Cry1 cryptochrome circadian regulator 1 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Cry1provided by RGD
Official Full Name: cryptochrome circadian regulator 1provided by RGD
Primary source: RGD:735083
See related: EnsemblRapid:ENSRNOG00000006622 AllianceGenome:RGD:735083
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
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 the related gene in mouse results in a shortened circadian cycle in complete darkness. [provided by RefSeq, Feb 2014]
Expression: Biased expression in Thymus (RPKM 50.5), Muscle (RPKM 47.4) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 7q13

Exon count:: 13

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	7	NC_086025.1 (20417526..20481791)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	7	NC_051342.1 (18529823..18594092)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	7	NC_005106.4 (24534593..24634098)

Chromosome 7 - NC_086025.1 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: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Low intensity near-infrared light promotes bone regeneration via circadian clock protein cryptochrome 1.
Title: Low intensity near-infrared light promotes bone regeneration via circadian clock protein cryptochrome 1.
The model efficiently described the synchronous rhythmicity of core-clock genes and further predicted that their phases are mainly regulated by Per2 and Cry1 transcriptional delays and Rev-Erba and Cry1 degradation rates.
Title: Modeling circadian variability of core-clock and clock-controlled genes in four tissues of the rat.
We investigated the effect of aging on daily rhythms of various clock genes such as rPer1, rPer2, rCry1, rCry2 and rBmal1 in the SCN of male Wistar rats.
Title: Differential role of melatonin in restoration of age-induced alterations in daily rhythms of expression of various clock genes in suprachiasmatic nucleus of male Wistar rats.
Data indicate that dysregulated expression of key circadian clock genes, such as Bmal1 and Cry1, was detected after traumatic brain injury (TBI).
Title: Traumatic brain injury-induced dysregulation of the circadian clock.
N-nitroso-N-methylurea disrupted the expression of Cry1 in mammary glands of Fischer 344 rats
Title: Methylselenocysteine resets the rhythmic expression of circadian and growth-regulatory genes disrupted by nitrosomethylurea in vivo.
The rhythmic mRNA expression of clock genes (Clock, Bmal1, Cry1, and Dbp) is not attenuated in the liver and visceral adipose tissues of Goto-Kakizaki rats, a model of nonobese, type 2 diabetes, as compared to control Wistar rats.
Title: Clock gene expression in the liver and adipose tissues of non-obese type 2 diabetic Goto-Kakizaki rats.
Circadian expression of Cry1 and Cry2 mRNA in the suprachiasma nucleus displayed a circadian rhythm with a peak at the day/night transition, and there was a slightly different circadian pattern of expression of Cry1 and Cry2 in the eye.
Title: Cloning and circadian expression of rat Cry1.

Submit: New GeneRIF Correction

General gene information

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Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
NOT enables DNA (6-4) photolyase activity	ISO Inferred from Sequence Orthology more info
enables DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables DNA-binding transcription factor binding	ISO Inferred from Sequence Orthology more info
enables E-box binding	ISO Inferred from Sequence Orthology more info
enables FAD binding	IBA Inferred from Biological aspect of Ancestor more info
NOT enables deoxyribodipyrimidine photo-lyase activity	ISO Inferred from Sequence Orthology more info
enables double-stranded DNA binding	ISO Inferred from Sequence Orthology more info
enables histone deacetylase binding	ISO Inferred from Sequence Orthology more info
enables kinase binding	ISO Inferred from Sequence Orthology more info
enables nuclear receptor binding	ISO Inferred from Sequence Orthology more info
enables phosphatase binding	ISO Inferred from Sequence Orthology more info
enables photoreceptor activity	IEA Inferred from Electronic Annotation more info
enables protein kinase binding	ISO Inferred from Sequence Orthology more info

