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mmu_circAbcc2_564
Basic information of circular RNA
PanCircBase ID:
mmu_circAbcc2_564
mm39_Chr. Position ID:
chr19|43798909|43803253|+
Gene name:
Abcc2
Transcript:
ENSMUST00000026208.6
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
12,13,14,15,16
Exon/intron offsets:
0,645,1960,2719,4217
Genomic length:
4344
Exon/intron sizes in nt:
13,81,47,85,67,127
Flanking exon/introns:
chr19:43797154-43798909|chr19:43803253-43805235
Splice length:
564
Other database IDs:
CIRCpedia: MMU_CIRCpedia_39335, circAtlas: mmu-Abcc2_0002
Human Ortholog IDs:
Mature spliced Sequence:
ATCCTGAAATACTTTGCCTGGGAACCTTCCTTTAAAGAGCAAGTGAACAGCATTCGGAAGAAAGAACTCAGGAACTTGCTGCGCTTCAGCCAGCTGCAGACGATTTTGATTTTCATCTTACACCTAACTCCAACCCTGGTGTCCGTGATCACATTTTCTGTTTACGTCCTGGTGGATAGTCAAAATGTTTTGAACGCGGAGAAGGCTTTCACCTCCATCACCCTCTTCAATATCCTGCGCTTTCCTCTGGCCATGCTTCCCATGGTGATCTCTTCAGTCATCCAGGCCAGCGTCTCTGTAGACCGGCTGGAGCAGTACCTGGGAAGCGATGATCTGGACTTGTCTGCCATTCGCCATGTCTGCCATTTTGATAAAGCTGTGCAGTTCTCAGAAGCCTCTTTTACTTGGGACCGGGACTTGGAAGCCACAATCCAAGATGTGAACCTGGACATAAAACCAGGCCAACTGGTGGCTGTGGTGGGCACTGTAGGCTCTGGGAAGTCCTCTTTGATATCAGCCATGCTGGGAGAAATGGAGAATGTCCATGGGCATATCACCATCAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GCACTGTAGGCTCTGGGAAG
60.11
CGCAGCAAGTTCCTGAGTTC
59.49
166
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AGGCTCTGGGAAGTCCTCTT
59.88
CGCAGCAAGTTCCTGAGTTC
59.49
159
PCR template sequence:
ACTGGTGGCTGTGGTGGGCACTGTAGGCTCTGGGAAGTCCTCTTTGATATCAGCCATGCTGGGAGAAATGGAGAATGTCCATGGGCATATCACCATCAAGATCCTGAAATACTTTGCCTGGGAACCTTCCTTTAAAGAGCAAGTGAACAGCATTCGGAAGAAAGAACTCAGGAACTTGCTGCGCTTCAGCCAGCTGCAGA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
5
Interacting miRNAs (#binding sites)
mmu-miR-139-5p(1), mmu-miR-136-5p(1), mmu-miR-29b-1-5p(1), mmu-miR-296-3p(1), mmu-miR-338-3p(1)
siRNAs for circular RNA silencing
Junction sequence
TATCACCATCAAGATCCTGAAATACT
siRNA sets
TATTTCAGGATCTTGATGG, TTTCAGGATCTTGATGGTG, GTATTTCAGGATCTTGATG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCABCC2_564_ORF_1
1.2016
0.348436296
0.991086054
876
ORF sequence:
ATGCTTCCCATGGTGATCTCTTCAGTCATCCAGGCCAGCGTCTCTGTAGACCGGCTGGAGCAGTACCTGGGAAGCGATGATCTGGACTTGTCTGCCATTCGCCATGTCTGCCATTTTGATAAAGCTGTGCAGTTCTCAGAAGCCTCTTTTACTTGGGACCGGGACTTGGAAGCCACAATCCAAGATGTGAACCTGGACATAAAACCAGGCCAACTGGTGGCTGTGGTGGGCACTGTAGGCTCTGGGAAGTCCTCTTTGATATCAGCCATGCTGGGAGAAATGGAGAATGTCCATGGGCATATCACCATCAAGATCCTGAAATACTTTGCCTGGGAACCTTCCTTTAAAGAGCAAGTGAACAGCATTCGGAAGAAAGAACTCAGGAACTTGCTGCGCTTCAGCCAGCTGCAGACGATTTTGATTTTCATCTTACACCTAACTCCAACCCTGGTGTCCGTGATCACATTTTCTGTTTACGTCCTGGTGGATAGTCAAAATGTTTTGAACGCGGAGAAGGCTTTCACCTCCATCACCCTCTTCAATATCCTGCGCTTTCCTCTGGCCATGCTTCCCATGGTGATCTCTTCAGTCATCCAGGCCAGCGTCTCTGTAGACCGGCTGGAGCAGTACCTGGGAAGCGATGATCTGGACTTGTCTGCCATTCGCCATGTCTGCCATTTTGATAAAGCTGTGCAGTTCTCAGAAGCCTCTTTTACTTGGGACCGGGACTTGGAAGCCACAATCCAAGATGTGAACCTGGACATAAAACCAGGCCAACTGGTGGCTGTGGTGGGCACTGTAGGCTCTGGGAAGTCCTCTTTGATATCAGCCATGCTGGGAGAAATGGAGAATGTCCATGGGCATATCACCATCAAG
Peptide sequence:
MLPMVISSVIQASVSVDRLEQYLGSDDLDLSAIRHVCHFDKAVQFSEASFTWDRDLEATIQDVNLDIKPGQLVAVVGTVGSGKSSLISAMLGEMENVHGHITIKILKYFAWEPSFKEQVNSIRKKELRNLLRFSQLQTILIFILHLTPTLVSVITFSVYVLVDSQNVLNAEKAFTSITLFNILRFPLAMLPMVISSVIQASVSVDRLEQYLGSDDLDLSAIRHVCHFDKAVQFSEASFTWDRDLEATIQDVNLDIKPGQLVAVVGTVGSGKSSLISAMLGEMENVHGHITIK
IRESfinder result
IRESfinder score
0.654756376
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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