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mmu_circMed13_1666
Basic information of circular RNA
PanCircBase ID:
mmu_circMed13_1666
mm39_Chr. Position ID:
chr11|86210173|86236854|-
Gene name:
Med13
Transcript:
ENSMUST00000043624.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
7
Exon/intron indexes:
9,8,7,6,5,4,3
Exon/intron offsets:
0,8454,9099,9820,11640,12535,26512
Genomic length:
26681
Exon/intron sizes in nt:
684,111,163,195,198,146,169
Flanking exon/introns:
chr11:86199738-86210173|chr11:86236854-86246099
Splice length:
1666
Other database IDs:
circBase: mmu_circ_0003501, CIRCpedia: MMU_CIRCpedia_32400, circAtlas: mmu-Med13_0008
circAtlas: hsa-MED13_0011, CIRCpedia: HSA_CIRCpedia_143785
Human Ortholog IDs:
Mature spliced Sequence:
AAGAGGAAGATGGAGTATGGGAGAATGGCCTTTCCTATGAATGCCGTACTTTGCTTTTCAAAGCAGTTCACAATCTGTTGGAGCGATGTTTGATGAACCGAAACTTTGTACGAATTGGCAAGTGGTTTGTGAAGCCATATGAGAAAGATGAAAAACCTATAAATAAAAGTGAACACTTGTCCTGCTCTTTCACCTTTTTCTTGCATGGAGACAGCAATGTTTGTACCAGTGTGGAAATTAACCAACATCAACCTGTATACCTTCTCAGTGAAGAGCATGTCACCCTTGCTCAACAGTCTAATAGCCCATTTCAAGTTATCTTAAGTCCATTTGGACTAAATGGCACTCTCACGGGACAGGCTTTCAAGATGTCTGATTCAGCTACGAAAAAATTAATTGGTGAATGGAAACAGTTCTATCCTATTTCATGTGGTTTGAAGGAGATGTCTGAGGAGAAACAGGACGATATGGATTGGGAAGACGATTCTTTGGCTGCGGTGGAAGTTCTTGTTGCGGGTGTCCGAATGATCTACCCAGCATGCTTTGTGCTAGTCCCTCAGTCAGACATTCCTGCTCCTAGCTCTGTGGGAGCTTCTCACTGTTCAGCTTCTTGCTTGGGTATCCATCAAGTGCCTGCTTCCACAAGAGATCCTGCTATGTCTTCAGTTACTCTCACTCCACCTACATCTCCTGAGGAAGTCCAAACAGTTGATCCTCAGTCCGCACAGAAGTGGGTCAAATTTTCTTCAGTATCCGATGGCTTCAGCACTGACAGTACTAGCCATCATGGTGGGAAAATACCCAGAAAATTAGCAAATCATGTGGTGGATAGAGTCTGGCAAGAATGTAATATGAACAGATTACAGAACAAGAGGAAGTATTCTGCTACATCCAGCGGCCTGTGTGAGGAAGAGACTGCCGATAAAATAGGATGCTGGGACTTTGTTGAAGCCACACAAAGAACAAGCTGCAGTTGTTTGAGGCATAAAAGTCTCAAGACAAGAAATACTGGGCAACAAGGACAGGCACCATCTTTAGGGCAGCAACAGCAAGTACTTCCTAAGCACAAGACCAATGAGAAGCAAGACAAGAGTGAGAAGCCACAGAAGCGCCCCTTGACTCCCTTTCACCATCGTGTATCAGTTAGTGATGAGATTGGCATGGACACAGATTCAGCCAGCCAAAGACTTGTGATCTCTGCTGCAGATAGTCAAGTGAGGTTTTCAAACATCCGAACTAATGATGTAGCAAAGACTCCTCAGATGCATGGCACTGAACTGGCAAATTCACCTCAGCCTCCCCCACTTAGTCCTCATCCTTGTGATGTGGTTGATGAAGGAGTGACTAAAACACCTTCAACTCCGCAGAGTCAACATTTTTATCAAATGCCAACACCGGATCCCTTGGTTCCTACCAAACCAATGGAAGATAGGATAGACAGTTTGTCCCAGTCTTTCCCACCTCCATTTCAGGAAGCTGTAGAACCTACCGTGTATGTTGGTACAGCAGTAAGCTTGGAAGAAGATGAAGCTAATGTAGCCTGGAAGTATTACAAAGTCCCAAAGAAAAAAGATGTAGAATTTTTACCACCTCAACTTCCAAATGATAAATTCAAGGATGATCCAGTTGGACCTTTTGGACAGGAAAGTGTAACATCAGTTACAGA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TCCAGTTGGACCTTTTGGACA
59.43
CGGTTCATCAAACATCGCTCC
59.94
145
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AGTTGGACCTTTTGGACAGGA
59.15
CGGTTCATCAAACATCGCTCC
59.94
142
PCR template sequence:
AAAAAGATGTAGAATTTTTACCACCTCAACTTCCAAATGATAAATTCAAGGATGATCCAGTTGGACCTTTTGGACAGGAAAGTGTAACATCAGTTACAGAAAGAGGAAGATGGAGTATGGGAGAATGGCCTTTCCTATGAATGCCGTACTTTGCTTTTCAAAGCAGTTCACAATCTGTTGGAGCGATGTTTGATGAACCG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
