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mmu_circAtp2c1_1152
Basic information of circular RNA
PanCircBase ID:
mmu_circAtp2c1_1152
mm39_Chr. Position ID:
chr9|105308693|105330042|-
Gene name:
Atp2c1
Transcript:
ENSMUST00000177293.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
11
Exon/intron indexes:
14,13,12,11,10,9,8,7,6,5,4
Exon/intron offsets:
0,1159,3557,7846,11271,11451,13723,14557,17327,20309,21280
Genomic length:
21349
Exon/intron sizes in nt:
98,171,157,105,90,96,98,125,67,76,69
Flanking exon/introns:
chr9:105301419-105308693|chr9:105330042-105330732
Splice length:
1152
Other database IDs:
circAtlas: mmu-Atp2c1_0039
Human Ortholog IDs:
Mature spliced Sequence:
GGTATTGTCATTGGAACAGGAGAAAATTCTGAATTTGGAGAGGTCTTTAAGATGATGCAGGCAGAAGAAGCACCAAAAACTCCTCTGCAGAAGAGCATGGACCTCTTAGGCAAGCAGCTGTCCTTTTACTCCTTTGGTATAATAGGTATCATCATGTTGGTTGGCTGGTTACTAGGAAAAGACATTCTGGAAATGTTCACTATTAGTGTAAGCTTGGCTGTAGCTGCAATTCCTGAAGGCCTGCCTATTGTGGTCACGGTGACTCTAGCCCTTGGTGTTATGAGAATGGTGAAGAAAAGGGCTATTGTAAAGAAATTGCCTATTGTGGAAACACTGGGCTGCTGTAATGTGATTTGTTCAGATAAAACTGGAACCCTGACGAAGAACGAGATGACTGTTACTCACATCCTCACTTCCGATGGCCTGCATGCTGAGGTCACTGGAGTTGGCTATAATCAGTTTGGTGAAGTGATCGTTGATGGTGATGTTGTTCATGGATTTTATAACCCAGCTGTTAGCAGAATTGTTGAGGCAGGCTGTGTGTGCAATGATGCTGTAATTAGGAACAACACTCTGATGGGAAAGCCAACTGAAGGAGCCTTAATCGCTCTTGCTATGAAGATGGGTCTTGATGGACTGCAACAAGACTACATCAGGAAAGCTGAATACCCTTTTAGTTCTGAGCAGAAGTGGATGGCTGTTAAGTGTGTGCACCGAACACAGCAGGACAGACCAGAGATTTGTTTTATGAAGGGTGCTTATGAGCAGGTGATTAAGTATTGTACTACATACAACAGCAAAGGGCAGACTTTGGCACTTACCCAGCAGCAGAGAGATTTGTATCAACAAGAGAAGGCACGGATGGGCTCAGCGGGACTCAGAGTTCTTGCCTTGGCGTCTGGTCCGGAACTGGGGCAGCTGACCTTCCTTGGCCTGGTCGGAATCATTGACCCTCCTAGAACTGGTGTGAAGGAAGCTGTCACAACACTCATTGCCTCAGGAGTCTCCATCAAAATGATCACTGGAGATTCTCAGGAGACTGCAATTGCCATCGCTAGTCGTCTGGGATTGTACTCTAAGACTTCACAGTCCGTGTCTGGGGAAGAAGTCGATACAATGGAGGTGCAGCACCTTTCACAGATAGTGCCAAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CTTCACAGTCCGTGTCTGGG
60.32
TGCTTCTTCTGCCTGCATCA
59.96
143
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
