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mmu_circKansl3_2398
Basic information of circular RNA
PanCircBase ID:
mmu_circKansl3_2398
mm39_Chr. Position ID:
chr1|36382331|36404733|-
Gene name:
Kansl3
Transcript:
ENSMUST00000010597.10
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
18
Exon/intron indexes:
20,19,18,17,16,15,14,13,12,11,10,9,8,7,6,5,4,3
Exon/intron offsets:
0,422,819,1665,2134,2587,5274,5567,6151,8382,8675,10343,10521,10847,11398,14789,15119,22231
Genomic length:
22402
Exon/intron sizes in nt:
13,42,23,11,01,31,82,10,00,00,00,00,00,00,00,00,00,00,00,00,00,00,00,000
Flanking exon/introns:
chr1:36376732-36382331|chr1:36404733-36406849
Splice length:
2398
Other database IDs:
circAtlas: mmu-Kansl3_0006
circAtlas: hsa-SCAF8_0001
Human Ortholog IDs:
Mature spliced Sequence:
TGAGTCAGACGTTCCAATAGATGTGGAGACGGTCACGGCAACTCCTGTTCCACTTTATGACAATCAGAAGGCAAGAAGTGTGATGAACGAGTGTGAACGGCACGTGATCTTCGCCAGGACAGATGCAGATGCTCCTCCTCCGCCAGAAGACTGGGAAGAACATGTCAACAGGACTGGCTGGACAGTGGCTCAGAATAAGCTATTTAACAAGATCCTCAAAGCCCTGCAGTCTGACCGGCTTGCACGATTGGCCAATGAAGGGGCTTGCAATGAGCCTGTGCTGCGTCGCGTGGCTGTGGACAAGTGTGCAAGGAGGGTGCGGCAGGCGCTGGCAAGTGTCAGCTGGGACACCAAGCTGACCCAGTGGCTGCACACCACCCTCGTGGAGACCCTGAGCCTGCCCATGCTGGCTGCTTACTTGGATGCCCTGCAGACACTGAAAGGGAAGATCCCAACTTTGATAGATCGGATGCTTGTGTCGTCCAACACCAAAACTGGGGCTGCAGGAGCGGAGGCCTTGTCCCTTCTCCTCAAGAGGCCCTGGGACCCTGCTGTTGGTGTGCTTTCACATAACAAACCAAGCAAGCTCCCTGGTTCTCCTTTGATTCTCATCGTCTCCTCTGGTCCCTCCAGCTCTGTGTTCCCTGCCTCACGCCGCCACCGCTTCTGGCAGTCTCAGCTCTCCTGCTTAGGCAAGGTCATCCCTGTAGCGACCCATCTACTGAACAATGGCAGTGGGGTAGGAGTTCTGCAGTGCCTCGAACACATGATTGGGGCCGTGAGAAGCAAAGTGCTAGAGATTCACAGCCATTTCCCACACAAACCCATCATCCTGATTGGATGGAATACGGGAGCTTTGGTGGCCTGTCATGTGTCTGTGATGGAGTACGTCACTGCTGTTGTCTGCCTTGGGTTTCCTCTGCTTACTGTGGATGGACCCAGGGGGGATGTGGACGATCCCCTCCTGGACATGAAGACTCCAGTCCTCTTCGTCATTGGTCAGAATTCTCTACAGTGTCACCCTGAAGCCATGGAGGACTTCCGGGAAAAGATTCGAGCAGAAAATAGCTTGGTGGTGGTTGGGGGAGCTGATGATAATCTCAGAATAAGCAAAGCAAAGAAGAAATCAGAGGGCCTGACTCAGAGCATGGTGGACAGATGTATTCAGGATGAGATTGTAGACTTCCTGACTGGAGTGCTCACTCGTGCTGAGGGTCATGTGGGCTCTGAGCCTCGGGATCAGGATGCTGAGAAGAAGAAGAAACCCCGGGACTTGACCCGAAGAGACCTGGCCTTTGAAATTCCTGAGCGAGGCAGTCGTCCTGCTTCCCCAGCTGCCAGGCTCCCCACATCCCCCTCAGGCTCAGAGGATCTCTCCAGTGTGTCCAGCAGCCCCACCTCTAGCCCTAAGACCAAAGTGACCACAGTGACCTCTACCCAGAAATCAAGTCAGATTGGGACCTCCCAGCTGCTGAAAAGACATGTGCAGAGGACAGAAGCTGTGCTGACCCACAGACAAGCCCAAGTTCCCATTTCATCAGAATCAGTGGAGGACATAGAGAAAGAAGAGCTTCGGGTCCAGCTTAAGAGGCACCATTCTTCCAGTCCTCTTCCTGGAGCAAAGCCTTCCAAGCGACCAAAGATCAAAGTGTCCCTGATCTCCCAAGGGGACACAGTTGGAGGACCTTGCACTCTTTCTCAAGGTGGAACACCTGAAGCTGCCGGAGGGAAGCCCATCACCATGACCCTGGGAGCTTCAGCAGGAGCCAAGGAACTCACTGGACTTCTCACTACAGCCAAGTCAAGTTCTTCTGAAGGTGGAGGTACAGCCAGCACAACCCCATCTGTGGCTTCCAGCAGTGCCACACCTAATGCTATCCACACGCTGCAGAGCCGCTTGGTGGCCACTTCTCCAGGCAGCTCCCTTCCAGGGACCGCTTCAGCCAGCAGCCTCCTCCAGGGCCTCAGCTTCAGCTTACAGGATATTAGCAGCAAGACCTCTGGCCTCCCAGGAAGTCCCTCCCCAGGGCCAGCCCCACAGGCCACCAGTGTGAAATTGCCAACCCCCATGCAGAGTCTGGGTGCCATCACCACAGGCACGAGCACCATTGTCCGTACCATCCCTGTGGCCACCACTCTCTCCTCCTTGGGTGCCACTCCTGGTGGGAAGCCCACTGCCATCCACCAGCTGCTGACCAATGGGAGCCTCGCTAAGTTGGCAAGCAGCCTACCTGGCTTGGCTCAGATTTCCAACCAAGCATCAGGCTTAAAGGTCCCCACCACCATTACTCTGACGCTGCGTGGCCAGCCAAGCAGAATTACCACGCTAAGCCCTATGGGGTCAGGGGCAACGCCGTCCGAGGAGCCCAACTCCCAGATGCTACCATCTAGTTCACAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TGGCCAGCCAAGCAGAATTA
59.96
AAGTGGAACAGGAGTTGCCG
60.54
152
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GCCAAGCAGAATTACCACGC
60.18
AAGTGGAACAGGAGTTGCCG
60.54
146
PCR template sequence:
GCGTGGCCAGCCAAGCAGAATTACCACGCTAAGCCCTATGGGGTCAGGGGCAACGCCGTCCGAGGAGCCCAACTCCCAGATGCTACCATCTAGTTCACAGTGAGTCAGACGTTCCAATAGATGTGGAGACGGTCACGGCAACTCCTGTTCCACTTTATGACAATCAGAAGGCAAGAAGTGTGATGAACGAGTGTGAACGG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
16
Interacting miRNAs (#binding sites)
mmu-miR-127-5p(2), mmu-miR-484(2), mmu-miR-9-5p(1), mmu-miR-298-5p(1), mmu-miR-216a-5p(1), mmu-miR-709(1), mmu-miR-24-3p(1), mmu-miR-136-5p(1), mmu-miR-22-3p(1), mmu-miR-301b-3p(1), mmu-miR-183-5p(1), mmu-miR-27a-5p(1), mmu-miR-1198-5p(1), mmu-miR-697(1), mmu-miR-1904(1), mmu-miR-544-5p(1)
siRNAs for circular RNA silencing
Junction sequence
ATCTAGTTCACAGTGAGTCAGACGTT
siRNA sets
AACGTCTGACTCACTGTGA, TGACTCACTGTGAACTAGA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCKANSL3_2398_ORF_1
1.0879
0.270306028
0.9999995
2319
ORF sequence:
ATGAACGAGTGTGAACGGCACGTGATCTTCGCCAGGACAGATGCAGATGCTCCTCCTCCGCCAGAAGACTGGGAAGAACATGTCAACAGGACTGGCTGGACAGTGGCTCAGAATAAGCTATTTAACAAGATCCTCAAAGCCCTGCAGTCTGACCGGCTTGCACGATTGGCCAATGAAGGGGCTTGCAATGAGCCTGTGCTGCGTCGCGTGGCTGTGGACAAGTGTGCAAGGAGGGTGCGGCAGGCGCTGGCAAGTGTCAGCTGGGACACCAAGCTGACCCAGTGGCTGCACACCACCCTCGTGGAGACCCTGAGCCTGCCCATGCTGGCTGCTTACTTGGATGCCCTGCAGACACTGAAAGGGAAGATCCCAACTTTGATAGATCGGATGCTTGTGTCGTCCAACACCAAAACTGGGGCTGCAGGAGCGGAGGCCTTGTCCCTTCTCCTCAAGAGGCCCTGGGACCCTGCTGTTGGTGTGCTTTCACATAACAAACCAAGCAAGCTCCCTGGTTCTCCTTTGATTCTCATCGTCTCCTCTGGTCCCTCCAGCTCTGTGTTCCCTGCCTCACGCCGCCACCGCTTCTGGCAGTCTCAGCTCTCCTGCTTAGGCAAGGTCATCCCTGTAGCGACCCATCTACTGAACAATGGCAGTGGGGTAGGAGTTCTGCAGTGCCTCGAACACATGATTGGGGCCGTGAGAAGCAAAGTGCTAGAGATTCACAGCCATTTCCCACACAAACCCATCATCCTGATTGGATGGAATACGGGAGCTTTGGTGGCCTGTCATGTGTCTGTGATGGAGTACGTCACTGCTGTTGTCTGCCTTGGGTTTCCTCTGCTTACTGTGGATGGACCCAGGGGGGATGTGGACGATCCCCTCCTGGACATGAAGACTCCAGTCCTCTTCGTCATTGGTCAGAATTCTCTACAGTGTCACCCTGAAGCCATGGAGGACTTCCGGGAAAAGATTCGAGCAGAAAATAGCTTGGTGGTGGTTGGGGGAGCTGATGATAATCTCAGAATAAGCAAAGCAAAGAAGAAATCAGAGGGCCTGACTCAGAGCATGGTGGACAGATGTATTCAGGATGAGATTGTAGACTTCCTGACTGGAGTGCTCACTCGTGCTGAGGGTCATGTGGGCTCTGAGCCTCGGGATCAGGATGCTGAGAAGAAGAAGAAACCCCGGGACTTGACCCGAAGAGACCTGGCCTTTGAAATTCCTGAGCGAGGCAGTCGTCCTGCTTCCCCAGCTGCCAGGCTCCCCACATCCCCCTCAGGCTCAGAGGATCTCTCCAGTGTGTCCAGCAGCCCCACCTCTAGCCCTAAGACCAAAGTGACCACAGTGACCTCTACCCAGAAATCAAGTCAGATTGGGACCTCCCAGCTGCTGAAAAGACATGTGCAGAGGACAGAAGCTGTGCTGACCCACAGACAAGCCCAAGTTCCCATTTCATCAGAATCAGTGGAGGACATAGAGAAAGAAGAGCTTCGGGTCCAGCTTAAGAGGCACCATTCTTCCAGTCCTCTTCCTGGAGCAAAGCCTTCCAAGCGACCAAAGATCAAAGTGTCCCTGATCTCCCAAGGGGACACAGTTGGAGGACCTTGCACTCTTTCTCAAGGTGGAACACCTGAAGCTGCCGGAGGGAAGCCCATCACCATGACCCTGGGAGCTTCAGCAGGAGCCAAGGAACTCACTGGACTTCTCACTACAGCCAAGTCAAGTTCTTCTGAAGGTGGAGGTACAGCCAGCACAACCCCATCTGTGGCTTCCAGCAGTGCCACACCTAATGCTATCCACACGCTGCAGAGCCGCTTGGTGGCCACTTCTCCAGGCAGCTCCCTTCCAGGGACCGCTTCAGCCAGCAGCCTCCTCCAGGGCCTCAGCTTCAGCTTACAGGATATTAGCAGCAAGACCTCTGGCCTCCCAGGAAGTCCCTCCCCAGGGCCAGCCCCACAGGCCACCAGTGTGAAATTGCCAACCCCCATGCAGAGTCTGGGTGCCATCACCACAGGCACGAGCACCATTGTCCGTACCATCCCTGTGGCCACCACTCTCTCCTCCTTGGGTGCCACTCCTGGTGGGAAGCCCACTGCCATCCACCAGCTGCTGACCAATGGGAGCCTCGCTAAGTTGGCAAGCAGCCTACCTGGCTTGGCTCAGATTTCCAACCAAGCATCAGGCTTAAAGGTCCCCACCACCATTACTCTGACGCTGCGTGGCCAGCCAAGCAGAATTACCACGCTAAGCCCTATGGGGTCAGGGGCAACGCCGTCCGAGGAGCCCAACTCCCAGATGCTACCATCTAGTTCACAGTGA
Peptide sequence:
MNECERHVIFARTDADAPPPPEDWEEHVNRTGWTVAQNKLFNKILKALQSDRLARLANEGACNEPVLRRVAVDKCARRVRQALASVSWDTKLTQWLHTTLVETLSLPMLAAYLDALQTLKGKIPTLIDRMLVSSNTKTGAAGAEALSLLLKRPWDPAVGVLSHNKPSKLPGSPLILIVSSGPSSSVFPASRRHRFWQSQLSCLGKVIPVATHLLNNGSGVGVLQCLEHMIGAVRSKVLEIHSHFPHKPIILIGWNTGALVACHVSVMEYVTAVVCLGFPLLTVDGPRGDVDDPLLDMKTPVLFVIGQNSLQCHPEAMEDFREKIRAENSLVVVGGADDNLRISKAKKKSEGLTQSMVDRCIQDEIVDFLTGVLTRAEGHVGSEPRDQDAEKKKKPRDLTRRDLAFEIPERGSRPASPAARLPTSPSGSEDLSSVSSSPTSSPKTKVTTVTSTQKSSQIGTSQLLKRHVQRTEAVLTHRQAQVPISSESVEDIEKEELRVQLKRHHSSSPLPGAKPSKRPKIKVSLISQGDTVGGPCTLSQGGTPEAAGGKPITMTLGASAGAKELTGLLTTAKSSSSEGGGTASTTPSVASSSATPNAIHTLQSRLVATSPGSSLPGTASASSLLQGLSFSLQDISSKTSGLPGSPSPGPAPQATSVKLPTPMQSLGAITTGTSTIVRTIPVATTLSSLGATPGGKPTAIHQLLTNGSLAKLASSLPGLAQISNQASGLKVPTTITLTLRGQPSRITTLSPMGSGATPSEEPNSQMLPSSSQ
IRESfinder result
IRESfinder score
0.492275335
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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