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mmu_circAbca8b_1004
Basic information of circular RNA
PanCircBase ID:
mmu_circAbca8b_1004
mm39_Chr. Position ID:
chr11|109826541|109833183|-
Gene name:
Abca8b
Transcript:
ENSMUST00000020948.15
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
9
Exon/intron indexes:
37,36,35,34,33,32,31,30,29
Exon/intron offsets:
0,626,981,1991,2177,2723,5096,5830,6521
Genomic length:
6642
Exon/intron sizes in nt:
80,14,11,20,95,76,16,10,00,00,000
Flanking exon/introns:
chr11:109825604-109826541|chr11:109833183-109836592
Splice length:
1004
Other database IDs:
circAtlas: mmu-Abca8b_0023
CIRCpedia: HSA_CIRCpedia_368852
Human Ortholog IDs:
Mature spliced Sequence:
AATTTCTCCAAGAAACAATGATGTGTATCAAAACCCAGAAGAGCCAGAAGATGAGGATGAAGATGTTCAAATGGAGAGAATGAGAACAGCGAATGCCTTGGTATCCACCAGTTTTGATGAGAAGCCAGTCATCATTGCCAGCTGCCTACGCAAAGAATATGCAGGGAAGCAGAAGCATTGCCTTTCCAAGAAGAAGGCCAAGATAGCCACTAGGAATGTCTCGTTTTGTGTCAGGAAAGGTGAGATTCTAGGATTGTTGGGACACAATGGAGCTGGCAAAAGTACATCTCTTAAAATGATAAGTGGAGACACAAAAGTCACAGCTGGGCAGGTGTTACTGAAAGGGAGCAGAGAAGGGGACACCCCGGGGTTCCTGGGGTACTGTCCTCAGGAGAATGCTCTGTGGCCCAACCTCACTGTGAAGGAGCACCTGGAGATATTTGCTGCAGTGAGGGGCTTGCGCAAAAGTCACGCTGCAGTCGCCATCACAAGGTTGGCAGATGCGCTCAAGCTGCAGGACCAGCTGAAGTCTCCTGTGAAGACGCTGTCAGAGGGAGTGAAGAGAAAGCTGTGCTTCGTGCTGAGCATCCTGGGGAACCCATCTATATTGCTTCTAGATGAGCCGTCCACTGGGCTGGATCCTGAGGGGCAGCAGCAAATATGGCAAGCAATCAGGGCCATCATAAAAAATACAGACAGGGGTGCCCTGCTGACCACCCATTACATGGCAGAGGCTGAGGCTCTGTGTGACCGAGTGGCCATCCTGGTGTCTGGAAGGCTGAGGTGTATTGGATCCATCCAACATCTCAAAAGCAAATTTGGCAAAGATTACCTGCTGGAGATGAAGGTGAAGACCCTCGAGCAGGTGGAGCCCCTCAATACGGAGATCCTCAGGCTTTTTCCCCAGGCTTCTAGGCAGGAACGGTACTCTTCTCTGATGGCTTACAAATTACCAGTGGAAGCTGTACAGCCTTTATCCCAAGCTTTCTTCAAGTTAGAGAAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CAGGCTTCTAGGCAGGAACG
60.46
CATCTTCTGGCTCTTCTGGGT
59.44
153
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CAGGCTTCTAGGCAGGAACG
60.46
TCTTCTGGCTCTTCTGGGTT
58.27
151
PCR template sequence:
CAGGCTTCTAGGCAGGAACGGTACTCTTCTCTGATGGCTTACAAATTACCAGTGGAAGCTGTACAGCCTTTATCCCAAGCTTTCTTCAAGTTAGAGAAAGAATTTCTCCAAGAAACAATGATGTGTATCAAAACCCAGAAGAGCCAGAAGATGAGGATGAAGATGTTCAAATGGAGAGAATGAGAACAGCGAATGCCTTG
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-136-5p(2), mmu-miR-101a-3p(1), mmu-miR-205-5p(1), mmu-miR-377-3p(1), mmu-miR-5101(1), mmu-miR-1904(1)
siRNAs for circular RNA silencing
Junction sequence
AAGTTAGAGAAAGAATTTCTCCAAGA
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCABCA8B_1004_ORF_1
1.0778
0.210458816
0.992708797
1017
ORF sequence:
ATGGAGAGAATGAGAACAGCGAATGCCTTGGTATCCACCAGTTTTGATGAGAAGCCAGTCATCATTGCCAGCTGCCTACGCAAAGAATATGCAGGGAAGCAGAAGCATTGCCTTTCCAAGAAGAAGGCCAAGATAGCCACTAGGAATGTCTCGTTTTGTGTCAGGAAAGGTGAGATTCTAGGATTGTTGGGACACAATGGAGCTGGCAAAAGTACATCTCTTAAAATGATAAGTGGAGACACAAAAGTCACAGCTGGGCAGGTGTTACTGAAAGGGAGCAGAGAAGGGGACACCCCGGGGTTCCTGGGGTACTGTCCTCAGGAGAATGCTCTGTGGCCCAACCTCACTGTGAAGGAGCACCTGGAGATATTTGCTGCAGTGAGGGGCTTGCGCAAAAGTCACGCTGCAGTCGCCATCACAAGGTTGGCAGATGCGCTCAAGCTGCAGGACCAGCTGAAGTCTCCTGTGAAGACGCTGTCAGAGGGAGTGAAGAGAAAGCTGTGCTTCGTGCTGAGCATCCTGGGGAACCCATCTATATTGCTTCTAGATGAGCCGTCCACTGGGCTGGATCCTGAGGGGCAGCAGCAAATATGGCAAGCAATCAGGGCCATCATAAAAAATACAGACAGGGGTGCCCTGCTGACCACCCATTACATGGCAGAGGCTGAGGCTCTGTGTGACCGAGTGGCCATCCTGGTGTCTGGAAGGCTGAGGTGTATTGGATCCATCCAACATCTCAAAAGCAAATTTGGCAAAGATTACCTGCTGGAGATGAAGGTGAAGACCCTCGAGCAGGTGGAGCCCCTCAATACGGAGATCCTCAGGCTTTTTCCCCAGGCTTCTAGGCAGGAACGGTACTCTTCTCTGATGGCTTACAAATTACCAGTGGAAGCTGTACAGCCTTTATCCCAAGCTTTCTTCAAGTTAGAGAAAGAATTTCTCCAAGAAACAATGATGTGTATCAAAACCCAGAAGAGCCAGAAGATGAGGATGAAGATGTTCAAATGGAGAGAATGA
Peptide sequence:
MERMRTANALVSTSFDEKPVIIASCLRKEYAGKQKHCLSKKKAKIATRNVSFCVRKGEILGLLGHNGAGKSTSLKMISGDTKVTAGQVLLKGSREGDTPGFLGYCPQENALWPNLTVKEHLEIFAAVRGLRKSHAAVAITRLADALKLQDQLKSPVKTLSEGVKRKLCFVLSILGNPSILLLDEPSTGLDPEGQQQIWQAIRAIIKNTDRGALLTTHYMAEAEALCDRVAILVSGRLRCIGSIQHLKSKFGKDYLLEMKVKTLEQVEPLNTEILRLFPQASRQERYSSLMAYKLPVEAVQPLSQAFFKLEKEFLQETMMCIKTQKSQKMRMKMFKWRE
IRESfinder result
IRESfinder score
0.384547421
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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