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mmu_ciSdf2_4813
Basic information of circular RNA
PanCircBase ID:
mmu_ciSdf2_4813
mm39_Chr. Position ID:
chr11|78136996|78141809|+
Gene name:
Sdf2
Transcript:
ENSMUST00000002133.9
CircRNA type:
Circular intronic (ci)RNA
Exon/Intron count:
1
Exon/intron indexes:
1
Exon/intron offsets:
0
Genomic length:
4813
Exon/intron sizes in nt:
4813
Flanking exon/introns:
chr11:78136996-78141841
Splice length:
4813
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GTACAGAGGGGGACTCACCGCTCTGGGTGGGCTGCCTAGGCCGGGTGAGCCTAGAAGGGGCGGGGCCTCGGAGTCTGAGGGCGTGGTCTGGGAAAGTTAGCCGTGCCCTATTTCTTGAAGAGGACGACGAGTTGCCAAGGAAACTTAGTCCTAATGTTAGTTTCTGTTTGATGAGCTGTGGGCCAAACGTGTTACATATATACTTTCCGGTTTTTAACATTGTATTGAGGACAGATACTAAAGTTATTTTCTTAGGTGAGTAAATAGACCTAGAGATATTGCTCAAAGCCAGCTAGTGAATGATGGAGACAGGGTTTAATCCAAATCTGTGCAGGTTCAAAATCTTTCAGATTCCATGGGCTGCCACTATTTTGTGCTGGAGAGAGGAGCATTTAGAGCAAGACAACATAAGCTGAATCTCAGATTTTAAATGTCACCTATTTTTAGCTCATATTTTTTGACACTCTAACTTAGCAATAACTTTCTTGTAAAGAATTTAAGCATTGACAGACATTGCAGAGGAAAGTCTGTTTTTTATCATGTGCAATTAAAATACTCACTTATTCGTGGGCTCATTCATTTGGCCTAGATTTAAAGAGCACTTTTAGTGTGTCTCGTATTGTTCTAGATACAGGAAATACAGTAGTGAATCAAACAATAAAACAAGACTAATGGGCAGGCGTGGTGGCCTAGGTCTGTAATTGTAGCACTCAAAAGGTTGAAGCAGGATTGTAACTTCAAGATCAGCCTAGCCTATATAGTGGGGGCTGTCTCAAAACAACAGAAGTTCAAAGGCTGGTAATTACTTCAGTGTTAGAGTATTTGCCGAGCATACGGAAAGCTTCTGCCCCCACACTGGAGGAAATAAAGTCATGAAGTTCGACAGGAGGTGTACTTGTGATATAATTTGAATGATTGATGATGCTATTTGCTAGAAAGGAAGTGACCTTCTAAGATGGTTAGTCTGTTCACAACTCTCAGAACCTGTCTTACCAGTTTAGTCCAGGGAGTATGTAGTCTTTACATTCCTAACCACCTCATTCAGTAAACACCTACTCAGGCTTACTACATTCTTTTTTTTTTTTTTTTTCTTTTTCTCGAGACAGGGTTTCTCTGTGTAGCCCTGGCTGTCCTGGAACTCACTTTGTAGACCAGGCTGGCCTCGAACTCAGAAATCCGCCTGCTGCTGCCTCCCAAGTGCTGGGATTAAAGGCATGCGCCACCACTGCCCGGCAGTTTTACTACGTTTTAATTTAATGTTTCCTGCTCTGGCTCTACTAAATAAAAATGGAGTTAGGCTGGGCGGTGGTGGTAGAGCAGGAGGCATTTAGTCTTAATATTCTGGAGGCAGAGAGAGGCAGGATCTCTGAAGACAGCCACTCTACCTAGAGAATTTCAGACCAGCCAGTGCTACACAGTGAGACACTGCCTCAACAAACAAAAATCCAAATTAGCAGTCGGGTGGTGGTGGGCCATTCCTTTAATCCCAACACTTAGGAAGCAGAGGCAGGTGGATCTCTTTGAATTTCAGGTCAGCCTGGTCTACAGAGTGAGTTCCAAGACAGCTAGGACTACACAGAGAAACCCTGTCTCGATAAAAAAATAAAAATCAAAAAATCAAAATCATTTAAACGAAGAACTTGGATTAGCCCTCTTGGGGGATGGGTTTGTGCATCATCTATTCAGATGCTAATTTCTATGCTTCTCTTTAACTGCAGTCCAGAAGTTGGCCAGGTTAAGCACTTCCAGTTTCAGTGTTATGCAAAAATTGTTATCCGTCACCTCTGATTGGTTAATAAAGAGCTGATTCAGCCAATGACTGAGCAGAGGAGAGAGGGAAGGCAGGACTTCCCGTCCCAGTCATGGGGTCCCACAGAGGAGTGAGAAGGGGTTGGGGGAGGAAGAAGAAAAGAAGATATGGAGGGACCAGGAGTGGCCATGAGAACACAGGTGGAGCAGAGTGGGGCTGATGAGGCTCAGGTCACAGGTGAACGACCATGAGGCTGGGGAGTAGCCAAGCTAGCACAGTAGAATAGATGACTTTCTGTCTAGCTATAGGGCTCACAGCCTTTTAATACATTTATTAGGTTCCTGTGCCTTTTATTCAGGGACCAAAAAGGACTAGAATGGACCAAGAAACGCCTTGTCCTTATTTGGGAGCAAAAGGGGTGGAGCAAATCCCCCAATTACTTTTACATAGCCCAATACCTGATGATAGTACATTTTCCTTTTTAAGAGCTACAGCTGCTGGGCAGTGGTGGCGCATACTTTTAATCCCAGCACTTGGGAGGCAGAGGCAGCGGATTTCTGAATTGGAGGCCAGCCTGGTCTACAAAGTGAGTTCCAGGACAGCCAGGGCTACACAGAGAAACCCAGTCTTGAAAAACAAACAAGCAAACAAAAGAGCTACAGTTATTTACATACATACAGTTACTCAATGTTTTCACCATGCACAATTATATTAGCTAAGGTATGGCTACAAATTTGTATGATCTAAAAATATTTTATTGTGGCTTTTTGAGACAAGGCTTTACTATACAGTCCTAACTAGAGTAAAACTTGCCAAAAGACAACTTGGGGCGTGTTGACTGTCTCCTACTGTGAATCTTCAGAATTGAACTCAAGTATAACTCCAAAATACCTTTAACCATTGATCCAATTCATTGGCTCTTTTTATGCTTAGATTTGTGTATCACTGGGCTTGGTGACCCTGTTTCAAAACAAGAAAGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTATGTATGTTCGTGAGTGTTTTTTTCAAGATGGTTTCTGTGTGTAACAGAGCCCTGACTGTCCTGGAACTCACAGACATCTGCCTGCCTCTGCCTTGGTATGCTACCATGCCTGACTCCCTTTTATAGTTTTTACCTGAGTTCTGGAAATTGATGTTAAGCTAGCATGGCTAATACTTTTTCCCACTAAGCCATCTCCCTTGCCCCCACTCTGTGTCTTGAGGCATGATCTATCATGGGGACCTGGGGCTCACCAGGCTGGCTAGGCTGGCTTGGCAGTAAGCTGAAGGCTGCTTGTGACATCTTCCCAGTGCTGGGATTACGGGCACAGTTCACAGTGCCTGTCCTTTTTTATGTGGGTTCTGAAGGTGGAACTCGAATAATCAGGCCTGGTAACCAGAAAACAACTTGCAGGCATCATTCTCTTTCTACTGTGTGGCTCTGGGGTGGAACTTAGGCTGGGGCTTAGGCAGCCTGTGCCTTCACCCTTGGGTATCTCCCTGGTCCTTTCACACCCGTTTAAGCGTACTCATTGAGTGTGTCTTAAATGTCAATGTTGTGGAAGTAATATATTCCCAAACGTATGTTTCCTCCCCTCCATGCCATTTGTGACACGGGGCACATCCTTGGCCCCAGAAGAGGAAGGGCTTAGGTTGAGCTCCCTTGGCCTGTCTTTTATCAGTTTAATTAGTTGTACTGTTAGCTCTGGTTAGTGCAGAAAGGGAGCCAAAAGCTCACAGGCTACTACTCAGTTTTACAAGACCCCATTCAGGGAAAAGAAAGGCTGGTATTGGGCTGGAGAGATGGCTCAGCAGTTAAGAGTACTGACTGCTCTTCCAAAGGTCCTGAGTTCAAATCCCAGCAACCACATGGTTGCTCACAGTCATCTTTAATGAGATCTGATGCCCTCTTCTGGTGCATCTGAAGACAACTACAGTGTACTTAGATATATTAATAAATTAAAAAAAAAAAAAAGAAAGGCTGGTATTTGCCAACAATATCCAGGTTCTTGGATACATTCCTTAGGAAGGGGGTCTCAATCCTAGAGAGGGCATACCTAGCATGGGTACCCCTCAATCAGAGGATCAGAGGAAGGCTAACTGATGACCCCGTGGGTGATCTCAGACCATCACACATGCCATGATTCATGGTGGTGGGGCCCCCCATCTTGGCAGGACCTCAGTGGGAGATGTGAAGTTGTCATTGGCAGTCACAGCAACAGCTGCTGCAGTCCCTCTTCTCTATGCTCTCACTACCTCCCAGGATGGATCTCCAGCTACTCAGACATGGCCTTCTGGGATTGGGTACCTTAGCTGGAACTCCTCTGCTAACCTTTCTCTCAATCCCAGAATCCCCAGCAGGAGGAGTAAGGAGCATCCAAGTATCCAGTATCTTTAGAAGGTAGCTTTTTCATAGCCAATGATATCAAGTTCTCTGCACATAACTCTAGACCTAAAACCTGTTTTTCTTCATACTCTGGCTATTTAGCATCTTGTCTCGTGATTTGGCTGAATTCATCACAGCTACAGAGGATCGAATTCATGTGCTTGTCCAAGGCCTTAAAGGTTCAATGAAGATTCACAAATGGCTCTCACAGGACATCTTATTCCATAGTCAGTATGCTACAACTTGGTGTCCTTGCGTCTGTCCTTAGTTCAGTCACAGTCATGACTGGTGTTCCATAATACCCAGTGTTTAAGAAATGTTGGTGGCTGGAGAGATGGCTCAGCTGGTTAAGAGCACTAACTGCTCTTCCAGAGGTTCTGAGTTAAATTCCCAGCAACCACATGGTGGCTCAAAACCATCTGAAATGGGATCTGATGCCTTCTTCTGGTGTGTCTGAAGACAGCTACAGTGTACTATATATATATAATGATTAAGTAAATCTTAAAAAAAAAAAAAAGGAGTGAAATGTCAAGATCTAGAGATGCTGTAGAAGGAGGTGTGATAGAGGTTTTCCTAGGAGCCAAGCAAGCTTAGCAGAAGTTTTCCTTGATTACTCCCATCAAGGCACAAACAGCTTGTCAGGGCGTTGGTCATCCCCAGACTGC
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GCACAAACAGCTTGTCAGGG
59.97
TAACTTTCCCAGACCACGCC
59.96
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GGCACAAACAGCTTGTCAGG
59.97
TAACTTTCCCAGACCACGCC
59.96
141
PCR template sequence:
AGGTTTTCCTAGGAGCCAAGCAAGCTTAGCAGAAGTTTTCCTTGATTACTCCCATCAAGGCACAAACAGCTTGTCAGGGCGTTGGTCATCCCCAGACTGCGTACAGAGGGGGACTCACCGCTCTGGGTGGGCTGCCTAGGCCGGGTGAGCCTAGAAGGGGCGGGGCCTCGGAGTCTGAGGGCGTGGTCTGGGAAAGTTAG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
54
Interacting miRNAs (#binding sites)
mmu-miR-382-5p(3), mmu-miR-5101(3), mmu-miR-1a-3p(2), mmu-miR-206-3p(2), mmu-miR-298-5p(2), mmu-miR-709(2), mmu-miR-339-5p(2), mmu-miR-494-3p(2), mmu-miR-466d-3p(2), mmu-miR-3087-3p(2), mmu-miR-3470b(2), mmu-miR-466b-3p(2), mmu-miR-670-5p(2), mmu-miR-124-3p(1), mmu-miR-20b-5p(1), mmu-miR-134-5p(1), mmu-miR-296-5p(1), mmu-let-7a-5p(1), mmu-miR-16-5p(1), mmu-miR-200a-3p(1), mmu-miR-141-3p(1), mmu-miR-93-5p(1), mmu-miR-20a-5p(1), mmu-miR-17-5p(1), mmu-miR-32-5p(1), mmu-let-7e-5p(1), mmu-let-7b-5p(1), mmu-miR-34c-5p(1), mmu-miR-34a-5p(1), mmu-miR-31-5p(1), mmu-miR-200c-3p(1), mmu-miR-101a-3p(1), mmu-let-7c-5p(1), mmu-miR-146a-5p(1), mmu-let-7d-5p(1), mmu-miR-149-5p(1), mmu-miR-136-5p(1), mmu-miR-351-5p(1), mmu-miR-382-3p(1), mmu-miR-22-3p(1), mmu-miR-411-3p(1), mmu-miR-501-3p(1), mmu-miR-182-5p(1), mmu-miR-370-3p(1), mmu-miR-324-3p(1), mmu-miR-34b-5p(1), mmu-miR-297a-5p(1), mmu-miR-98-5p(1), mmu-miR-1187(1), mmu-miR-335-3p(1), mmu-miR-532-5p(1), mmu-miR-484(1), mmu-miR-490-3p(1), mmu-miR-146b-5p(1)
siRNAs for circular RNA silencing
Junction sequence
ATCCCCAGACTGCGTACAGAGGGGGA
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
NA
NA
NA
NA
NA
ORF sequence:
NA
Peptide sequence:
NA
IRESfinder result
IRESfinder score
0.770276564
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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