) 3 4
  5. 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 48

Products for RAI1 Gene

Sources for RAI1 Gene

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