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mmu_circSetdb1_3049
Basic information of circular RNA
PanCircBase ID:
mmu_circSetdb1_3049
mm39_Chr. Position ID:
chr3|95244459|95257184|-
Gene name:
Setdb1
Transcript:
ENSMUST00000124638.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
10
Exon/intron indexes:
13,12,11,10,9,8,7,6,5,4
Exon/intron offsets:
0,2758,3013,4185,4507,8377,9466,9847,10847,12690
Genomic length:
12725
Exon/intron sizes in nt:
1884,156,151,130,191,74,202,126,100,35
Flanking exon/introns:
chr3:95236028-95244459|chr3:95257184-95261852
Splice length:
3049
Other database IDs:
CIRCpedia: MMU_CIRCpedia_227369, circAtlas: mmu-Setdb1_0003
Human Ortholog IDs:
Mature spliced Sequence:
GTGATGCTGGGAGCAGAACTCCAAAAGACCAGAAGCTTCGTGAAGCTATGGCTGCCTTAAGAAAATCAGCTCAAGATGTCCAGAAGTTCATGGATGCTGTCAACAAGAAAAGCAGTTCTCAAGATCTACATAAAGGAACCTTGGGTCAGGTGTCTGGAGAACTGAGCAAAGATGGGGACCTGATAGTCAGCATGCGGATTCTGGGCAAGAAGAGGACTAAGACATGGCACAAAGGCACCCTTATTGCCATCCAGACTGTTGGGCTAGGAAAAAAATACAAAGTGAAATTTGACAACAAAGGAAAGAGTCTGCTATCTGGGAACCATATTGCCTATGATTACCACCCTCCCGCTGACAAGCTGTTTGTGGGCAGTCGAGTGGTGGCCAAGTACAAAGATGGAAATCAGGTCTGGCTTTATGCTGGCATTGTAGCTGAGACCCCTAACGTCAAGAACAAGCTCAGATTTTTAATTTTTTTTGATGATGGCTATGCTTCCTATGTCACTCAGTCAGAGCTTTATCCCATTTGCCGACCACTAAAAAAGACTTGGGAGGACATAGAAGATAGCTCCTGCCGAGACTTCATAGAGGAATATATCACTGCCTATCCAAACCGCCCAATGGTACTTCTCAAGAGTGGGCAGCTTATCAAGACTGAGTGGGAAGGCACATGGTGGAAGTCTCGAGTTGAAGAGGTGGATGGCAGCCTAGTCAGGATCCTCTTTCTGGATGACAAAAGATGTGAGTGGATATATCGAGGCTCTACACGCCTGGAACCTATGTTTAGTATGAAGACATCCTCAGCCTCTGCAATGGAGAAGAAGCAAGGGGGGCAACTCAGAACCCGTCCTAATATGGGTGCTGTGAGGAGCAAAGGTCCTGTTGTTCAGTATACACAGGATCTAACTGGTACTGGAATCCAGTTTAAGCCCATGGAGCCCCTACAGCCTATAGCTCCACCGGCCCCACTTCCTATACCTCCTCTTTCCCCCCAAGCAGCTGACACTGACTTAGAAAGCCAACTTGCACAATCACGGAAACAAGTAGCCAAGAAGAGCACATCATTCCGACCAGGATCTGTGGGCTCCGGCCATTCCTCCCCTACTTCATCCACACTCAGTGAAAATGTGTCTGCTGGGAAACTTGGGATAAACCAGACATATCGGTCACCTTTGGCCTCAGTAACATCTACCCCAGCATCTGCAGCCCCTCCAGTCCCTCCAGTCCCACCAGGGCCTCCAACCCCTCCAGGGCCTCCAGCTCCTCCAGGGCCTCTAGCTCCTCCAGCCTTCCATGGCATGTTAGAGCGGGCACCAGCTGAGCCCTCCTACCGAGCCCCCATGGAGAAGCTTTTCTATTTACCTCATGTCTGCAGTTACACTTGTTTGTCCCGGATCAGACCCATGAGAAACGAACAGTATCGGGGCAAGAACCCTCTATTAGTTCCACTTCTGTATGACTTCCGGAGGATGACAGCACGGCGCAGAGTTAACCGCAAAATGGGCTTTCATGTAATCTATAAGACACCCTGTGGTCTCTGCCTTCGGACGATGCAGGAGATAGAGCGCTACCTTTTTGAGACTGGCTGTGACTTTCTGTTCCTGGAGATGTTCTGTTTGGATCCATATGTTCTTGTTGACAGAAAGTTTCAACCCTTTAAGCCTTTTTACTATATTTTGGACATCACCTATGGCAAGGAAGATGTTCCCCTGTCCTGTGTTAATGAGATTGACACAACTCCCCCACCCCAGGTGGCCTACAGCAAGGAACGCATTCCTGGCAAGGGTGTTTTCATTAACACAGGCCCTGAATTTCTGGTTGGCTGTGACTGCAAGGATGGGTGTCGGGATAAGTGAGTTGGTGGGGTGTACAGGCATTGCTGTCTCTGCCTTCAGGTTTATTACAGTTGCTTTTCTTTTCTTTTTTATTTGTATTGCTTTCCCTGTTTTCCTTTACCTCCTCTTTCAGCTAGAGTTCTGCTAAGGTCATTATGAAATACAGATACAGAAACTGGGTACAGTGGCACATACCTGTAACTTCAGAATTTGAAATTCAGCATTGTGGCAGTTTCATCTTGAGTTCTGGGCCAGCCTAGGCTTCATAATAACTTTGAAGCTAGGCTGAGCTAGCTACGCAGTGAGATCTTATTGAAAGAGAGAGAGAGAGAGGGAGAATGAATGAACATGAGATAGGGAGACCAGGGTCTGATCGTCTTAAATGTCCCCAGGAGTAACCCTGGAAATGTAGGGGTTATGTTCTGTTCCTGTCTCCTCTTGCTGTTTCTGTCTCCCCTTAACCTTTCATCCTTGTGTTCACCATTTAGATTCTACTTTATTCTCACTGTATCTTACTCATGCTTTTTCTCACTACCTTTACCTTATCCCCATCCTCTGTTATTGGTTGATTTTTGCCCTAAGGTAAGGTTTGTTGAGGGAGTCCCTGGTGACTAAGGATGAGGCCTCGAAAGTTCCTCGCAAGGGAAAGAGTTTCCATAACCAAGATCTGCTTAAAAATATGGCTTTAGCTCCACCTTTCCTACAGCTCGGCCTGCTTCATATTCAGCATGGCCCTGGAGGTTAGAGCCTTTGGTATTTCTCACATTTTAGGAAGTCCTTGCCAACAAAGTCACTCAGCCAGTGCACCTCCTGTGCACTCAGCCAGTGGTACCACACATGGGCACCTTGGGCCTGGCAGAGCCTGACCTGAGATGAATGACTGCAGCTAGCAAGTCCTAAGTTGTGGACTCAACTCAGTTTTGATTTAAGACCGCTCAAGCTGGCCCAGAACTTACTAGCTGAGGATAGCAGTTAACTCCTGATCCTCCCACCTCTATGTCTCAGATATTGGATTACAGATGTAGATCACTGTGTCCAGTTCCCATCCTCATGAACCTCAGAAAACCACAACTCTAGTCACCCTTTTCTCTCTGCAGATCCAAATGTGCCTGCCACCAGCTAACTATCCAGGCCACAGCCTGTACCCCAGGGGGCCAAGTCAACCCTAACTCTGGCTACCAGTATAAAAGACTAGAAGAGTGTCTGCCCACAGG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GGGCCAAGTCAACCCTAACT
59.6
AGCATCCATGAACTTCTGGACA
59.69
161
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GGGCCAAGTCAACCCTAACT
59.6
ACAGCATCCATGAACTTCTGGA
59.69
163
PCR template sequence:
ACCAGCTAACTATCCAGGCCACAGCCTGTACCCCAGGGGGCCAAGTCAACCCTAACTCTGGCTACCAGTATAAAAGACTAGAAGAGTGTCTGCCCACAGGGTGATGCTGGGAGCAGAACTCCAAAAGACCAGAAGCTTCGTGAAGCTATGGCTGCCTTAAGAAAATCAGCTCAAGATGTCCAGAAGTTCATGGATGCTGT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
26
Interacting miRNAs (#binding sites)
mmu-miR-150-5p(1), mmu-miR-146a-5p(1), mmu-miR-298-5p(1), mmu-miR-132-3p(1), mmu-miR-709(1), mmu-miR-320-3p(1), mmu-miR-214-3p(1), mmu-miR-128-3p(1), mmu-miR-24-3p(1), mmu-miR-22-3p(1), mmu-miR-224-5p(1), mmu-miR-705(1), mmu-miR-27a-5p(1), mmu-miR-466a-5p(1), mmu-miR-1198-5p(1), mmu-miR-466p-5p(1), mmu-miR-190b-5p(1), mmu-miR-673-5p(1), mmu-miR-3087-3p(1), mmu-miR-484(1), mmu-miR-1904(1), mmu-miR-574-5p(1), mmu-miR-146b-5p(1), mmu-miR-296-3p(1), mmu-miR-202-3p(1), mmu-miR-338-3p(1)
siRNAs for circular RNA silencing
Junction sequence
GTCTGCCCACAGGGTGATGCTGGGAG
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
0.667915244
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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