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mmu_circRobo2_843
Basic information of circular RNA
PanCircBase ID:
mmu_circRobo2_843
mm39_Chr. Position ID:
chr16|73778868|73843825|-
Gene name:
Robo2
Transcript:
ENSMUST00000117785.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
6
Exon/intron indexes:
8,7,6,5,4,3
Exon/intron offsets:
0,3607,33890,53004,63841,64799
Genomic length:
64957
Exon/intron sizes in nt:
1,72,12,51,28,13,91,21,000
Flanking exon/introns:
chr16:73775501-73778868|chr16:73843825-74149438
Splice length:
843
Other database IDs:
CIRCpedia: MMU_CIRCpedia_215140, circAtlas: mmu-Robo2_0018
circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_148049
Human Ortholog IDs:
Mature spliced Sequence:
TATTGCGAGATGACTTCCGGCAAAACCCCACAGATGTGGTAGTCGCAGCTGGAGAGCCTGCAATCTTGGAGTGCCAGCCACCACGGGGACACCCAGAACCAACCATCTACTGGAAAAAGGACAAAGTCCGAATTGATGACAAGGAAGAGAGAATAAGTATCCGTGGTGGGAAGCTGATGATCTCTAATACTAGGAAAAGCGATGCTGGCATGTACACCTGTGTGGGAACCAATATGGTGGGAGAAAGGGACAGCGACCCTGCAGAGCTCACTGTCTTTGAACGACCCACATTTCTCAGGAGGCCAATTAACCAGGTGGTGCTAGAGGAAGAAGCTGTAGAATTCCGTTGTCAGGTCCAAGGAGATCCCCAGCCAACGGTGAGGTGGAAAAAAGATGATGCAGACTTGCCGAGAGGAAGGTATGATATCAAAGATGACTACACGCTGAGAATTAAAAAGGCCATGAGTACTGATGAAGGTACCTATGTGTGTATTGCTGAGAATCGGGTGGGAAAAGTGGAAGCCTCTGCTACCCTCACTGTCCGAGCTCCTCCACAGTTTGTGGTTAGGCCAAGAGATCAGATCGTTGCTCAAGGCCGAACAGTGACATTCCCCTGTGAAACTAAAGGAAACCCACAGCCAGCTGTTTTTTGGCAGAAAGAAGGCAGCCAGAACCTACTTTTCCCGAATCAACCTCAGCAGCCCAACAGCCGATGTTCAGTGTCGCCCACGGGGGACCTCACCATCACCAACATCCAGCGTTCAGATGCGGGTTACTACATCTGCCAGGCCCTAACCGTGGCAGGAAGCATTTTAGCTAAAGCACAGTTGGAAGTTACTGACG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TCACCAACATCCAGCGTTCA
59.89
CCAAGATTGCAGGCTCTCCA
60.03
168
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GCGGGTTACTACATCTGCCA
59.82
CCAAGATTGCAGGCTCTCCA
60.03
145
PCR template sequence:
ATCACCAACATCCAGCGTTCAGATGCGGGTTACTACATCTGCCAGGCCCTAACCGTGGCAGGAAGCATTTTAGCTAAAGCACAGTTGGAAGTTACTGACGTATTGCGAGATGACTTCCGGCAAAACCCCACAGATGTGGTAGTCGCAGCTGGAGAGCCTGCAATCTTGGAGTGCCAGCCACCACGGGGACACCCAGAACC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
9
Interacting miRNAs (#binding sites)
mmu-miR-135a-5p(1), mmu-miR-211-5p(1), mmu-miR-204-5p(1), mmu-miR-29b-3p(1), mmu-miR-29a-3p(1), mmu-miR-29c-3p(1), mmu-miR-191-5p(1), mmu-miR-218-5p(1), mmu-miR-338-3p(1)
siRNAs for circular RNA silencing
Junction sequence
GAAGTTACTGACGTATTGCGAGATGA
siRNA sets
