Human Gene PER1 (uc010cns.3) Description and Page Index
  Description: Homo sapiens period circadian clock 1 (PER1), mRNA.
RefSeq Summary (NM_002616): This gene is a member of the Period family of genes and is expressed in a circadian pattern in the suprachiasmatic nucleus, the primary circadian pacemaker in the mammalian brain. Genes in this family encode components of the circadian rhythms of locomotor activity, metabolism, and behavior. This gene is upregulated by CLOCK/ARNTL heterodimers but then represses this upregulation in a feedback loop using PER/CRY heterodimers to interact with CLOCK/ARNTL. Polymorphisms in this gene may increase the risk of getting certain cancers. Alternative splicing has been observed in this gene; however, these variants have not been fully described. [provided by RefSeq, Jan 2014]. Publication Note: This RefSeq record includes a subset of the publications that are available for this gene. Please see the Gene record to access additional publications. ##Evidence-Data-START## Transcript exon combination :: AF022991.1, AK291061.1 [ECO:0000332] RNAseq introns :: mixed/partial sample support SAMEA1965299, SAMEA1966682 [ECO:0000350] ##Evidence-Data-END## ##RefSeq-Attributes-START## MANE Ensembl match :: ENST00000317276.9/ ENSP00000314420.4 RefSeq Select criteria :: based on conservation, expression, longest protein ##RefSeq-Attributes-END##
Transcript (Including UTRs)
   Position: hg19 chr17:8,043,788-8,045,509 Size: 1,722 Total Exon Count: 2 Strand: -
Coding Region
   Position: hg19 chr17:8,044,386-8,045,344 Size: 959 Coding Exon Count: 2 

Page IndexSequence and LinksGenetic AssociationsMalaCardsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureOther SpeciesmRNA DescriptionsPathways
Other NamesModel InformationMethods
Data last updated: 2013-06-15

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr17:8,043,788-8,045,509)mRNA (may differ from genome)Protein (164 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblExonPrimerGeneCardsGeneNetwork
H-INVHGNCLynxMGIPubMedStanford SOURCE
TreefamWikipedia

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): PER1
CDC HuGE Published Literature: PER1
Positive Disease Associations: autism , delayed sleep phase syndrome
Related Studies:
  1. autism
    Nicholas, B. et al. 2007, Association of Per1 and Npas2 with autistic disorder, Mol Psychiatry 2007. [PubMed 17264841]
  2. delayed sleep phase syndrome
    Ebisawa, T. et al. 2001, Association of structural polymorphisms in the human period3 gene with delayed sleep phase syndrome., EMBO reports. 2001 Apr;2(4):342-6. [PubMed 11306557]
    Our results suggest that structural polymorphisms in the hPer3 gene may be implicated in the pathogenesis of DSPS.

-  MalaCards Disease Associations
  MalaCards Gene Search: PER1
Diseases sorted by gene-association score: periodic limb movement disorder (9), advanced sleep phase syndrome (8), autistic disorder (1)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
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-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 118.39 RPKM in Skin - Not Sun Exposed (Suprapubic)
Total median expression: 2452.30 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -62.80165-0.381 Picture PostScript Text
3' UTR -237.80598-0.398 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
 Protein Sequence    
 Alignment    

-  Descriptions from all associated GenBank mRNAs
  AB088477 - Homo sapiens KIAA0482 mRNA for KIAA0482 protein.
AF022991 - Homo sapiens Rigui (RIGUI) mRNA, complete cds.
JD109162 - Sequence 90186 from Patent EP1572962.
JD271965 - Sequence 252989 from Patent EP1572962.
JD423797 - Sequence 404821 from Patent EP1572962.
JD055334 - Sequence 36358 from Patent EP1572962.
JD559056 - Sequence 540080 from Patent EP1572962.
JD092382 - Sequence 73406 from Patent EP1572962.
JD518232 - Sequence 499256 from Patent EP1572962.
AK291061 - Homo sapiens cDNA FLJ77255 complete cds, highly similar to Homo sapiens period homolog 1 (Drosophila) (PER1), mRNA.
BC137346 - Homo sapiens period homolog 1 (Drosophila), mRNA (cDNA clone MGC:168967 IMAGE:9021344), complete cds.
BC144593 - Homo sapiens cDNA clone IMAGE:9053123.
JD100158 - Sequence 81182 from Patent EP1572962.
JD308072 - Sequence 289096 from Patent EP1572962.
JD157271 - Sequence 138295 from Patent EP1572962.
JD414210 - Sequence 395234 from Patent EP1572962.
JD320301 - Sequence 301325 from Patent EP1572962.
AB002107 - Homo sapiens hPer mRNA, complete cds.
AB383894 - Synthetic construct DNA, clone: pF1KSDA0482, Homo sapiens PER1 gene for period circadian protein homolog 1, complete cds, without stop codon, in Flexi system.
BC150151 - Homo sapiens cDNA clone IMAGE:40134409.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa04710 - Circadian rhythm - mammal

BioCarta from NCI Cancer Genome Anatomy Project
h_circadianPathway - Circadian Rhythms

-  Other Names for This Gene
  Alternate Gene Symbols: BC150151
UCSC ID: uc010cns.3
RefSeq Accession: NM_002616

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: BC150151.1
exon count: 2CDS single in 3' UTR: no RNA size: 530
ORF size: 495CDS single in intron: no Alignment % ID: 99.80
txCdsPredict score: 1161.00frame shift in genome: no % Coverage: 96.04
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 236# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.