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mmu_circItch_750
Basic information of circular RNA
PanCircBase ID:
mmu_circItch_750
mm39_Chr. Position ID:
chr2|155048212|155055022|+
Gene name:
Itch
Transcript:
ENSMUST00000029126.15
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
6
Exon/intron indexes:
17,18,19,20,21,22
Exon/intron offsets:
0,2766,3694,4147,6044,6705
Genomic length:
6810
Exon/intron sizes in nt:
89,16,01,34,14,11,21,100
Flanking exon/introns:
chr2:155045272-155048212|chr2:155055022-155059910
Splice length:
750
Other database IDs:
circAtlas: mmu-Itch_0013
circAtlas: hsa-SCAF8_0001
Human Ortholog IDs:
Mature spliced Sequence:
ATCATGAGCTTCAGCCCGCAAGACCTGAGAAGACGTTTGTGGGTGATTTTCCCAGGAGAAGAAGGTTTAGATTATGGAGGTGTAGCAAGAGAATGGTTCTTTCTTTTGTCACATGAAGTGTTGAACCCAATGTATTGCCTGTTTGAATATGCAGGGAAGGATAACTACTGCCTGCAGATAAACCCCGCTTCTTACATCAATCCAGACCACCTGAAATACTTTCGTTTTATTGGCAGATTTATTGCCATGGCTCTGTTTCATGGGAAATTCATAGATACCGGATTTTCTTTACCATTCTATAAACGTATCCTGAATAAACCAGTTGGACTGAAGGATTTAGAATCTATTGATCCAGAATTTTATAATTCGCTCATCTGGGTTAAAGAAAACAACATTGAAGAATGTGGTTTGGAAATGTACTTCTCAGTTGATAAAGAAATTCTAGGTGAAATTAAGAGTCATGATTTGAAACCCAATGGTGGCAATATTCTTGTGACAGAAGAAAACAAGGAGGAATACATCAGGATGGTAGCTGAGTGGAGGTTGTCTCGAGGTGTTGAAGAACAGACACAAGCTTTCTTTGAGGGCTTTAATGAAATTCTTCCTCAGCAATATTTGCAATATTTTGATGCGAAGGAATTAGAGGTTCTTCTGTGTGGGATGCAGGAGATTGATTTGAATGACTGGCAGAGACATGCCATCTACCGCCACTACACCAGAACAAGCAAGCAGATCATGTGGTTTTGGCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TCTGTGTGGGATGCAGGAGA
60.55
CCCACAAACGTCTTCTCAGGT
60.2
143
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TCTGTGTGGGATGCAGGAGA
60.55
ACCCACAAACGTCTTCTCAGG
60.2
144
PCR template sequence:
TCTGTGTGGGATGCAGGAGATTGATTTGAATGACTGGCAGAGACATGCCATCTACCGCCACTACACCAGAACAAGCAAGCAGATCATGTGGTTTTGGCAGATCATGAGCTTCAGCCCGCAAGACCTGAGAAGACGTTTGTGGGTGATTTTCCCAGGAGAAGAAGGTTTAGATTATGGAGGTGTAGCAAGAGAATGGTTCT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
9
Interacting miRNAs (#binding sites)
mmu-miR-137-3p(1), mmu-miR-431-5p(1), mmu-miR-29b-1-5p(1), mmu-miR-127-5p(1), mmu-miR-29b-2-5p(1), mmu-miR-377-3p(1), mmu-miR-207(1), mmu-miR-5101(1), mmu-miR-188-3p(1)
siRNAs for circular RNA silencing
Junction sequence
GTGGTTTTGGCAGATCATGAGCTTCA
siRNA sets
TGAAGCTCATGATCTGCCA, CATGATCTGCCAAAACCAC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCITCH_750_ORF_1
