top of page
mmu_circYthdc1_1522
Basic information of circular RNA
PanCircBase ID:
mmu_circYthdc1_1522
mm39_Chr. Position ID:
chr5|86963487|86975980|+
Gene name:
Ythdc1
Transcript:
ENSMUST00000119339.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
9
Exon/intron indexes:
2,3,4,5,6,7,8,9,10
Exon/intron offsets:
0,835,1278,4457,5623,6967,7162,11098,12326
Genomic length:
12493
Exon/intron sizes in nt:
1,02,32,94,27,90,95,10,00,00,00,000
Flanking exon/introns:
chr5:86952450-86963487|chr5:86975980-86978412
Splice length:
1522
Other database IDs:
circAtlas: mmu-Ythdc1_0006
Human Ortholog IDs:
Mature spliced Sequence:
ATGGGGAACTTAATGTTTTGGATGATATTTTGACTGAAGTACCAGAACAGGATGATGAATTGTATAATCCAGAGAGTGAACAAGATAAAAATGAGAAAAAAGGATCAAAAAGAAAAAGTGAGAGAATGGAGTCTACTGACACCAAGCGACAAAAACCTTCCATCCATTCAAGACAATTGATTTCTAAGCCACTAAGCTCATCTGTAAGCAATAATAAAAGAATAGTTAGTACAAAAGGAAAGTCGGTTACAGAATATAAAAATGAGGAATATCAAAGATCTGAAAGGAACAAGCGTCTAGATGCTGATCGAAAAATTCGTCTGTCAAGCAGTTCCTCTAGAGAACCTTACAAGAGTCAACCAGAAAAAACTTGTCTACGGAAAAGGGATTCTGAAAGAAGGGCCAAGTCTCCTACACCAGATGGTTCTGAGAGAATTGGGCTTGAAGTTGATAGACGTGCAAGCAGATCCAGCCAGTCTTCAAAGGAAGAGGTGAACTCTGAAGACTATGGCTCTGACCACGAGACAGGAAGCAGTGGTTCTTCTGAACAGGGCAACAACACTGAGAATGAGGAGGAAGGAGGGGAGGAAGATGTAGAGGAAGATGAAGAGGTAGATGAAGATGCAGAAGATGATGAGGAAGTGGATGAAGATGCAGAGGAGGAGGAGGAAGAGGATGAAGAGGAAGAAGAGGATGAGGACGAGGATGAAGAGGAAGAAGAATATGAACAGGATGAGAGAGATCAGAAGGAAGAAGGGAATGATTATGACACCCGAAGTGAGGCCAGTGATTCTGGTTCCGAGTCTGTTTCCTTCACAGATGGATCTGTCAGATCTGGGTCAGGAACAGATGGATCAGATGAGAAAAAGAAGGAAAGGAAGAGAGCTCGAGGCATATCACCCATTGTCTTTGATAGAAGTGGCAGTTCTGCATCAGAGTCATATGCAGATCAAACCAGTAAACTCAAATATGTCCTTCAGGATGCAAGATTTTTCCTCATAAAGAGTAATAACCATGAGAATGTGTCTCTTGCCAAAGCAAAGGGTGTATGGTCCACATTGCCTGTAAATGAGAAGAAATTAAATCTTGCATTTAGATCTGCAAGGAGTGTTATATTAATATTTTCTGTCAGAGAAAGTGGAAAATTTCAAGGTTTTGCCAGATTGTCTTCAGAATCACACCATGGCGGATCTCCTATACACTGGGTGCTTCCAGCAGGAATGAGTGCTAAAATGCTTGGAGGTGTTTTTAAAATAGACTGGATTTGCAGGCGTGAATTACCCTTTACTAAATCAGCTCATCTCACCAATCCCTGGAATGAACATAAGCCAGTAAAGATTGGACGTGATGGACAGGAAATTGAACTTGAATGTGGAACTCAGCTTTGTCTTCTGTTTCCCCCTGATGAAAGTATTGACTTGTATCAGCTCATTCATAAAATGCGTCACAAGAGAAGAATGCATTCTCAGCCTCGATCAAGAGGACGTCCATCCCGTCGAGAACCAGTCCGGGATGTGGGAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TGCGTCACAAGAGAAGAATGC
59.2
TCATCATCCTGTTCTGGTACTTCA
59.22
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GCGTCACAAGAGAAGAATGCA
59.2
ACAATTCATCATCCTGTTCTGGT
58.07
144
PCR template sequence:
ATCAGCTCATTCATAAAATGCGTCACAAGAGAAGAATGCATTCTCAGCCTCGATCAAGAGGACGTCCATCCCGTCGAGAACCAGTCCGGGATGTGGGAAGATGGGGAACTTAATGTTTTGGATGATATTTTGACTGAAGTACCAGAACAGGATGATGAATTGTATAATCCAGAGAGTGAACAAGATAAAAATGAGAAAAA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
12
Interacting miRNAs (#binding sites)