14
Interacting miRNAs (#binding sites)
mmu-miR-221-3p(2), mmu-miR-222-3p(2), mmu-miR-205-5p(1), mmu-miR-216a-5p(1), mmu-miR-382-3p(1), mmu-miR-541-5p(1), mmu-miR-342-5p(1), mmu-miR-342-3p(1), mmu-miR-300-3p(1), mmu-miR-335-3p(1), mmu-miR-452-3p(1), mmu-miR-3065-5p(1), mmu-miR-350-3p(1), mmu-miR-338-3p(1)
siRNAs for circular RNA silencing
Junction sequence
CATCAGTTACAGAAAGAGGAAGATGG
siRNA sets
TTCCTCTTTCTGTAACTGA, TCTTCCTCTTTCTGTAACT, CTTCCTCTTTCTGTAACTG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCMED13_1666_ORF_1
0.9588
0.034526494
0.999738907
1614
ORF sequence:
ATGAACCGAAACTTTGTACGAATTGGCAAGTGGTTTGTGAAGCCATATGAGAAAGATGAAAAACCTATAAATAAAAGTGAACACTTGTCCTGCTCTTTCACCTTTTTCTTGCATGGAGACAGCAATGTTTGTACCAGTGTGGAAATTAACCAACATCAACCTGTATACCTTCTCAGTGAAGAGCATGTCACCCTTGCTCAACAGTCTAATAGCCCATTTCAAGTTATCTTAAGTCCATTTGGACTAAATGGCACTCTCACGGGACAGGCTTTCAAGATGTCTGATTCAGCTACGAAAAAATTAATTGGTGAATGGAAACAGTTCTATCCTATTTCATGTGGTTTGAAGGAGATGTCTGAGGAGAAACAGGACGATATGGATTGGGAAGACGATTCTTTGGCTGCGGTGGAAGTTCTTGTTGCGGGTGTCCGAATGATCTACCCAGCATGCTTTGTGCTAGTCCCTCAGTCAGACATTCCTGCTCCTAGCTCTGTGGGAGCTTCTCACTGTTCAGCTTCTTGCTTGGGTATCCATCAAGTGCCTGCTTCCACAAGAGATCCTGCTATGTCTTCAGTTACTCTCACTCCACCTACATCTCCTGAGGAAGTCCAAACAGTTGATCCTCAGTCCGCACAGAAGTGGGTCAAATTTTCTTCAGTATCCGATGGCTTCAGCACTGACAGTACTAGCCATCATGGTGGGAAAATACCCAGAAAATTAGCAAATCATGTGGTGGATAGAGTCTGGCAAGAATGTAATATGAACAGATTACAGAACAAGAGGAAGTATTCTGCTACATCCAGCGGCCTGTGTGAGGAAGAGACTGCCGATAAAATAGGATGCTGGGACTTTGTTGAAGCCACACAAAGAACAAGCTGCAGTTGTTTGAGGCATAAAAGTCTCAAGACAAGAAATACTGGGCAACAAGGACAGGCACCATCTTTAGGGCAGCAACAGCAAGTACTTCCTAAGCACAAGACCAATGAGAAGCAAGACAAGAGTGAGAAGCCACAGAAGCGCCCCTTGACTCCCTTTCACCATCGTGTATCAGTTAGTGATGAGATTGGCATGGACACAGATTCAGCCAGCCAAAGACTTGTGATCTCTGCTGCAGATAGTCAAGTGAGGTTTTCAAACATCCGAACTAATGATGTAGCAAAGACTCCTCAGATGCATGGCACTGAACTGGCAAATTCACCTCAGCCTCCCCCACTTAGTCCTCATCCTTGTGATGTGGTTGATGAAGGAGTGACTAAAACACCTTCAACTCCGCAGAGTCAACATTTTTATCAAATGCCAACACCGGATCCCTTGGTTCCTACCAAACCAATGGAAGATAGGATAGACAGTTTGTCCCAGTCTTTCCCACCTCCATTTCAGGAAGCTGTAGAACCTACCGTGTATGTTGGTACAGCAGTAAGCTTGGAAGAAGATGAAGCTAATGTAGCCTGGAAGTATTACAAAGTCCCAAAGAAAAAAGATGTAGAATTTTTACCACCTCAACTTCCAAATGATAAATTCAAGGATGATCCAGTTGGACCTTTTGGACAGGAAAGTGTAACATCAGTTACAGAAAGAGGAAGATGGAGTATGGGAGAATGGCCTTTCCTATGA
Peptide sequence:
MNRNFVRIGKWFVKPYEKDEKPINKSEHLSCSFTFFLHGDSNVCTSVEINQHQPVYLLSEEHVTLAQQSNSPFQVILSPFGLNGTLTGQAFKMSDSATKKLIGEWKQFYPISCGLKEMSEEKQDDMDWEDDSLAAVEVLVAGVRMIYPACFVLVPQSDIPAPSSVGASHCSASCLGIHQVPASTRDPAMSSVTLTPPTSPEEVQTVDPQSAQKWVKFSSVSDGFSTDSTSHHGGKIPRKLANHVVDRVWQECNMNRLQNKRKYSATSSGLCEEETADKIGCWDFVEATQRTSCSCLRHKSLKTRNTGQQGQAPSLGQQQQVLPKHKTNEKQDKSEKPQKRPLTPFHHRVSVSDEIGMDTDSASQRLVISAADSQVRFSNIRTNDVAKTPQMHGTELANSPQPPPLSPHPCDVVDEGVTKTPSTPQSQHFYQMPTPDPLVPTKPMEDRIDSLSQSFPPPFQEAVEPTVYVGTAVSLEEDEANVAWKYYKVPKKKDVEFLPPQLPNDKFKDDPVGPFGQESVTSVTERGRWSMGEWPFL
IRESfinder result
IRESfinder score
0.613127789
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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