0.8193
0.097684014
0.999417533
1497
ORF sequence:
ATGAGCTTCAGCCCGCAAGACCTGAGAAGACGTTTGTGGGTGATTTTCCCAGGAGAAGAAGGTTTAGATTATGGAGGTGTAGCAAGAGAATGGTTCTTTCTTTTGTCACATGAAGTGTTGAACCCAATGTATTGCCTGTTTGAATATGCAGGGAAGGATAACTACTGCCTGCAGATAAACCCCGCTTCTTACATCAATCCAGACCACCTGAAATACTTTCGTTTTATTGGCAGATTTATTGCCATGGCTCTGTTTCATGGGAAATTCATAGATACCGGATTTTCTTTACCATTCTATAAACGTATCCTGAATAAACCAGTTGGACTGAAGGATTTAGAATCTATTGATCCAGAATTTTATAATTCGCTCATCTGGGTTAAAGAAAACAACATTGAAGAATGTGGTTTGGAAATGTACTTCTCAGTTGATAAAGAAATTCTAGGTGAAATTAAGAGTCATGATTTGAAACCCAATGGTGGCAATATTCTTGTGACAGAAGAAAACAAGGAGGAATACATCAGGATGGTAGCTGAGTGGAGGTTGTCTCGAGGTGTTGAAGAACAGACACAAGCTTTCTTTGAGGGCTTTAATGAAATTCTTCCTCAGCAATATTTGCAATATTTTGATGCGAAGGAATTAGAGGTTCTTCTGTGTGGGATGCAGGAGATTGATTTGAATGACTGGCAGAGACATGCCATCTACCGCCACTACACCAGAACAAGCAAGCAGATCATGTGGTTTTGGCAGATCATGAGCTTCAGCCCGCAAGACCTGAGAAGACGTTTGTGGGTGATTTTCCCAGGAGAAGAAGGTTTAGATTATGGAGGTGTAGCAAGAGAATGGTTCTTTCTTTTGTCACATGAAGTGTTGAACCCAATGTATTGCCTGTTTGAATATGCAGGGAAGGATAACTACTGCCTGCAGATAAACCCCGCTTCTTACATCAATCCAGACCACCTGAAATACTTTCGTTTTATTGGCAGATTTATTGCCATGGCTCTGTTTCATGGGAAATTCATAGATACCGGATTTTCTTTACCATTCTATAAACGTATCCTGAATAAACCAGTTGGACTGAAGGATTTAGAATCTATTGATCCAGAATTTTATAATTCGCTCATCTGGGTTAAAGAAAACAACATTGAAGAATGTGGTTTGGAAATGTACTTCTCAGTTGATAAAGAAATTCTAGGTGAAATTAAGAGTCATGATTTGAAACCCAATGGTGGCAATATTCTTGTGACAGAAGAAAACAAGGAGGAATACATCAGGATGGTAGCTGAGTGGAGGTTGTCTCGAGGTGTTGAAGAACAGACACAAGCTTTCTTTGAGGGCTTTAATGAAATTCTTCCTCAGCAATATTTGCAATATTTTGATGCGAAGGAATTAGAGGTTCTTCTGTGTGGGATGCAGGAGATTGATTTGAATGACTGGCAGAGACATGCCATCTACCGCCACTACACCAGAACAAGCAAGCAGATCATGTGGTTTTGGCAG
Peptide sequence:
MSFSPQDLRRRLWVIFPGEEGLDYGGVAREWFFLLSHEVLNPMYCLFEYAGKDNYCLQINPASYINPDHLKYFRFIGRFIAMALFHGKFIDTGFSLPFYKRILNKPVGLKDLESIDPEFYNSLIWVKENNIEECGLEMYFSVDKEILGEIKSHDLKPNGGNILVTEENKEEYIRMVAEWRLSRGVEEQTQAFFEGFNEILPQQYLQYFDAKELEVLLCGMQEIDLNDWQRHAIYRHYTRTSKQIMWFWQIMSFSPQDLRRRLWVIFPGEEGLDYGGVAREWFFLLSHEVLNPMYCLFEYAGKDNYCLQINPASYINPDHLKYFRFIGRFIAMALFHGKFIDTGFSLPFYKRILNKPVGLKDLESIDPEFYNSLIWVKENNIEECGLEMYFSVDKEILGEIKSHDLKPNGGNILVTEENKEEYIRMVAEWRLSRGVEEQTQAFFEGFNEILPQQYLQYFDAKELEVLLCGMQEIDLNDWQRHAIYRHYTRTSKQIMWFWQ
IRESfinder result
IRESfinder score
0.779223785
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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