TCATCTCGCAATACGTCAG, CATCTCGCAATACGTCAGT, ATCTCGCAATACGTCAGTA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCROBO2_843_ORF_1
0.9673
0.26734707
0.999796332
1509
ORF sequence:
ATGATCTCTAATACTAGGAAAAGCGATGCTGGCATGTACACCTGTGTGGGAACCAATATGGTGGGAGAAAGGGACAGCGACCCTGCAGAGCTCACTGTCTTTGAACGACCCACATTTCTCAGGAGGCCAATTAACCAGGTGGTGCTAGAGGAAGAAGCTGTAGAATTCCGTTGTCAGGTCCAAGGAGATCCCCAGCCAACGGTGAGGTGGAAAAAAGATGATGCAGACTTGCCGAGAGGAAGGTATGATATCAAAGATGACTACACGCTGAGAATTAAAAAGGCCATGAGTACTGATGAAGGTACCTATGTGTGTATTGCTGAGAATCGGGTGGGAAAAGTGGAAGCCTCTGCTACCCTCACTGTCCGAGCTCCTCCACAGTTTGTGGTTAGGCCAAGAGATCAGATCGTTGCTCAAGGCCGAACAGTGACATTCCCCTGTGAAACTAAAGGAAACCCACAGCCAGCTGTTTTTTGGCAGAAAGAAGGCAGCCAGAACCTACTTTTCCCGAATCAACCTCAGCAGCCCAACAGCCGATGTTCAGTGTCGCCCACGGGGGACCTCACCATCACCAACATCCAGCGTTCAGATGCGGGTTACTACATCTGCCAGGCCCTAACCGTGGCAGGAAGCATTTTAGCTAAAGCACAGTTGGAAGTTACTGACGTATTGCGAGATGACTTCCGGCAAAACCCCACAGATGTGGTAGTCGCAGCTGGAGAGCCTGCAATCTTGGAGTGCCAGCCACCACGGGGACACCCAGAACCAACCATCTACTGGAAAAAGGACAAAGTCCGAATTGATGACAAGGAAGAGAGAATAAGTATCCGTGGTGGGAAGCTGATGATCTCTAATACTAGGAAAAGCGATGCTGGCATGTACACCTGTGTGGGAACCAATATGGTGGGAGAAAGGGACAGCGACCCTGCAGAGCTCACTGTCTTTGAACGACCCACATTTCTCAGGAGGCCAATTAACCAGGTGGTGCTAGAGGAAGAAGCTGTAGAATTCCGTTGTCAGGTCCAAGGAGATCCCCAGCCAACGGTGAGGTGGAAAAAAGATGATGCAGACTTGCCGAGAGGAAGGTATGATATCAAAGATGACTACACGCTGAGAATTAAAAAGGCCATGAGTACTGATGAAGGTACCTATGTGTGTATTGCTGAGAATCGGGTGGGAAAAGTGGAAGCCTCTGCTACCCTCACTGTCCGAGCTCCTCCACAGTTTGTGGTTAGGCCAAGAGATCAGATCGTTGCTCAAGGCCGAACAGTGACATTCCCCTGTGAAACTAAAGGAAACCCACAGCCAGCTGTTTTTTGGCAGAAAGAAGGCAGCCAGAACCTACTTTTCCCGAATCAACCTCAGCAGCCCAACAGCCGATGTTCAGTGTCGCCCACGGGGGACCTCACCATCACCAACATCCAGCGTTCAGATGCGGGTTACTACATCTGCCAGGCCCTAACCGTGGCAGGAAGCATTTTAGCTAAAGCACAGTTGGAAGTTACTGAC
Peptide sequence:
MISNTRKSDAGMYTCVGTNMVGERDSDPAELTVFERPTFLRRPINQVVLEEEAVEFRCQVQGDPQPTVRWKKDDADLPRGRYDIKDDYTLRIKKAMSTDEGTYVCIAENRVGKVEASATLTVRAPPQFVVRPRDQIVAQGRTVTFPCETKGNPQPAVFWQKEGSQNLLFPNQPQQPNSRCSVSPTGDLTITNIQRSDAGYYICQALTVAGSILAKAQLEVTDVLRDDFRQNPTDVVVAAGEPAILECQPPRGHPEPTIYWKKDKVRIDDKEERISIRGGKLMISNTRKSDAGMYTCVGTNMVGERDSDPAELTVFERPTFLRRPINQVVLEEEAVEFRCQVQGDPQPTVRWKKDDADLPRGRYDIKDDYTLRIKKAMSTDEGTYVCIAENRVGKVEASATLTVRAPPQFVVRPRDQIVAQGRTVTFPCETKGNPQPAVFWQKEGSQNLLFPNQPQQPNSRCSVSPTGDLTITNIQRSDAGYYICQALTVAGSILAKAQLEVTD
IRESfinder result
IRESfinder score
0.386294961
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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