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mmu_circApbb2_1784
Basic information of circular RNA
PanCircBase ID:
mmu_circApbb2_1784
mm39_Chr. Position ID:
chr5|66520060|66700960|-
Gene name:
Apbb2
Transcript:
ENSMUST00000162366.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
9
Exon/intron indexes:
10,9,8,7,6,5,4,3,2
Exon/intron offsets:
0,2256,28909,29054,37358,88750,99380,129340,180744
Genomic length:
180900
Exon/intron sizes in nt:
1,28,14,76,18,62,06,81,00,00,00,000
Flanking exon/introns:
chr5:66470772-66520060|chr5:66700960-66775910
Splice length:
1784
Other database IDs:
CIRCpedia: MMU_CIRCpedia_223390, circAtlas: mmu-Apbb2_0031
Human Ortholog IDs:
Mature spliced Sequence:
GTTGAGCCTCTGTAGGGAGCTGCTGTGCTCTCCAGCCAAGCATGCTGTGGTCAGATCTGCCCAGCCCTGGAATAGAATCCTTTGCCGGATGGAAAATCCATAAAAGAAAGCTCTTGTGAAGAGCTGATTCCCACCTGCTGACTTAAGTGCGCCCAGCTAGCCCTCTCTCTGTTTCTGGAGTCCTTGGGAGTTCCTGAGTCCCCCACTCACACGCTGACTGTCGCTATGGGCAGAAGGTACCCAGAGGCTCGAGGGTGTCCAAGCAGCTCATATCTCAAATTATAACCTGTTTCCTGCACCATTGCTGACGTCCAACGATCCATGTCAGAAGTACTTCCAGCTGACTCAGGTGTTGGCACCTTGGCAGTGTTTATGGCCAGCAGCGGATCCACAGACATTGCAAACCGGAACAGCCCAGCCACACCACCAAATACCCTCAATCTCCGTTCCTCCCACAATGAACTATTAAATGCAGAGATCAAACACTCAGATGCCAAGAACAGCACGCCCCCCAAATGCAGGAAAAAATATGCACTGACTAATATTCAGGCGGCCATGGGCCTCTCGGATCCAGCTGTACAGCCCCTGCTGGGAAACGGCTCTGCCAACATCAAGCTGGTTAAAAATGGGGAGAACCAGCTCCGCAAGGCTGCAGAACAGGGGCAGCAGGACCCCAACAAGAACCTCAGCCCTGCAGCCGTCATCAACCTAACCTCCGAGAAGCTGGAGGTTAAAGATCCCCACCCACAGGAGTCTTCAGGCTGTGAGATTTTGCCCTCCCAGCCCAGGAGAACTAAGAGCTTCCTCAATTACTATGCAGACCTGGAAACCTCGGCTAGAGAGCTAGGGCAGAACCTGGGCCCCTGCCAAGGGGTTGGAGAGGAGAAAGCCCAGCCTGGCCCAGGCCAGGCCCCAGTAGTCATTGGGAATGGTGACTTGCTGCCACAGAAACCAAACAAACCCCAATCCAGCCCAGAGGATGGCCAAGTAGCCACAGTATCGTCCAGCCCAGAGACCAAGAAAGACCACCCTAAAACAGGAGCCAAAACCGACTGTGCCCTCCATCGGATCCAGAACCTGGCACCAAGTGACGAGGAATCCAGCTGGACGACGCTGTCCCAAGACAGTGCCTCCCCCAGCTCCCCAGATGAAACAGATATCTGGAGTGATCACTCATTTCAGACAGATCCCGATTTGCCGCCGGGCTGGAAGAGAGTCAATGACATTGCCGGGACCTATTACTGGCACATCCCAACAGGGACGACTCAATGGGAACGGCCTGTCTCCATCCCAGCAGATCTCCACGGCTCTAGGAAAGGGTCACTTAGTTCTGTAACGCCATCGCCCACCCCAGAGAATGAGGATTTGCACGCAGCCACAGTTAACCCAGACCCCAGTTTAAAAGAGTTTGAAGGAGCAACGCTACGCTATGCATCCTTGAAACTCAGAAACGCCCCTCATGGTGATGACGATGATTCTTGTAGTATCAACAGTGACCCAGAAGCCAAGTGTTTTGCTGTGCGTTCTCTGGGCTGGGTAGAGATGGCCGAGGAGGACCTTGCCCCCGGGAAGAGCAGTGTCGCTGTCAACAACTGCATCCGACAGCTTTCCTACTGCAAAAACGACATCCGGGACACAGTCGGCATCTGGGGAGAGGGCAAAGACATGTACCTGAGCCTGGAAAACGACATGCTCAGCCTGGTGGACCCCATGGACCGCTCCGTGTTACACTCCCAGCCCATCGTGAACATCCGAGTGTGGGGCGTGGGCCGAGACAACGGCCG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TCGTGAACATCCGAGTGTGG
60.04
GGATTTTCCATCCGGCAAAGG
59.86
142
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CCCATCGTGAACATCCGAGT
59.82
GGATTTTCCATCCGGCAAAGG
59.86
146
PCR template sequence:
ACGACATGCTCAGCCTGGTGGACCCCATGGACCGCTCCGTGTTACACTCCCAGCCCATCGTGAACATCCGAGTGTGGGGCGTGGGCCGAGACAACGGCCGGTTGAGCCTCTGTAGGGAGCTGCTGTGCTCTCCAGCCAAGCATGCTGTGGTCAGATCTGCCCAGCCCTGGAATAGAATCCTTTGCCGGATGGAAAATCCA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
