RAI1 Gene (Protein Coding)

Retinoic Acid Induced 1

GC17P017682
GIFtS:
41
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 ass... See more...

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 4
  • 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 Alacrima, Achalasia, And Mental Retardation Syndrome. Among its related pathways are BMAL1-CLOCK,NPAS2 activates circadian gene expression and Circadian rythm related genes. Gene Ontology (GO) annotations related to this gene include enhancer binding. An important paralog of this gene is TCF20.

UniProtKB/Swiss-Prot Summary 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.

Additional gene information for RAI1 Gene

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for RAI1 Gene

Genomics for RAI1 Gene

GeneHancer (GH) Regulatory Elements for RAI1 Gene

Promoters and enhancers for RAI1 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around RAI1 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the RAI1 gene promoter:
  • MAZR
  • NF-kappaB
  • NF-kappaB1
  • Pax-5
  • SREBP-1a
  • SREBP-1b
  • SREBP-1c

Genomic Locations for RAI1 Gene

Genomic Locations for RAI1 Gene
chr17:17,681,458-17,811,453
(GRCh38/hg38)
Size:
129,996 bases
Orientation:
Plus strand
chr17:17,584,787-17,714,767
(GRCh37/hg19)
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 Structure • Gene Density

RefSeq DNA sequence for RAI1 Gene

Proteins for RAI1 Gene

Products:

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  • 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

Protein Expression for RAI1 Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Post-translational modifications for RAI1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for RAI1 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for RAI1 Gene

Domains & Families for RAI1 Gene

Gene Families for RAI1 Gene

Human Protein Atlas (HPA):
  • Disease related genes
  • Plasma proteins
  • Predicted intracellular proteins

Protein Domains for RAI1 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for RAI1 Gene

GenScript: Design optimal peptide antigens:
  • Retinoic acid-induced protein 1 (RAI1_HUMAN)
genes like me logo Genes that share domains with RAI1: view

No data available for Graphical View of Domain Structure and UniProtKB/Swiss-Prot for RAI1 Gene

Function for RAI1 Gene

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Molecular function for RAI1 Gene

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

Phenotypes From GWAS Catalog for RAI1 Gene

Gene Ontology (GO) - Molecular Function for RAI1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003700 DNA-binding transcription factor activity IBA 21873635
GO:0005515 protein binding IPI 16189514
GO:0035326 enhancer binding IDA 22578325
GO:0044212 transcription regulatory region DNA binding IBA 21873635
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

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for RAI1

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
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for RAI1 gene
Compartment Confidence
nucleus 5
mitochondrion 4
cytosol 2
extracellular 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoplasm (4)
See all subcellular structures

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 BioSystems pathway 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 by RNA polymerase II IEA --
GO:0032922 circadian regulation of gene expression IEA,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

Products:

  1. Drug

(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

Products:

  1. CRISPR
  2. miRNA
  3. Inhibitory RNA
  4. Clone

mRNA/cDNA for RAI1 Gene

(1) REFSEQ mRNAs :
(8) Additional mRNA sequences :
(109) Selected AceView cDNA sequences:
(7) Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for RAI1

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

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  1. Primer
  2. Gene Expression Assay

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

mRNA expression in normal human tissues for RAI1 Gene
mRNA expression by GTEx for RAI1 GenemRNA expression by BioGPS 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, 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.

Evidence on tissue expression from TISSUES for RAI1 Gene

  • Nervous system(4.3)
  • Muscle(4.1)