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	ISO Inferred from Sequence Orthology more info
involved_in circadian regulation of gene expression	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of_or_within circadian rhythm	ISO Inferred from Sequence Orthology more info
involved_in circadian rhythm	ISO Inferred from Sequence Orthology more info
involved_in circadian rhythm	ISS Inferred from Sequence or Structural Similarity more info
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	ISO Inferred from Sequence Orthology more info
involved_in entrainment of circadian clock by photoperiod	ISS Inferred from Sequence or Structural Similarity more info
involved_in gluconeogenesis	ISO Inferred from Sequence Orthology more info
involved_in gluconeogenesis	ISS Inferred from Sequence or Structural Similarity more info
involved_in glucose homeostasis	ISO Inferred from Sequence Orthology more info
involved_in glucose homeostasis	ISS Inferred from Sequence or Structural Similarity more info
involved_in lipid storage	ISO Inferred from Sequence Orthology more info
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	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of DNA-templated transcription	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of G protein-coupled receptor signaling pathway	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of G protein-coupled receptor signaling pathway	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of circadian rhythm	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of circadian rhythm	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of glucocorticoid receptor signaling pathway	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of glucocorticoid receptor signaling pathway	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of glucocorticoid secretion	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of gluconeogenesis	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of gluconeogenesis	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of protein ubiquitination	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of protein ubiquitination	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of transcription by RNA polymerase II	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of gluconeogenesis	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of protein ubiquitination	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of protein ubiquitination	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of DNA damage checkpoint	ISO Inferred from Sequence Orthology more info
involved_in regulation of DNA damage checkpoint	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of circadian rhythm	ISO Inferred from Sequence Orthology more info
involved_in regulation of circadian rhythm	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of gluconeogenesis	ISO Inferred from Sequence Orthology more info
involved_in response to activity	ISO Inferred from Sequence Orthology more info
involved_in response to activity	ISS Inferred from Sequence or Structural Similarity more info
involved_in response to glucagon	ISO Inferred from Sequence Orthology more info
involved_in response to glucagon	ISS Inferred from Sequence or Structural Similarity more info
involved_in response to insulin	ISO Inferred from Sequence Orthology more info
involved_in response to light stimulus	ISO Inferred from Sequence Orthology more info
involved_in response to light stimulus	ISS Inferred from Sequence or Structural Similarity more info
involved_in signal transduction in response to DNA damage	ISO Inferred from Sequence Orthology more info
involved_in signal transduction in response to DNA damage	ISS Inferred from Sequence or Structural Similarity more info

Component	Evidence Code	Pubs
is_active_in cytoplasm	IBA Inferred from Biological aspect of Ancestor more info
located_in mitochondrion	ISO Inferred from Sequence Orthology more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	ISO Inferred from Sequence Orthology more info
located_in nucleus	ISS Inferred from Sequence or Structural Similarity more info

General protein information

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Preferred Names: cryptochrome-1

Names: cryptochrome 1 (photolyase-like); cryptochrome circadian clock 1

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_198750.2 → NP_942045.2 cryptochrome-1

See identical proteins and their annotated locations for NP_942045.2

Status: PROVISIONAL

Source sequence(s)

BC107677

UniProtKB/Swiss-Prot

Q32Q86, Q717B5

UniProtKB/TrEMBL

A6IFE1

Related

ENSRNOP00000009124.4, ENSRNOT00000009124.7

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_036323735.1-RS_2024_02

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

Reference GRCr8

Genomic

NC_086025.1 Reference GRCr8

Range

20417526..20481791

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_008765225.4 → XP_008763447.1 cryptochrome-1 isoform X1

See identical proteins and their annotated locations for XP_008763447.1

UniProtKB/Swiss-Prot

Q32Q86, Q717B5

UniProtKB/TrEMBL

A6IFE1

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
XM_063263193.1 → XP_063119263.1 cryptochrome-1 isoform X1

UniProtKB/Swiss-Prot

Q32Q86, Q717B5

UniProtKB/TrEMBL

A6IFE1