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mmu_circClock_1258
Basic information of circular RNA
PanCircBase ID:
mmu_circClock_1258
mm39_Chr. Position ID:
chr5|76374779|76388793|-
Gene name:
Clock
Transcript:
ENSMUST00000202651.4
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
8
Exon/intron indexes:
22,21,20,19,18,17,16,15
Exon/intron offsets:
0,2425,3232,4463,8833,9349,10088,13938
Genomic length:
14014
Exon/intron sizes in nt:
295,206,195,153,90,101,142,76
Flanking exon/introns:
chr5:76364725-76374779|chr5:76388793-76389716
Splice length:
1258
Other database IDs:
CIRCpedia: MMU_CIRCpedia_29282, circAtlas: mmu-Clock_0038
Human Ortholog IDs:
Mature spliced Sequence:
TTATGCAGAAGTTAGGGCTGAAAGACGGCGAGAACTTGGCATTGAAGAGTCTCTTCCTGAGACAGCTGCTGACAAAAGCCAAGATTCTGGGTCTGACAATCGTATCAACACAGTGAGTCTCAAGGAAGCACTGGAAAGGTTTGATCACAGCCCAACTCCTTCTGCCTCCTCTAGAAGCTCACGAAAGTCATCTCACACCGCAGTCTCAGACCCTTCCTCCACACCGACAAAGATCCCTACTGATACTAGCACTCCTCCCAGACAGCATTTGCCAGCTCATGAAAAGATGACACAGCGGAGGTCGTCCTTCAGCAGTCAGTCCATAAACTCCCAGTCAGTTGGTCCATCATTAACACAGCCAGCGATGTCTCAAGCTGCAAATTTACCAATTCCACAAGGCATGTCACAGTTTCAGTTTTCAGCTCAGTTAGGAGCCATGCAGCATCTAAAAGACCAGCTAGAGCAGCGGACACGGATGATAGAGGCAAATATTCATCGGCAGCAAGAAGAACTAAGGAAAATTCAAGAGCAACTTCAGATGGTCCATGGTCAAGGGCTACAGATGTTTTTGCAGCAATCAAACCCTGGATTGAATTTTGGTTCTGTTCAACTTTCCTCTGGAAATTCTAATATCCAGCAACTCACACCTGTAAATATGCAAGGCCAGGTTGTCCCTGCTAACCAGGTTCAGAGTGGACATATCAGCACAGGCCAGCACATGATACAGCAACAGACTTTACAAAGTACATCAACTCAGCAGAGTCAACAGAGTGTAATGAGTGGACACAGTCAGCAGACGTCTCTTCCAAGTCAGACACCGAGCACTCTCACAGCCCCACTGTACAATACGATGGTGATTTCCCAGCCTGCAGCTGGGAGCATGGTCCAGATTCCATCCAGTATGCCACAGAACAGTACCCAGAGTGCTACAGTCACTACGTTCACTCAGGACAGACAGATAAGATTTTCTCAAGGTCAGCAACTTGTGACCAAATTAGTGACTGCTCCTGTAGCTTGTGGGGCCGTCATGGTACCAAGTACCATGCTTATGGGTCAGGTGGTGACTGCCTATCCTACCTTCGCCACACAACAGCAGCAGGCACAGACATTATCGGTAACACAACAGCAGCAGCAGCAGCAGCAGCAGCCACCACAGCAACAGCAACAACAACAGCAGAGTTCCCAGGAACAGCAGCTTCCTTCAGTTCAGCAGCCAGCTCAGGCCCAGCTGGGCCAGCCACCACAGCAGTTCTTACAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TCCTTCAGTTCAGCAGCCAG
59.96
GGCTTTTGTCAGCAGCTGTC
60.04
141
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
ACAACAGCAGAGTTCCCAGG
59.89
