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mmu_ciEdem2_4093
Basic information of circular RNA
PanCircBase ID:
mmu_ciEdem2_4093
mm39_Chr. Position ID:
chr2|155564461|155568554|-
Gene name:
Edem2
Transcript:
ENSMUST00000040833.5
CircRNA type:
Circular intronic (ci)RNA
Exon/Intron count:
1
Exon/intron indexes:
3
Exon/intron offsets:
0
Genomic length:
4093
Exon/intron sizes in nt:
4093
Flanking exon/introns:
chr2:155564457-155568554
Splice length:
4093
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GTAAGTATCCCATCTGTTTGTTTCCCACTCTGTCATTGCCCAACCGACATCCTTCCTCTTTTAATAGCTTGTCTGTGGGTGCAAAGTAAATTCCTCCCCTAGGCCTTTCATCTCATGATTCTGAGCCACCAGACTCTGGTTACCCAACTGCATAGGAGGGAATGCCAAGTTCCAAGAGAAACCAACTCGCACAGGTTCATTTGTTCGTTGAGCAAATATTTGCAGGGGGCCTGTGGTAGACATGCATAGCTCAGTGAGAGACAGAGGGACATTGACACCGTCCTTTTCAAAAGCTTATTATATTCTAGTTAGCCACGTGCAGTGACAAAAAGAGAATAACAAAGCCAACCACTCTGTCACATACATGGCTTGTACGAAGTCCTTTACAGGTTATACTAGTCACTTTCTATCATCGCGGCGACCACACGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAACATCTTAAAAGGAGGAAGAATGTATTTTGGCTCACAGTCCCAGAGGCCTCATACACGGTGGCCTACCCCATGTGCTTGGGCAATAATGTGGCAGAGAGATGATGCTTTGTCTCATGGTTGATAGGAGTCAGAGATCAGGAGACAGGAATGGGCCAAGGACAAGGTACCCACCCCAAGTTGTGCCTCCCACCCCCAACTTACTTCCTCCACTTGATAAGGTTTCCATAACCTGTGCTGCCTCCTGGGAACCTAGGCTTCGCGCAGCTTGTCATGATTGCTTCTTACTCAAATTGCAACACATGCATTGTGCTATTTAGTCCCTTCCCATAGTCTCCTGGCTTTATTAGTTCATTCTTTTATTCCTTTTTACAGCTGAGGAAATAGGATTCTTAGGAATGCAATGCTGAGAAAGGTAAAAACAGAACTCGGACCTAAACTTAACTTTATGTGACACCAATCCTTGATTGCCTTCTGCCCTGCTTACTCCCTTCCAGGGTTTTGTTGTTTAGCCAGGAAGACCTCAAACTTGGTAATCCTCTTGCCTCAGCCTCCCAAGTGCTGAGATTATAAAGATTTACCAGTATGCCTGGCCACTTCTCATTTTTATACATCTATAGTATTTATATGACTATGAACACTACGTAGATATGGTTTGGCTTATACTTTTTGTTTAATGTTAATTTGTATGTTTCTATCTATCTATCAATCTATCAAATATTTATTGAGGACAGCTATGTACCAAGCATGGTGCTAAACTTTGAAGTCAAAATGGTAGGTTCAAACAGAAATGATCTACACTTACCTGGAGTTTGAGATGTTAGCACCAGGATCAAAAAATAGCAATAAAAGATGATAACCACATATTGAGGCCAAAGCTTTGTATTGCAAAGGCCCAAACACAAAATGATCTGGTGTGTGCCTTTAGCTCTGGCACTCAGAAAGAAGAAGCAGAGGCAGGCTGATCTCTGAGGTCAAGGAGTGACCTGTGGAGTGAGTTCCAGGACAGCTAGAGCTATATAAAAGAAACTATCTCAAAAAAAAAAAAAAACCCTAAACAAACAACAAACACCGATCTGACCTAGCCAAGGATTTTGGAGAACTTCTCTGAGGCAGTGATGTGCAGCTGGAGTTAGAATTTGACGGAGAAGCTGGCAGTAACTGGGAAGGTGATAGAAGAGGGTGCTGTAGGCCAGCTAGCATGGAGGCTTTGTGGCAGGAGAGTAAAGCGGGTGAGTGGAAGGGAGGCAGTGTGCTGGGGTTGAGAGAGAGAAGGGTATGTGGGGTCTGGAGGTGGACGCTCCACTTCACCGCATTGTGATCATTCACTGGACAATACAGGAGCTCCACTGGCATCTCTTACGTACAAGTCAGGAAGTGGTGAGATGACAGCTTTGAGATCACTGGCCGCCTTGTAAACAAGATTTGTGTTCTCATTCACCACATTTGCCAAGTAATTGCTTCCTGAGCTGTGTCTGGCACTCTGAGGAAGTACAAGAATGGGAGATGCCTCTGCTGTTGTGAAGGGGAACGGAGACCCTAACAGTAGAATACATAGAGCTCAGAAGGACTTTTAGAAGAAGAAAAGGTTGAGAGAAGTACCAGGCATCCTAGAGTAGGTGACACAGGCCAGGGAAGGCTTGGATTTATAAATGGAAGACGTAGGAGGGAGCTACTTCTGGTGGAGGAAACAGGAAACTGAGGAAGACTGGGCACAGAGGAAGGTGAATGGTGAAAGAGACAGGACAGAGGTAGGCTGGCTCCAGGTCCTAGAGAAACTGAGTGTTGGGATAGTCAGGAATTGTCTGGGCTACAAATTGCAGAACCTCGATTCAACTGACTGAGATAAGAAGACAAACTTACTGAATCAGATAACTAAAAAGCCCAGGTCAAGGCTGACCTCAGACCCGATCCAGACAGACAAATGACGTCAATCAGAGTCCCCTTCCACCTTTTATCTCTGCTTTCTTGGCTGCTGTGTTCTCAGTCTCCATAAAAGGTCGGTCAGCCAATTGCCATTCCTATCTCCTTCTTCGCAAGTTTAAGAAACAGTATGTTCAAAGAAGCACCCTTCCCCCTTAGTCCAAGCAGTAAGTCTTCATAGGTCAGGCTTGGGTCACATATATATTCCCGAACTGTCTCTGGTAAAGGGGTATGGTATTACGGCTGATACCAGTAAGACACCCACTCCACAGCTGGGGACATGGGGTCCTGAATTACAGGAGTGACTCTGGGAAGAAGAGTATTCAAGGGAAATTTGGGGTGATAATAGCAGAAAAAACGGTAATATTATGTGTCAAGCTAGGTGGGGTGGCACGTGACTGTAAACGCAGCGATAGTTGGAGTCGGGAACATCAGCAGTCCGAGGCCATTCTTGCCTTACATAGTGAGTTCGAGGCCAGCCTGGTCTGTACGAGAACATCTCAAACAAACAAGTTTGTTCTCTCCCTCCCTCCCTCCTCCTCTCTCTCCTTCTCTCCCCTCCCCTATCCCCTCTCTCTCTCCATGTATGTATATTCATATACAACACATATATGTATATACAAGTATATATGTAGATGCACATATACATATCTAGCATTGGACTAGATTTAACCAGATTTATTTTCCCAAGTAAAGGAAAGGATATGGTTTAGGCGATAGACTACTTGCCTTCTGCATGCAGCCATGAGTTCAATCCCCATCAACCTCAGATGGATAAGAACCACAAAGCTACATGAAAATGCGACTCATCCTTTAAGCATACGGTTTGGGGGCTGGAGAGGTGGCTCAGTGGTTAAGAGAACTGTTACTCTCGCAGAGGACCTAAGTTTCGGTCTCAGTACCCATACGGTAGCTCACAGCCATCTGCAACTCCAGTGGGAGGAGACCCACCCCACCTCACCCCACACACTTCTCTCCTCCAAGAGCAGCAAGTGCCAACGTGGCACTCTTGACTATGGAGGCAAAACACTCACACACGCAAATAACATTTTCAAAAAGGAAAAGAAAAGCCAAAAGGTAATTTCTTTTTTCTTTTAGCAATGAGTCAGCTACTCGACGATGCCATCAGAGACAGGCTCTTTGTCCCTTCCTAGTCACCCGTCGTTGGCTTTTATTCTCATGTTTTACCCCGTGGTGAAACACAGCTGCCACCACACCAGAAACTGAGTCTGCTTGCAAGGCAGAAAAGCAGGGGCAGAATAGAAACCATGCTAGCCATATCTGCCATCAGGAAAAGATTTGTTCCCAAAGGTGTACTTCACAAGGACCCCGGTTAGGGCGACACCGCGAAGGAGGCGGGGAACGGTAGTGCCAGGGTTCTTGGCCTCTGTGGCAGAGGCTTTGGGATAAAGAGGACTGGGAAGCAGCTGGTGCTGTTTTCCACAAAGTGGGGAGGACAGAGAGGTAGAAACAATTGCTGTCCACTTCCGATCCCCGCTTTGTTTATGTGGGATCCCTTTAAATGGGCGCCAGGAAACCACGCGGGCTGGGTTTCTGCGAGGTTGCTGGCTCAGTGTACCCGAACCCAGGACAGAGAGGTTCTGACTGAAAAGTGTGGGTCACACCAGCACCTGAACTGTTTCCGTGCCCAGAGGAGCCACGTGGTCAGGGTTCTCTTTCATT