ACTTCACAGTCCGTGTCTGG
59.61
TGCTTCTTCTGCCTGCATCA
59.96
144
PCR template sequence:
CGCTAGTCGTCTGGGATTGTACTCTAAGACTTCACAGTCCGTGTCTGGGGAAGAAGTCGATACAATGGAGGTGCAGCACCTTTCACAGATAGTGCCAAAGGGTATTGTCATTGGAACAGGAGAAAATTCTGAATTTGGAGAGGTCTTTAAGATGATGCAGGCAGAAGAAGCACCAAAAACTCCTCTGCAGAAGAGCATGG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
15
Interacting miRNAs (#binding sites)
mmu-miR-7a-1-3p(2), mmu-miR-9-5p(1), mmu-miR-199a-5p(1), mmu-miR-92a-3p(1), mmu-miR-335-5p(1), mmu-miR-298-5p(1), mmu-miR-136-5p(1), mmu-miR-22-3p(1), mmu-miR-96-5p(1), mmu-miR-194-5p(1), mmu-miR-297a-5p(1), mmu-miR-384-3p(1), mmu-miR-1199-5p(1), mmu-miR-1904(1), mmu-miR-323-3p(1)
siRNAs for circular RNA silencing
Junction sequence
GATAGTGCCAAAGGGTATTGTCATTG
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCATP2C1_1152_ORF_1
1.1216
0.16441342
0.999998899
2253
ORF sequence:
ATGATGCAGGCAGAAGAAGCACCAAAAACTCCTCTGCAGAAGAGCATGGACCTCTTAGGCAAGCAGCTGTCCTTTTACTCCTTTGGTATAATAGGTATCATCATGTTGGTTGGCTGGTTACTAGGAAAAGACATTCTGGAAATGTTCACTATTAGTGTAAGCTTGGCTGTAGCTGCAATTCCTGAAGGCCTGCCTATTGTGGTCACGGTGACTCTAGCCCTTGGTGTTATGAGAATGGTGAAGAAAAGGGCTATTGTAAAGAAATTGCCTATTGTGGAAACACTGGGCTGCTGTAATGTGATTTGTTCAGATAAAACTGGAACCCTGACGAAGAACGAGATGACTGTTACTCACATCCTCACTTCCGATGGCCTGCATGCTGAGGTCACTGGAGTTGGCTATAATCAGTTTGGTGAAGTGATCGTTGATGGTGATGTTGTTCATGGATTTTATAACCCAGCTGTTAGCAGAATTGTTGAGGCAGGCTGTGTGTGCAATGATGCTGTAATTAGGAACAACACTCTGATGGGAAAGCCAACTGAAGGAGCCTTAATCGCTCTTGCTATGAAGATGGGTCTTGATGGACTGCAACAAGACTACATCAGGAAAGCTGAATACCCTTTTAGTTCTGAGCAGAAGTGGATGGCTGTTAAGTGTGTGCACCGAACACAGCAGGACAGACCAGAGATTTGTTTTATGAAGGGTGCTTATGAGCAGGTGATTAAGTATTGTACTACATACAACAGCAAAGGGCAGACTTTGGCACTTACCCAGCAGCAGAGAGATTTGTATCAACAAGAGAAGGCACGGATGGGCTCAGCGGGACTCAGAGTTCTTGCCTTGGCGTCTGGTCCGGAACTGGGGCAGCTGACCTTCCTTGGCCTGGTCGGAATCATTGACCCTCCTAGAACTGGTGTGAAGGAAGCTGTCACAACACTCATTGCCTCAGGAGTCTCCATCAAAATGATCACTGGAGATTCTCAGGAGACTGCAATTGCCATCGCTAGTCGTCTGGGATTGTACTCTAAGACTTCACAGTCCGTGTCTGGGGAAGAAGTCGATACAATGGAGGTGCAGCACCTTTCACAGATAGTGCCAAAGGGTATTGTCATTGGAACAGGAGAAAATTCTGAATTTGGAGAGGTCTTTAAGATGATGCAGGCAGAAGAAGCACCAAAAACTCCTCTGCAGAAGAGCATGGACCTCTTAGGCAAGCAGCTGTCCTTTTACTCCTTTGGTATAATAGGTATCATCATGTTGGTTGGCTGGTTACTAGGAAAAGACATTCTGGAAATGTTCACTATTAGTGTAAGCTTGGCTGTAGCTGCAATTCCTGAAGGCCTGCCTATTGTGGTCACGGTGACTCTAGCCCTTGGTGTTATGAGAATGGTGAAGAAAAGGGCTATTGTAAAGAAATTGCCTATTGTGGAAACACTGGGCTGCTGTAATGTGATTTGTTCAGATAAAACTGGAACCCTGACGAAGAACGAGATGACTGTTACTCACATCCTCACTTCCGATGGCCTGCATGCTGAGGTCACTGGAGTTGGCTATAATCAGTTTGGTGAAGTGATCGTTGATGGTGATGTTGTTCATGGATTTTATAACCCAGCTGTTAGCAGAATTGTTGAGGCAGGCTGTGTGTGCAATGATGCTGTAATTAGGAACAACACTCTGATGGGAAAGCCAACTGAAGGAGCCTTAATCGCTCTTGCTATGAAGATGGGTCTTGATGGACTGCAACAAGACTACATCAGGAAAGCTGAATACCCTTTTAGTTCTGAGCAGAAGTGGATGGCTGTTAAGTGTGTGCACCGAACACAGCAGGACAGACCAGAGATTTGTTTTATGAAGGGTGCTTATGAGCAGGTGATTAAGTATTGTACTACATACAACAGCAAAGGGCAGACTTTGGCACTTACCCAGCAGCAGAGAGATTTGTATCAACAAGAGAAGGCACGGATGGGCTCAGCGGGACTCAGAGTTCTTGCCTTGGCGTCTGGTCCGGAACTGGGGCAGCTGACCTTCCTTGGCCTGGTCGGAATCATTGACCCTCCTAGAACTGGTGTGAAGGAAGCTGTCACAACACTCATTGCCTCAGGAGTCTCCATCAAAATGATCACTGGAGATTCTCAGGAGACTGCAATTGCCATCGCTAGTCGTCTGGGATTGTACTCTAAGACTTCACAGTCCGTGTCTGGGGAAGAAGTCGATACAATGGAGGTGCAGCACCTTTCACAGATAGTGCCAAAG
Peptide sequence:
MMQAEEAPKTPLQKSMDLLGKQLSFYSFGIIGIIMLVGWLLGKDILEMFTISVSLAVAAIPEGLPIVVTVTLALGVMRMVKKRAIVKKLPIVETLGCCNVICSDKTGTLTKNEMTVTHILTSDGLHAEVTGVGYNQFGEVIVDGDVVHGFYNPAVSRIVEAGCVCNDAVIRNNTLMGKPTEGALIALAMKMGLDGLQQDYIRKAEYPFSSEQKWMAVKCVHRTQQDRPEICFMKGAYEQVIKYCTTYNSKGQTLALTQQQRDLYQQEKARMGSAGLRVLALASGPELGQLTFLGLVGIIDPPRTGVKEAVTTLIASGVSIKMITGDSQETAIAIASRLGLYSKTSQSVSGEEVDTMEVQHLSQIVPKGIVIGTGENSEFGEVFKMMQAEEAPKTPLQKSMDLLGKQLSFYSFGIIGIIMLVGWLLGKDILEMFTISVSLAVAAIPEGLPIVVTVTLALGVMRMVKKRAIVKKLPIVETLGCCNVICSDKTGTLTKNEMTVTHILTSDGLHAEVTGVGYNQFGEVIVDGDVVHGFYNPAVSRIVEAGCVCNDAVIRNNTLMGKPTEGALIALAMKMGLDGLQQDYIRKAEYPFSSEQKWMAVKCVHRTQQDRPEICFMKGAYEQVIKYCTTYNSKGQTLALTQQQRDLYQQEKARMGSAGLRVLALASGPELGQLTFLGLVGIIDPPRTGVKEAVTTLIASGVSIKMITGDSQETAIAIASRLGLYSKTSQSVSGEEVDTMEVQHLSQIVPK
IRESfinder result
IRESfinder score
0.530708103
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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