mmu-miR-137-3p(1), mmu-miR-320-3p(1), mmu-miR-381-3p(1), mmu-miR-29b-1-5p(1), mmu-miR-182-5p(1), mmu-miR-192-5p(1), mmu-miR-370-3p(1), mmu-miR-541-5p(1), mmu-miR-215-5p(1), mmu-miR-410-3p(1), mmu-miR-344d-3p(1), mmu-miR-188-3p(1)
siRNAs for circular RNA silencing
Junction sequence
GGGATGTGGGAAGATGGGGAACTTAA
siRNA sets
TTCCCCATCTTCCCACATC, TTAAGTTCCCCATCTTCCC, TCCCCATCTTCCCACATCC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCYTHDC1_1522_ORF_1
1.0479
0.13388176
0.999918395
1695
ORF sequence:
ATGGACAGGAAATTGAACTTGAATGTGGAACTCAGCTTTGTCTTCTGTTTCCCCCTGATGAAAGTATTGACTTGTATCAGCTCATTCATAAAATGCGTCACAAGAGAAGAATGCATTCTCAGCCTCGATCAAGAGGACGTCCATCCCGTCGAGAACCAGTCCGGGATGTGGGAAGATGGGGAACTTAATGTTTTGGATGATATTTTGACTGAAGTACCAGAACAGGATGATGAATTGTATAATCCAGAGAGTGAACAAGATAAAAATGAGAAAAAAGGATCAAAAAGAAAAAGTGAGAGAATGGAGTCTACTGACACCAAGCGACAAAAACCTTCCATCCATTCAAGACAATTGATTTCTAAGCCACTAAGCTCATCTGTAAGCAATAATAAAAGAATAGTTAGTACAAAAGGAAAGTCGGTTACAGAATATAAAAATGAGGAATATCAAAGATCTGAAAGGAACAAGCGTCTAGATGCTGATCGAAAAATTCGTCTGTCAAGCAGTTCCTCTAGAGAACCTTACAAGAGTCAACCAGAAAAAACTTGTCTACGGAAAAGGGATTCTGAAAGAAGGGCCAAGTCTCCTACACCAGATGGTTCTGAGAGAATTGGGCTTGAAGTTGATAGACGTGCAAGCAGATCCAGCCAGTCTTCAAAGGAAGAGGTGAACTCTGAAGACTATGGCTCTGACCACGAGACAGGAAGCAGTGGTTCTTCTGAACAGGGCAACAACACTGAGAATGAGGAGGAAGGAGGGGAGGAAGATGTAGAGGAAGATGAAGAGGTAGATGAAGATGCAGAAGATGATGAGGAAGTGGATGAAGATGCAGAGGAGGAGGAGGAAGAGGATGAAGAGGAAGAAGAGGATGAGGACGAGGATGAAGAGGAAGAAGAATATGAACAGGATGAGAGAGATCAGAAGGAAGAAGGGAATGATTATGACACCCGAAGTGAGGCCAGTGATTCTGGTTCCGAGTCTGTTTCCTTCACAGATGGATCTGTCAGATCTGGGTCAGGAACAGATGGATCAGATGAGAAAAAGAAGGAAAGGAAGAGAGCTCGAGGCATATCACCCATTGTCTTTGATAGAAGTGGCAGTTCTGCATCAGAGTCATATGCAGATCAAACCAGTAAACTCAAATATGTCCTTCAGGATGCAAGATTTTTCCTCATAAAGAGTAATAACCATGAGAATGTGTCTCTTGCCAAAGCAAAGGGTGTATGGTCCACATTGCCTGTAAATGAGAAGAAATTAAATCTTGCATTTAGATCTGCAAGGAGTGTTATATTAATATTTTCTGTCAGAGAAAGTGGAAAATTTCAAGGTTTTGCCAGATTGTCTTCAGAATCACACCATGGCGGATCTCCTATACACTGGGTGCTTCCAGCAGGAATGAGTGCTAAAATGCTTGGAGGTGTTTTTAAAATAGACTGGATTTGCAGGCGTGAATTACCCTTTACTAAATCAGCTCATCTCACCAATCCCTGGAATGAACATAAGCCAGTAAAGATTGGACGTGATGGACAGGAAATTGAACTTGAATGTGGAACTCAGCTTTGTCTTCTGTTTCCCCCTGATGAAAGTATTGACTTGTATCAGCTCATTCATAAAATGCGTCACAAGAGAAGAATGCATTCTCAGCCTCGATCAAGAGGACGTCCATCCCGTCGAGAACCAGTCCGGGATGTGGGA
Peptide sequence:
MDRKLNLNVELSFVFCFPLMKVLTCISSFIKCVTREECILSLDQEDVHPVENQSGMWEDGELNVLDDILTEVPEQDDELYNPESEQDKNEKKGSKRKSERMESTDTKRQKPSIHSRQLISKPLSSSVSNNKRIVSTKGKSVTEYKNEEYQRSERNKRLDADRKIRLSSSSSREPYKSQPEKTCLRKRDSERRAKSPTPDGSERIGLEVDRRASRSSQSSKEEVNSEDYGSDHETGSSGSSEQGNNTENEEEGGEEDVEEDEEVDEDAEDDEEVDEDAEEEEEEDEEEEEDEDEDEEEEEYEQDERDQKEEGNDYDTRSEASDSGSESVSFTDGSVRSGSGTDGSDEKKKERKRARGISPIVFDRSGSSASESYADQTSKLKYVLQDARFFLIKSNNHENVSLAKAKGVWSTLPVNEKKLNLAFRSARSVILIFSVRESGKFQGFARLSSESHHGGSPIHWVLPAGMSAKMLGGVFKIDWICRRELPFTKSAHLTNPWNEHKPVKIGRDGQEIELECGTQLCLLFPPDESIDLYQLIHKMRHKRRMHSQPRSRGRPSRREPVRDVG
IRESfinder result
IRESfinder score
0.516684532
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
bottom of page