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GTCACACCAGCACCTGAACT
60.18
CTTTGCACCCACAGACAAGC
59.97
151
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TCACACCAGCACCTGAACTG
60.18
CTTTGCACCCACAGACAAGC
59.97
150
PCR template sequence:
ACCCAGGACAGAGAGGTTCTGACTGAAAAGTGTGGGTCACACCAGCACCTGAACTGTTTCCGTGCCCAGAGGAGCCACGTGGTCAGGGTTCTCTTTCATTGTAAGTATCCCATCTGTTTGTTTCCCACTCTGTCATTGCCCAACCGACATCCTTCCTCTTTTAATAGCTTGTCTGTGGGTGCAAAGTAAATTCCTCCCCT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
39
Interacting miRNAs (#binding sites)
mmu-miR-297a-5p(3), mmu-miR-135a-5p(2), mmu-miR-31-5p(2), mmu-miR-185-5p(2), mmu-miR-29b-2-5p(2), mmu-miR-466a-5p(2), mmu-miR-1187(2), mmu-miR-5101(2), mmu-miR-3087-3p(2), mmu-miR-124-3p(1), mmu-miR-137-3p(1), mmu-miR-134-5p(1), mmu-miR-29b-3p(1), mmu-miR-29a-3p(1), mmu-miR-29c-3p(1), mmu-miR-298-5p(1), mmu-miR-216a-5p(1), mmu-miR-143-3p(1), mmu-miR-139-5p(1), mmu-miR-495-3p(1), mmu-miR-434-3p(1), mmu-miR-433-3p(1), mmu-miR-494-3p(1), mmu-miR-96-5p(1), mmu-miR-182-5p(1), mmu-miR-192-5p(1), mmu-miR-215-5p(1), mmu-miR-362-5p(1), mmu-miR-340-5p(1), mmu-miR-324-3p(1), mmu-miR-466d-3p(1), mmu-miR-705(1), mmu-miR-539-5p(1), mmu-miR-669d-5p(1), mmu-miR-188-3p(1), mmu-miR-3065-5p(1), mmu-miR-466b-3p(1), mmu-miR-574-5p(1), mmu-miR-7a-1-3p(1)
siRNAs for circular RNA silencing
Junction sequence
GTTCTCTTTCATTGTAAGTATCCCAT
siRNA sets
ATGGGATACTTACAATGAA, GATACTTACAATGAAAGAG, ATACTTACAATGAAAGAGA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIEDEM2_4093_ORF_5
0.6935
-0.097997731
0.067947775
267
ORF sequence:
ATGTGGGATCCCTTTAAATGGGCGCCAGGAAACCACGCGGGCTGGGTTTCTGCGAGGTTGCTGGCTCAGTGTACCCGAACCCAGGACAGAGAGGTTCTGACTGAAAAGTGTGGGTCACACCAGCACCTGAACTGTTTCCGTGCCCAGAGGAGCCACGTGGTCAGGGTTCTCTTTCATTGTAAGTATCCCATCTGTTTGTTTCCCACTCTGTCATTGCCCAACCGACATCCTTCCTCTTTTAATAGCTTGTCTGTGGGTGCAAAGTAA
Peptide sequence:
MWDPFKWAPGNHAGWVSARLLAQCTRTQDREVLTEKCGSHQHLNCFRAQRSHVVRVLFHCKYPICLFPTLSLPNRHPSSFNSLSVGAK
IRESfinder result
IRESfinder score
0.695973277
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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