Phenotype-based relationships between genes and organs from Gene ORGANizer for RAI1 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • cardiovascular
  • digestive
  • immune
  • integumentary
  • nervous
  • respiratory
  • skeletal muscle
  • skeleton
  • urinary
Regions:
Head and neck:
  • brain
  • cheek
  • chin
  • cranial nerve
  • ear
  • eye
  • eyelid
  • face
  • forehead
  • head
  • jaw
  • larynx
  • lip
  • mandible
  • maxilla
  • middle ear
  • mouth
  • neck
  • nose
  • outer ear
  • pharynx
  • skull
  • tongue
  • tooth
  • vocal cord
Thorax:
  • bronchus
  • esophagus
  • heart
  • lung
  • rib
  • rib cage
  • trachea
Abdomen:
  • duodenum
  • intestine
  • kidney
  • large intestine
  • liver
  • pancreas
  • small intestine
  • stomach
Pelvis:
  • pelvis
  • rectum
Limb:
  • digit
  • finger
  • foot
  • hand
  • lower limb
  • toe
  • upper limb
General:
  • blood
  • blood vessel
  • hair
  • peripheral nerve
  • peripheral nervous system
  • skin
  • spinal column
  • spinal cord
  • vertebrae
genes like me logo Genes that share expression patterns with RAI1: view

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 33 32
  • 99.3 (n)
 OneToOne
dog
(Canis familiaris)
 Mammalia RAI1 33 32
  • 88.15 (n)
 OneToOne
cow
(Bos Taurus)
 Mammalia RAI1 33 32
  • 86.96 (n)
 OneToOne
mouse
(Mus musculus)
 Mammalia Rai1 17 33 32
  • 82.74 (n)
rat
(Rattus norvegicus)
 Mammalia Rai1 32
  • 82.29 (n)
platypus
(Ornithorhynchus anatinus)
 Mammalia RAI1 33
  • 66 (a)
 OneToOne
oppossum
(Monodelphis domestica)
 Mammalia RAI1 33
  • 64 (a)
 OneToOne
chicken
(Gallus gallus)
 Aves RAI1 33 32
  • 66.93 (n)
 OneToOne
lizard
(Anolis carolinensis)
 Reptilia RAI1 33
  • 45 (a)
 OneToOne
tropical clawed frog
(Silurana tropicalis)
 Amphibia rai1 32
  • 55.8 (n)
zebrafish
(Danio rerio)
 Actinopterygii RAI1 33
  • 20 (a)
 OneToOne
fruit fly
(Drosophila melanogaster)
 Insecta CG5098 33
  • 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)
Aminode:
Evolutionary constrained regions (ECRs) for RAI1: view image

Paralogs for RAI1 Gene

Paralogs for RAI1 Gene

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

Variants for RAI1 Gene

Products:

  1. SNP Genotyping and Copy Number Assay

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 Variation AA Info Type
rs1034894206 likely-benign, History of neurodevelopmental disorder 17,794,406(+) C/T coding_sequence_variant, synonymous_variant
rs1041313981 uncertain-significance, History of neurodevelopmental disorder 17,797,960(+) A/C/G coding_sequence_variant, missense_variant
rs104894633 pathogenic, Smith-Magenis syndrome 17,798,371(+) G/A coding_sequence_variant, missense_variant
rs104894634 pathogenic, Smith-Magenis syndrome 17,797,633(+) A/C/G coding_sequence_variant, missense_variant
rs1057519065 uncertain-significance, Smith-Magenis syndrome 17,794,696(+) G/A coding_sequence_variant, missense_variant

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)

Additional Variant Information for RAI1 Gene

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

SNP Genotyping and Copy Number Assay Products

Disorders for RAI1 Gene

MalaCards: The human disease database

(10) MalaCards diseases for RAI1 Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, DISEASES, Novoseek, and GeneCards

- 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, ECO:0000269 PubMed:24863970}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for RAI1

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
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 SR … Elsea SH (American journal of human genetics 2012) 3 4 56
  2. Web-based genome-wide association study identifies two novel loci and a substantial genetic component for Parkinson's disease. (PMID: 21738487) Do CB … Eriksson N (PLoS genetics 2011) 3 43 56
  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 JC (PloS one 2010) 3 43 56
  4. Polymorphisms in RAI and in genes of nucleotide and base excision repair are not associated with risk of testicular cancer. (PMID: 15885892) Laska MJ … Vogel U (Cancer letters 2005) 3 43 56
  5. RAI1 variations in Smith-Magenis syndrome patients without 17p11.2 deletions. (PMID: 15788730) Girirajan S … Elsea SH (Journal of medical genetics 2005) 3 23 56

ExternalLinks

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