Cry1 cryptochrome circadian regulator 1 [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Cry1provided by MGI
Official Full Name: cryptochrome circadian regulator 1provided by MGI
Primary source: MGI:MGI:1270841
See related: Ensembl:ENSMUSG00000020038 AllianceGenome:MGI:1270841
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as: Phll1
Summary: This gene encodes a flavin adenine dinucleotide-binding protein that is a key component of the circadian core oscillator complex, which regulates the circadian clock. 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 have been associated with altered sleep patterns. The encoded protein is widely conserved across plants and animals. Loss of this gene results in a shortened circadian cycle in complete darkness. [provided by RefSeq, Feb 2014]
Expression: Ubiquitous expression in thymus adult (RPKM 16.0), ovary adult (RPKM 8.5) and 27 other tissues See more
Orthologs: human all
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Genomic context

Location:: 10 C1; 10 41.63 cM

Exon count:: 15

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	10	NC_000076.7 (84967564..85020918, complement)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	10	NC_000076.6 (85131700..85185054, complement)

Chromosome 10 - NC_000076.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Mouse ENCODE transcriptome data
Description: RNA profiling data sets generated by the Mouse ENCODE project.
BioProject: PRJNA66167
Publication: PMID 25409824
Analysis date: n/a

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

CRY1/2 regulate rhythmic CYP2A5 in mouse liver through repression of E4BP4.
Title: CRY1/2 regulate rhythmic CYP2A5 in mouse liver through repression of E4BP4.
The circadian clock CRY1 regulates pluripotent stem cell identity and somatic cell reprogramming.
Title: The circadian clock CRY1 regulates pluripotent stem cell identity and somatic cell reprogramming.
The duper mutation reveals previously unsuspected functions of Cryptochrome 1 in circadian entrainment and heart disease.
Title: The duper mutation reveals previously unsuspected functions of Cryptochrome 1 in circadian entrainment and heart disease.
Hepatic GSK3beta-Dependent CRY1 Degradation Contributes to Diabetic Hyperglycemia.
Title: Hepatic GSK3β-Dependent CRY1 Degradation Contributes to Diabetic Hyperglycemia.
Restoration of H3k27me3 Modification Epigenetically Silences Cry1 Expression and Sensitizes Leptin Signaling to Reduce Obesity-Related Properties.
Title: Restoration of H3k27me3 Modification Epigenetically Silences Cry1 Expression and Sensitizes Leptin Signaling to Reduce Obesity-Related Properties.
Structural differences in the FAD-binding pockets and lid loops of mammalian CRY1 and CRY2 for isoform-selective regulation.
Title: Structural differences in the FAD-binding pockets and lid loops of mammalian CRY1 and CRY2 for isoform-selective regulation.
Restoring the Molecular Clockwork within the Suprachiasmatic Hypothalamus of an Otherwise Clockless Mouse Enables Circadian Phasing and Stabilization of Sleep-Wake Cycles and Reverses Memory Deficits.
Title: Restoring the Molecular Clockwork within the Suprachiasmatic Hypothalamus of an Otherwise Clockless Mouse Enables Circadian Phasing and Stabilization of Sleep-Wake Cycles and Reverses Memory Deficits.
CRYPTOCHROMES confer robustness, not rhythmicity, to circadian timekeeping.
Title: CRYPTOCHROMES confer robustness, not rhythmicity, to circadian timekeeping.
An in-depth neurobehavioral characterization shows anxiety-like traits, impaired habituation behavior, and restlessness in male Cryptochrome-deficient mice.
Title: An in-depth neurobehavioral characterization shows anxiety-like traits, impaired habituation behavior, and restlessness in male Cryptochrome-deficient mice.
Suppression of circadian clock protein cryptochrome 2 promotes osteoarthritis.
Title: Suppression of circadian clock protein cryptochrome 2 promotes osteoarthritis.

Submit: New GeneRIF Correction See all GeneRIFs (102)

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Targeted (2) 1 citation
Endonuclease-mediated (4) 1 citation

