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mmu_circClock_1101
Basic information of circular RNA
PanCircBase ID:
mmu_circClock_1101
mm39_Chr. Position ID:
chr5|76383612|76396309|-
Gene name:
Clock
Transcript:
ENSMUST00000202651.4
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
10
Exon/intron indexes:
18,17,16,15,14,13,12,11,10,9
Exon/intron offsets:
0,516,1255,5105,6104,7016,7313,9430,9656,12576
Genomic length:
12697
Exon/intron sizes in nt:
90,10,11,42,76,14,81,00,00,00,00,00,000
Flanking exon/introns:
chr5:76379395-76383612|chr5:76396309-76402220
Splice length:
1101
Other database IDs:
CIRCpedia: MMU_CIRCpedia_29284, circAtlas: mmu-Clock_0010
circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_376072
Human Ortholog IDs:
Mature spliced Sequence:
TCTGATCTTGTGGATCAAAGTATATTTAATTTTATCCCAGAGGGAGAACATTCAGAGGTTTATAAGATACTCTCTACTCATCTGCTGGAAAGTGACTCATTAACCCCTGAGTACTTAAAATCAAAAAATCAGTTAGAATTCTGTTGTCACATGCTTCGAGGAACAATAGACCCAAAGGAGCCATCCACCTATGAATATGTGAGATTTATAGGAAATTTTAAATCTTTAACCAGTGTATCAACTTCAACACACAATGGTTTTGAAGGAACTATACAACGCACACATAGGCCTTCTTATGAAGATAGAGTTTGTTTTGTAGCTACTGTCAGATTAGCTACACCTCAGTTCATCAAGGAAATGTGTACTGTTGAAGAACCAAATGAAGAGTTTACATCTAGACACAGTTTAGAATGGAAGTTTCTATTTTTAGATCACAGGGCACCACCAATAATAGGCTATTTGCCATTTGAAGTCTTGGGAACATCAGGCTATGATTACTATCATGTGGATGACCTAGAAAATCTGGCAAAATGTCACGAGCACTTAATGCAATATGGAAAAGGCAAATCGTGTTACTATAGATTCCTGACCAAAGGCCAGCAGTGGATATGGCTTCAGACTCATTATTATATTACTTACCATCAGTGGAATTCAAGGCCAGAGTTCATTGTTTGTACTCACACTGTAGTAAGTTATGCAGAAGTTAGGGCTGAAAGACGGCGAGAACTTGGCATTGAAGAGTCTCTTCCTGAGACAGCTGCTGACAAAAGCCAAGATTCTGGGTCTGACAATCGTATCAACACAGTGAGTCTCAAGGAAGCACTGGAAAGGTTTGATCACAGCCCAACTCCTTCTGCCTCCTCTAGAAGCTCACGAAAGTCATCTCACACCGCAGTCTCAGACCCTTCCTCCACACCGACAAAGATCCCTACTGATACTAGCACTCCTCCCAGACAGCATTTGCCAGCTCATGAAAAGATGACACAGCGGAGGTCGTCCTTCAGCAGTCAGTCCATAAACTCCCAGTCAGTTGGTCCATCATTAACACAGCCAGCGATGTCTCAAGCTGCAAATTTACCAATTCCACAAGGCATGTCACAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
ACTCCCAGTCAGTTGGTCCA
60.4
CTCTGAATGTTCTCCCTCTGGG
59.83
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
ACTCCCAGTCAGTTGGTCCA
60.4
CCTCTGAATGTTCTCCCTCTGG
59.83
141
PCR template sequence:
CAGCAGTCAGTCCATAAACTCCCAGTCAGTTGGTCCATCATTAACACAGCCAGCGATGTCTCAAGCTGCAAATTTACCAATTCCACAAGGCATGTCACAGTCTGATCTTGTGGATCAAAGTATATTTAATTTTATCCCAGAGGGAGAACATTCAGAGGTTTATAAGATACTCTCTACTCATCTGCTGGAAAGTGACTCAT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
6
Interacting miRNAs (#binding sites)
mmu-miR-9-5p(1), mmu-miR-709(1), mmu-miR-362-5p(1), mmu-miR-466a-5p(1), mmu-miR-1187(1), mmu-miR-466p-5p(1)
siRNAs for circular RNA silencing
Junction sequence
AGGCATGTCACAGTCTGATCTTGTGG
siRNA sets
AGATCAGACTGTGACATGC, ATCAGACTGTGACATGCCT, GATCAGACTGTGACATGCC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCCLOCK_1101_ORF_1
0.7358
-0.041698134
0.999977706
2052
ORF sequence:
ATGCTTCGAGGAACAATAGACCCAAAGGAGCCATCCACCTATGAATATGTGAGATTTATAGGAAATTTTAAATCTTTAACCAGTGTATCAACTTCAACACACAATGGTTTTGAAGGAACTATACAACGCACACATAGGCCTTCTTATGAAGATAGAGTTTGTTTTGTAGCTACTGTCAGATTAGCTACACCTCAGTTCATCAAGGAAATGTGTACTGTTGAAGAACCAAATGAAGAGTTTACATCTAGACACAGTTTAGAATGGAAGTTTCTATTTTTAGATCACAGGGCACCACCAATAATAGGCTATTTGCCATTTGAAGTCTTGGGAACATCAGGCTATGATTACTATCATGTGGATGACCTAGAAAATCTGGCAAAATGTCACGAGCACTTAATGCAATATGGAAAAGGCAAATCGTGTTACTATAGATTCCTGACCAAAGGCCAGCAGTGGATATGGCTTCAGACTCATTATTATATTACTTACCATCAGTGGAATTCAAGGCCAGAGTTCATTGTTTGTACTCACACTGTAGTAAGTTATGCAGAAGTTAGGGCTGAAAGACGGCGAGAACTTGGCATTGAAGAGTCTCTTCCTGAGACAGCTGCTGACAAAAGCCAAGATTCTGGGTCTGACAATCGTATCAACACAGTGAGTCTCAAGGAAGCACTGGAAAGGTTTGATCACAGCCCAACTCCTTCTGCCTCCTCTAGAAGCTCACGAAAGTCATCTCACACCGCAGTCTCAGACCCTTCCTCCACACCGACAAAGATCCCTACTGATACTAGCACTCCTCCCAGACAGCATTTGCCAGCTCATGAAAAGATGACACAGCGGAGGTCGTCCTTCAGCAGTCAGTCCATAAACTCCCAGTCAGTTGGTCCATCATTAACACAGCCAGCGATGTCTCAAGCTGCAAATTTACCAATTCCACAAGGCATGTCACAGTCTGATCTTGTGGATCAAAGTATATTTAATTTTATCCCAGAGGGAGAACATTCAGAGGTTTATAAGATACTCTCTACTCATCTGCTGGAAAGTGACTCATTAACCCCTGAGTACTTAAAATCAAAAAATCAGTTAGAATTCTGTTGTCACATGCTTCGAGGAACAATAGACCCAAAGGAGCCATCCACCTATGAATATGTGAGATTTATAGGAAATTTTAAATCTTTAACCAGTGTATCAACTTCAACACACAATGGTTTTGAAGGAACTATACAACGCACACATAGGCCTTCTTATGAAGATAGAGTTTGTTTTGTAGCTACTGTCAGATTAGCTACACCTCAGTTCATCAAGGAAATGTGTACTGTTGAAGAACCAAATGAAGAGTTTACATCTAGACACAGTTTAGAATGGAAGTTTCTATTTTTAGATCACAGGGCACCACCAATAATAGGCTATTTGCCATTTGAAGTCTTGGGAACATCAGGCTATGATTACTATCATGTGGATGACCTAGAAAATCTGGCAAAATGTCACGAGCACTTAATGCAATATGGAAAAGGCAAATCGTGTTACTATAGATTCCTGACCAAAGGCCAGCAGTGGATATGGCTTCAGACTCATTATTATATTACTTACCATCAGTGGAATTCAAGGCCAGAGTTCATTGTTTGTACTCACACTGTAGTAAGTTATGCAGAAGTTAGGGCTGAAAGACGGCGAGAACTTGGCATTGAAGAGTCTCTTCCTGAGACAGCTGCTGACAAAAGCCAAGATTCTGGGTCTGACAATCGTATCAACACAGTGAGTCTCAAGGAAGCACTGGAAAGGTTTGATCACAGCCCAACTCCTTCTGCCTCCTCTAGAAGCTCACGAAAGTCATCTCACACCGCAGTCTCAGACCCTTCCTCCACACCGACAAAGATCCCTACTGATACTAGCACTCCTCCCAGACAGCATTTGCCAGCTCATGAAAAGATGACACAGCGGAGGTCGTCCTTCAGCAGTCAGTCCATAAACTCCCAGTCAGTTGGTCCATCATTAACACAGCCAGCGATGTCTCAAGCTGCAAATTTACCAATTCCACAAGGCATGTCACAG
Peptide sequence:
MLRGTIDPKEPSTYEYVRFIGNFKSLTSVSTSTHNGFEGTIQRTHRPSYEDRVCFVATVRLATPQFIKEMCTVEEPNEEFTSRHSLEWKFLFLDHRAPPIIGYLPFEVLGTSGYDYYHVDDLENLAKCHEHLMQYGKGKSCYYRFLTKGQQWIWLQTHYYITYHQWNSRPEFIVCTHTVVSYAEVRAERRRELGIEESLPETAADKSQDSGSDNRINTVSLKEALERFDHSPTPSASSRSSRKSSHTAVSDPSSTPTKIPTDTSTPPRQHLPAHEKMTQRRSSFSSQSINSQSVGPSLTQPAMSQAANLPIPQGMSQSDLVDQSIFNFIPEGEHSEVYKILSTHLLESDSLTPEYLKSKNQLEFCCHMLRGTIDPKEPSTYEYVRFIGNFKSLTSVSTSTHNGFEGTIQRTHRPSYEDRVCFVATVRLATPQFIKEMCTVEEPNEEFTSRHSLEWKFLFLDHRAPPIIGYLPFEVLGTSGYDYYHVDDLENLAKCHEHLMQYGKGKSCYYRFLTKGQQWIWLQTHYYITYHQWNSRPEFIVCTHTVVSYAEVRAERRRELGIEESLPETAADKSQDSGSDNRINTVSLKEALERFDHSPTPSASSRSSRKSSHTAVSDPSSTPTKIPTDTSTPPRQHLPAHEKMTQRRSSFSSQSINSQSVGPSLTQPAMSQAANLPIPQGMSQ
IRESfinder result
IRESfinder score
0.69977078
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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