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mmu_circRobo2_1454
Basic information of circular RNA
PanCircBase ID:
mmu_circRobo2_1454
mm39_Chr. Position ID:
chr16|73730474|73768108|-
Gene name:
Robo2
Transcript:
ENSMUST00000117785.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
9
Exon/intron indexes:
20,19,18,17,16,15,14,13,12
Exon/intron offsets:
0,5144,6669,14616,22901,24717,28092,34181,37467
Genomic length:
37634
Exon/intron sizes in nt:
2,82,12,84,31,83,17,21,00,00,00,00,000
Flanking exon/introns:
chr16:73730059-73730474|chr16:73768108-73770040
Splice length:
1454
Other database IDs:
CIRCpedia: MMU_CIRCpedia_214175, circAtlas: mmu-Robo2_0005
circBase: hsa_circ_0124674, circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_138532
Human Ortholog IDs:
Mature spliced Sequence:
CCAATCGGTGAGCAATAGCTGGCAGACAGTGGCAAACCATGTTAAGACAACTCTGTATACAGTAAGGGGGCTGAGGCCCAACACAATCTACTTGTTTATGGTCAGAGCGATCAACCCACAAGGTCTCAGTGATCCAAGTCCTATGTCGGATCCTGTACGCACACAAGATATCAGCCCCCCAGCACAAGGAGTGGACCACAGACAGGTGCAGAAGGAATTAGGTGATGTCGTTGTTCGTCTCCATAATCCAGTTGTCCTGACACCTACAACTGTTCAAGTCACATGGACGGTGGACCGACAACCCCAGTTTATTCAGGGCTACAGAGTGATGTACCGTCAGACTTCGGGACTACAAGCCTCAACTGTGTGGCAGAATCTAGACGCCAAAGTCCCGACTGAGAGGAGTGCTGTCCTTGTGAATTTGAAAAAGGGGGTGACTTATGAAATTAAAGTCCGGCCGTATTTTAACGAGTTCCAAGGAATGGACAGTGAATCGAAAACAGTCCGAACCACTGAGGAAGCCCCAAGTGCCCCTCCCCAGTCTGTCACTGTGCTGACAGTTGGAAGTCACAACAGCACAAGCATCAGTGTTTCCTGGGATCCTCCACCAGCCGACCACCAGAATGGAATTATTCAGGAATATAAGATCTGGTGTCTGGGAAACGAAACGCGATTCCATATCAATAAAACGGTGGATGCAGCCATTCGCTCTGTAGTAATAGGTGGCTTGTTCCCTGGAATTCAGTACCGGGTAGAAGTGGCAGCTAGCACAAGTGCAGGGGTTGGAGTAAAAAGTGAACCACAGCCGATAATAATTGGGGGACGTAACGAAGTTGTCATTACTGAAAACAATAACAGCATCACTGAGCAAATCACGGATGTCGTGAAGCAACCGGCATTTATAGCTGGCATTGGTGGTGCCTGCTGGGTAATTCTGATGGGTTTTAGCATCTGGTTGTACTGGAGAAGAAAGAAGAGAAAGGGACTCAGCAATTATGCTGTAACATTTCAAAGAGGAGATGGAGGACTAATGAGCAATGGGAGCCGTCCAGGTCTTCTAAATGCTGGCGATCCCAATTACCCATGGCTTGCTGATTCTTGGCCAGCCACGAGTTTGCCAGTGAACAATAGCAATAGTGGCCCAAATGAAATTGGAAATTTTGGGCGTGGAGATGTGCTGCCTCCGGTGCCAGGCCAAGGGGATAAAACAGCGACCATGCTCTCGGATGGAGCCATTTATAGCAGCATTGACTTCACTACCAAAACCACTTACAACAGTTCCAGCCAAATAACACAGGCCACCCCATATGCCACTACACAAATCCTGCATTCAAACAGCATCCACGAACTGGCAGTTGATCTTCCTGATCCACAGTGGAAAAGCTCAGTTCAACAGAAGACAGACCTCATGGGATTTGGTTATTCGCTACCTGATCAGAACAAGGGGAACAACG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TCCACAGTGGAAAAGCTCAGT
59.51
AGATTGTGTTGGGCCTCAGC
60.61
175
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TCCACAGTGGAAAAGCTCAGT
59.51
GCCTCAGCCCCCTTACTGTA
60.98
163
PCR template sequence:
GTTGATCTTCCTGATCCACAGTGGAAAAGCTCAGTTCAACAGAAGACAGACCTCATGGGATTTGGTTATTCGCTACCTGATCAGAACAAGGGGAACAACGCCAATCGGTGAGCAATAGCTGGCAGACAGTGGCAAACCATGTTAAGACAACTCTGTATACAGTAAGGGGGCTGAGGCCCAACACAATCTACTTGTTTATG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
12
Interacting miRNAs (#binding sites)
mmu-miR-140-5p(1), mmu-miR-211-5p(1), mmu-miR-204-5p(1), mmu-miR-203-3p(1), mmu-miR-138-5p(1), mmu-miR-214-3p(1), mmu-miR-128-3p(1), mmu-miR-382-3p(1), mmu-miR-22-3p(1), mmu-miR-669d-5p(1), mmu-miR-3470b(1), mmu-miR-1199-5p(1)
siRNAs for circular RNA silencing
Junction sequence
AAGGGGAACAACGCCAATCGGTGAGC
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCROBO2_1454_ORF_1
0.8923
0.163531967
0.998981933
1368
ORF sequence:
ATGGTCAGAGCGATCAACCCACAAGGTCTCAGTGATCCAAGTCCTATGTCGGATCCTGTACGCACACAAGATATCAGCCCCCCAGCACAAGGAGTGGACCACAGACAGGTGCAGAAGGAATTAGGTGATGTCGTTGTTCGTCTCCATAATCCAGTTGTCCTGACACCTACAACTGTTCAAGTCACATGGACGGTGGACCGACAACCCCAGTTTATTCAGGGCTACAGAGTGATGTACCGTCAGACTTCGGGACTACAAGCCTCAACTGTGTGGCAGAATCTAGACGCCAAAGTCCCGACTGAGAGGAGTGCTGTCCTTGTGAATTTGAAAAAGGGGGTGACTTATGAAATTAAAGTCCGGCCGTATTTTAACGAGTTCCAAGGAATGGACAGTGAATCGAAAACAGTCCGAACCACTGAGGAAGCCCCAAGTGCCCCTCCCCAGTCTGTCACTGTGCTGACAGTTGGAAGTCACAACAGCACAAGCATCAGTGTTTCCTGGGATCCTCCACCAGCCGACCACCAGAATGGAATTATTCAGGAATATAAGATCTGGTGTCTGGGAAACGAAACGCGATTCCATATCAATAAAACGGTGGATGCAGCCATTCGCTCTGTAGTAATAGGTGGCTTGTTCCCTGGAATTCAGTACCGGGTAGAAGTGGCAGCTAGCACAAGTGCAGGGGTTGGAGTAAAAAGTGAACCACAGCCGATAATAATTGGGGGACGTAACGAAGTTGTCATTACTGAAAACAATAACAGCATCACTGAGCAAATCACGGATGTCGTGAAGCAACCGGCATTTATAGCTGGCATTGGTGGTGCCTGCTGGGTAATTCTGATGGGTTTTAGCATCTGGTTGTACTGGAGAAGAAAGAAGAGAAAGGGACTCAGCAATTATGCTGTAACATTTCAAAGAGGAGATGGAGGACTAATGAGCAATGGGAGCCGTCCAGGTCTTCTAAATGCTGGCGATCCCAATTACCCATGGCTTGCTGATTCTTGGCCAGCCACGAGTTTGCCAGTGAACAATAGCAATAGTGGCCCAAATGAAATTGGAAATTTTGGGCGTGGAGATGTGCTGCCTCCGGTGCCAGGCCAAGGGGATAAAACAGCGACCATGCTCTCGGATGGAGCCATTTATAGCAGCATTGACTTCACTACCAAAACCACTTACAACAGTTCCAGCCAAATAACACAGGCCACCCCATATGCCACTACACAAATCCTGCATTCAAACAGCATCCACGAACTGGCAGTTGATCTTCCTGATCCACAGTGGAAAAGCTCAGTTCAACAGAAGACAGACCTCATGGGATTTGGTTATTCGCTACCTGATCAGAACAAGGGGAACAACGCCAATCGGTGA
Peptide sequence:
MVRAINPQGLSDPSPMSDPVRTQDISPPAQGVDHRQVQKELGDVVVRLHNPVVLTPTTVQVTWTVDRQPQFIQGYRVMYRQTSGLQASTVWQNLDAKVPTERSAVLVNLKKGVTYEIKVRPYFNEFQGMDSESKTVRTTEEAPSAPPQSVTVLTVGSHNSTSISVSWDPPPADHQNGIIQEYKIWCLGNETRFHINKTVDAAIRSVVIGGLFPGIQYRVEVAASTSAGVGVKSEPQPIIIGGRNEVVITENNNSITEQITDVVKQPAFIAGIGGACWVILMGFSIWLYWRRKKRKGLSNYAVTFQRGDGGLMSNGSRPGLLNAGDPNYPWLADSWPATSLPVNNSNSGPNEIGNFGRGDVLPPVPGQGDKTATMLSDGAIYSSIDFTTKTTYNSSSQITQATPYATTQILHSNSIHELAVDLPDPQWKSSVQQKTDLMGFGYSLPDQNKGNNANR
IRESfinder result
IRESfinder score
0.493455454
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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