TTGTCAGCAGCTGTCTCAGG
59.97
166
PCR template sequence:
ACAGCAACAACAACAGCAGAGTTCCCAGGAACAGCAGCTTCCTTCAGTTCAGCAGCCAGCTCAGGCCCAGCTGGGCCAGCCACCACAGCAGTTCTTACAGTTATGCAGAAGTTAGGGCTGAAAGACGGCGAGAACTTGGCATTGAAGAGTCTCTTCCTGAGACAGCTGCTGACAAAAGCCAAGATTCTGGGTCTGACAAT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
3
Interacting miRNAs (#binding sites)
mmu-miR-3470b(2), mmu-miR-709(1), mmu-miR-190b-5p(1)
siRNAs for circular RNA silencing
Junction sequence
GCAGTTCTTACAGTTATGCAGAAGTT
siRNA sets
CTTCTGCATAACTGTAAGA, GCATAACTGTAAGAACTGC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCCLOCK_1258_ORF_1
1.089
0.098853419
0.985935526
987
ORF sequence:
ATGACACAGCGGAGGTCGTCCTTCAGCAGTCAGTCCATAAACTCCCAGTCAGTTGGTCCATCATTAACACAGCCAGCGATGTCTCAAGCTGCAAATTTACCAATTCCACAAGGCATGTCACAGTTTCAGTTTTCAGCTCAGTTAGGAGCCATGCAGCATCTAAAAGACCAGCTAGAGCAGCGGACACGGATGATAGAGGCAAATATTCATCGGCAGCAAGAAGAACTAAGGAAAATTCAAGAGCAACTTCAGATGGTCCATGGTCAAGGGCTACAGATGTTTTTGCAGCAATCAAACCCTGGATTGAATTTTGGTTCTGTTCAACTTTCCTCTGGAAATTCTAATATCCAGCAACTCACACCTGTAAATATGCAAGGCCAGGTTGTCCCTGCTAACCAGGTTCAGAGTGGACATATCAGCACAGGCCAGCACATGATACAGCAACAGACTTTACAAAGTACATCAACTCAGCAGAGTCAACAGAGTGTAATGAGTGGACACAGTCAGCAGACGTCTCTTCCAAGTCAGACACCGAGCACTCTCACAGCCCCACTGTACAATACGATGGTGATTTCCCAGCCTGCAGCTGGGAGCATGGTCCAGATTCCATCCAGTATGCCACAGAACAGTACCCAGAGTGCTACAGTCACTACGTTCACTCAGGACAGACAGATAAGATTTTCTCAAGGTCAGCAACTTGTGACCAAATTAGTGACTGCTCCTGTAGCTTGTGGGGCCGTCATGGTACCAAGTACCATGCTTATGGGTCAGGTGGTGACTGCCTATCCTACCTTCGCCACACAACAGCAGCAGGCACAGACATTATCGGTAACACAACAGCAGCAGCAGCAGCAGCAGCAGCCACCACAGCAACAGCAACAACAACAGCAGAGTTCCCAGGAACAGCAGCTTCCTTCAGTTCAGCAGCCAGCTCAGGCCCAGCTGGGCCAGCCACCACAGCAGTTCTTACAGTTATGCAGAAGTTAG
Peptide sequence:
MTQRRSSFSSQSINSQSVGPSLTQPAMSQAANLPIPQGMSQFQFSAQLGAMQHLKDQLEQRTRMIEANIHRQQEELRKIQEQLQMVHGQGLQMFLQQSNPGLNFGSVQLSSGNSNIQQLTPVNMQGQVVPANQVQSGHISTGQHMIQQQTLQSTSTQQSQQSVMSGHSQQTSLPSQTPSTLTAPLYNTMVISQPAAGSMVQIPSSMPQNSTQSATVTTFTQDRQIRFSQGQQLVTKLVTAPVACGAVMVPSTMLMGQVVTAYPTFATQQQQAQTLSVTQQQQQQQQQPPQQQQQQQQSSQEQQLPSVQQPAQAQLGQPPQQFLQLCRS
IRESfinder result
IRESfinder score
0.57991316
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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