15
Interacting miRNAs (#binding sites)
mmu-miR-200a-3p(1), mmu-miR-19b-3p(1), mmu-miR-122-5p(1), mmu-miR-19a-3p(1), mmu-miR-203-3p(1), mmu-miR-326-3p(1), mmu-miR-214-3p(1), mmu-miR-370-3p(1), mmu-miR-324-3p(1), mmu-miR-705(1), mmu-miR-29b-2-5p(1), mmu-miR-129-5p(1), mmu-miR-673-5p(1), mmu-miR-5101(1), mmu-miR-484(1)
siRNAs for circular RNA silencing
Junction sequence
GAGACAACGGCCGGTTGAGCCTCTGT
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCAPBB2_1784_ORF_1
0.9281
0.326664695
0.999880943
1566
ORF sequence:
ATGTCAGAAGTACTTCCAGCTGACTCAGGTGTTGGCACCTTGGCAGTGTTTATGGCCAGCAGCGGATCCACAGACATTGCAAACCGGAACAGCCCAGCCACACCACCAAATACCCTCAATCTCCGTTCCTCCCACAATGAACTATTAAATGCAGAGATCAAACACTCAGATGCCAAGAACAGCACGCCCCCCAAATGCAGGAAAAAATATGCACTGACTAATATTCAGGCGGCCATGGGCCTCTCGGATCCAGCTGTACAGCCCCTGCTGGGAAACGGCTCTGCCAACATCAAGCTGGTTAAAAATGGGGAGAACCAGCTCCGCAAGGCTGCAGAACAGGGGCAGCAGGACCCCAACAAGAACCTCAGCCCTGCAGCCGTCATCAACCTAACCTCCGAGAAGCTGGAGGTTAAAGATCCCCACCCACAGGAGTCTTCAGGCTGTGAGATTTTGCCCTCCCAGCCCAGGAGAACTAAGAGCTTCCTCAATTACTATGCAGACCTGGAAACCTCGGCTAGAGAGCTAGGGCAGAACCTGGGCCCCTGCCAAGGGGTTGGAGAGGAGAAAGCCCAGCCTGGCCCAGGCCAGGCCCCAGTAGTCATTGGGAATGGTGACTTGCTGCCACAGAAACCAAACAAACCCCAATCCAGCCCAGAGGATGGCCAAGTAGCCACAGTATCGTCCAGCCCAGAGACCAAGAAAGACCACCCTAAAACAGGAGCCAAAACCGACTGTGCCCTCCATCGGATCCAGAACCTGGCACCAAGTGACGAGGAATCCAGCTGGACGACGCTGTCCCAAGACAGTGCCTCCCCCAGCTCCCCAGATGAAACAGATATCTGGAGTGATCACTCATTTCAGACAGATCCCGATTTGCCGCCGGGCTGGAAGAGAGTCAATGACATTGCCGGGACCTATTACTGGCACATCCCAACAGGGACGACTCAATGGGAACGGCCTGTCTCCATCCCAGCAGATCTCCACGGCTCTAGGAAAGGGTCACTTAGTTCTGTAACGCCATCGCCCACCCCAGAGAATGAGGATTTGCACGCAGCCACAGTTAACCCAGACCCCAGTTTAAAAGAGTTTGAAGGAGCAACGCTACGCTATGCATCCTTGAAACTCAGAAACGCCCCTCATGGTGATGACGATGATTCTTGTAGTATCAACAGTGACCCAGAAGCCAAGTGTTTTGCTGTGCGTTCTCTGGGCTGGGTAGAGATGGCCGAGGAGGACCTTGCCCCCGGGAAGAGCAGTGTCGCTGTCAACAACTGCATCCGACAGCTTTCCTACTGCAAAAACGACATCCGGGACACAGTCGGCATCTGGGGAGAGGGCAAAGACATGTACCTGAGCCTGGAAAACGACATGCTCAGCCTGGTGGACCCCATGGACCGCTCCGTGTTACACTCCCAGCCCATCGTGAACATCCGAGTGTGGGGCGTGGGCCGAGACAACGGCCGGTTGAGCCTCTGTAGGGAGCTGCTGTGCTCTCCAGCCAAGCATGCTGTGGTCAGATCTGCCCAGCCCTGGAATAGAATCCTTTGCCGGATGGAAAATCCATAA
Peptide sequence:
MSEVLPADSGVGTLAVFMASSGSTDIANRNSPATPPNTLNLRSSHNELLNAEIKHSDAKNSTPPKCRKKYALTNIQAAMGLSDPAVQPLLGNGSANIKLVKNGENQLRKAAEQGQQDPNKNLSPAAVINLTSEKLEVKDPHPQESSGCEILPSQPRRTKSFLNYYADLETSARELGQNLGPCQGVGEEKAQPGPGQAPVVIGNGDLLPQKPNKPQSSPEDGQVATVSSSPETKKDHPKTGAKTDCALHRIQNLAPSDEESSWTTLSQDSASPSSPDETDIWSDHSFQTDPDLPPGWKRVNDIAGTYYWHIPTGTTQWERPVSIPADLHGSRKGSLSSVTPSPTPENEDLHAATVNPDPSLKEFEGATLRYASLKLRNAPHGDDDDSCSINSDPEAKCFAVRSLGWVEMAEEDLAPGKSSVAVNNCIRQLSYCKNDIRDTVGIWGEGKDMYLSLENDMLSLVDPMDRSVLHSQPIVNIRVWGVGRDNGRLSLCRELLCSPAKHAVVRSAQPWNRILCRMENP
IRESfinder result
IRESfinder score
0.456769233
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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