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

AB000777 (e-PCR)
- UniSTS:160015

RH136559 (e-PCR)
- UniSTS:210541

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables DNA-binding transcription factor binding	IPI Inferred from Physical Interaction more info	PubMed
enables E-box binding	IDA Inferred from Direct Assay more info	PubMed
enables FAD binding	IBA Inferred from Biological aspect of Ancestor more info
enables double-stranded DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables double-stranded DNA binding	ISO Inferred from Sequence Orthology more info
enables histone deacetylase binding	IPI Inferred from Physical Interaction more info	PubMed
enables kinase binding	IPI Inferred from Physical Interaction more info	PubMed
enables nuclear receptor binding	IPI Inferred from Physical Interaction more info	PubMed
enables nuclear receptor binding	ISO Inferred from Sequence Orthology more info
enables nucleotide binding	IEA Inferred from Electronic Annotation more info
enables phosphatase binding	ISO Inferred from Sequence Orthology more info
enables photoreceptor activity	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein kinase binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in circadian regulation of gene expression	IBA Inferred from Biological aspect of Ancestor more info
involved_in circadian regulation of gene expression	IGI Inferred from Genetic Interaction more info	PubMed
involved_in circadian regulation of gene expression	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within circadian rhythm	IDA Inferred from Direct Assay more info	PubMed
involved_in circadian rhythm	IEP Inferred from Expression Pattern more info	PubMed
acts_upstream_of_or_within circadian rhythm	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in circadian rhythm	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in entrainment of circadian clock by photoperiod	IBA Inferred from Biological aspect of Ancestor more info
involved_in entrainment of circadian clock by photoperiod	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in gluconeogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in glucose homeostasis	IGI Inferred from Genetic Interaction more info	PubMed
involved_in lipid storage	IGI Inferred from Genetic Interaction more info	PubMed
involved_in negative regulation of DNA-templated transcription	IBA Inferred from Biological aspect of Ancestor more info
involved_in negative regulation of DNA-templated transcription	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of DNA-templated transcription	IGI Inferred from Genetic Interaction more info	PubMed
involved_in negative regulation of DNA-templated transcription	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of DNA-templated transcription	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of G protein-coupled receptor signaling pathway	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of circadian rhythm	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of circadian rhythm	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of glucocorticoid receptor signaling pathway	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of glucocorticoid receptor signaling pathway	IGI Inferred from Genetic Interaction more info	PubMed
involved_in negative regulation of glucocorticoid secretion	IGI Inferred from Genetic Interaction more info	PubMed
involved_in negative regulation of gluconeogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of protein ubiquitination	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of transcription by RNA polymerase II	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of gluconeogenesis	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of protein ubiquitination	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of DNA damage checkpoint	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of circadian rhythm	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of gluconeogenesis	IEP Inferred from Expression Pattern more info	PubMed
involved_in regulation of gluconeogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in response to activity	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in response to glucagon	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in response to insulin	IGI Inferred from Genetic Interaction more info	PubMed
involved_in response to light stimulus	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within response to stimulus	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within rhythmic process	IEA Inferred from Electronic Annotation more info
involved_in signal transduction in response to DNA damage	IDA Inferred from Direct Assay more info	PubMed

Component	Evidence Code	Pubs
is_active_in cytoplasm	IBA Inferred from Biological aspect of Ancestor more info
located_in cytosol	TAS Traceable Author Statement more info
located_in mitochondrion	HDA more info	PubMed
located_in mitochondrion	IDA Inferred from Direct Assay more info	PubMed
located_in nucleoplasm	TAS Traceable Author Statement more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
located_in nucleus	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: cryptochrome-1

Names: cryptochrome 1 (photolyase-like)

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

NM_001428424.1 → NP_001415353.1 cryptochrome-1 isoform b

Status: VALIDATED

Source sequence(s)

AC100386, AC122238
NM_001428425.1 → NP_001415354.1 cryptochrome-1 isoform c

Status: VALIDATED

Source sequence(s)

AC100386, AC122238
NM_001428426.1 → NP_001415355.1 cryptochrome-1 isoform d

Status: VALIDATED

Source sequence(s)

AC100386
NM_001428427.1 → NP_001415356.1 cryptochrome-1 isoform e

Status: VALIDATED

Source sequence(s)

AC100386, AC122238
NM_001428428.1 → NP_001415357.1 cryptochrome-1 isoform e

Status: VALIDATED

Source sequence(s)

AC100386, AC122238
NM_001428429.1 → NP_001415358.1 cryptochrome-1 isoform f

Status: VALIDATED

Source sequence(s)

AC100386
NM_007771.4 → NP_031797.1 cryptochrome-1 isoform a

See identical proteins and their annotated locations for NP_031797.1

Status: VALIDATED

Description

Transcript Variant: This variant (1) encodes the longest isoform (a).

Source sequence(s)

AC100386, AC122238

Consensus CDS

CCDS24089.1

UniProtKB/Swiss-Prot

P97784

Related

ENSMUSP00000020227.10, ENSMUST00000020227.11

Conserved Domains (3) summary

COG0415
Location:6 → 491

PhrB; Deoxyribodipyrimidine photolyase [Replication, recombination and repair]

pfam00875
Location:5 → 167

DNA_photolyase; DNA photolyase

pfam03441
Location:213 → 486

FAD_binding_7; FAD binding domain of DNA photolyase

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCm39 C57BL/6J

Genomic

NC_000076.7 Reference GRCm39 C57BL/6J

Range

84967564..85020918 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_011243349.2 → XP_011241651.1 cryptochrome-1 isoform X2

Conserved Domains (1) summary

pfam03441
Location:129 → 327

FAD_binding_7; FAD binding domain of DNA photolyase
XM_030244860.1 → XP_030100720.1 cryptochrome-1 isoform X2

Conserved Domains (1) summary

pfam03441
Location:129 → 327

FAD_binding_7; FAD binding domain of DNA photolyase
XM_011243348.2 → XP_011241650.1 cryptochrome-1 isoform X1

Conserved Domains (2) summary

pfam03441
Location:250 → 448

FAD_binding_7; FAD binding domain of DNA photolyase

cl30787
Location:15 → 453

PhrB; Deoxyribodipyrimidine photolyase [Replication, recombination and repair]