Human Gene PER1 (uc010vur.1) 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 chr17:8,047,374-8,059,678 Size: 12,305 Total Exon Count: 18 Strand: -
Coding Region
   Position: hg19 chr17:8,047,902-8,059,672 Size: 11,771 Coding Exon Count: 18 

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

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr17:8,047,374-8,059,678)mRNA (may differ from genome)Protein (859 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblExonPrimerGeneCardsGeneNetwork
H-INVHGNCLynxMGIPubMedStanford SOURCE
TreefamUniProtKBWikipedia

-  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
  Press "+" in the title bar above to open this section.

-  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
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
3' UTR -236.27528-0.447 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.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR001610 - PAC
IPR000014 - PAS
IPR013655 - PAS_fold_3

Pfam Domains:
PF08447 - PAS fold
PF14598 - PAS domain

SCOP Domains:
55785 - PYP-like sensor domain (PAS domain)

ModBase Predicted Comparative 3D Structure on B4DI49
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  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 orthologGenome BrowserNo orthologNo ortholog
Gene DetailsGene Details Gene Details  
Gene SorterGene Sorter Gene Sorter  
 RGD FlyBase  
 Protein Sequence Protein Sequence  
 Alignment Alignment  

-  Descriptions from all associated GenBank mRNAs
  AB088477 - Homo sapiens KIAA0482 mRNA for KIAA0482 protein.
AF022991 - Homo sapiens Rigui (RIGUI) mRNA, complete cds.
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.
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.
BC028207 - Homo sapiens period homolog 1 (Drosophila), mRNA (cDNA clone IMAGE:5215552).
AK295410 - Homo sapiens cDNA FLJ59327 complete cds, highly similar to Period circadian protein 1.
KJ901631 - Synthetic construct Homo sapiens clone ccsbBroadEn_11025 PER1 gene, encodes complete protein.
CU688426 - Synthetic construct Homo sapiens gateway clone IMAGE:100019891 5' read PER1 mRNA.
BC072458 - Homo sapiens period homolog 1 (Drosophila), mRNA (cDNA clone IMAGE:6200422), complete cds.
KJ901632 - Synthetic construct Homo sapiens clone ccsbBroadEn_11026 PER1 gene, encodes complete protein.
CU687240 - Synthetic construct Homo sapiens gateway clone IMAGE:100022889 5' read PER1 mRNA.

-  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: AK295410, B4DI49, B4DI49_HUMAN
UCSC ID: uc010vur.1
RefSeq Accession: NM_002616
Protein: B4DI49

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: AK295410.1
exon count: 18CDS single in 3' UTR: no RNA size: 2981
ORF size: 2580CDS single in intron: no Alignment % ID: 99.93
txCdsPredict score: 5327.00frame shift in genome: no % Coverage: 100.00
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: 695# 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.