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mmu_circCcdc171_1949
Basic information of circular RNA
PanCircBase ID:
mmu_circCcdc171_1949
mm39_Chr. Position ID:
chr4|83573764|83614673|+
Gene name:
Ccdc171
Transcript:
ENSMUST00000053414.13
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
10
Exon/intron indexes:
12,13,14,15,16,17,18,19,20,21
Exon/intron offsets:
0,1808,2793,6188,7974,25477,26771,38219,38725,40723
Genomic length:
40909
Exon/intron sizes in nt:
107,66,201,168,189,505,117,227,183,186
Flanking exon/introns:
chr4:83553979-83573764|chr4:83614673-83661164
Splice length:
1949
Other database IDs:
circAtlas: mmu-Ccdc171_0006
circAtlas: hsa-CCDC171_0009, CIRCpedia: HSA_CIRCpedia_149070
Human Ortholog IDs:
Mature spliced Sequence:
GCGTCCACAAGGACAAAGATAAGCCTCCCAGCTTCTCCGTCGTCCTTGAGACTTTGAGGCGGACCTTGACAGATTACCAGAACAAGCTGGAAGATGCATCTAATGAGGAAAAGACATCCAACGAACTCGATTCCACCAAACAAAAGATTGAGACTCACATTAAAAATACAAAGGAGCTGCAGGATAAGCTGACGGAGGTCCATAAGGAGCTCAGTCACTTGCGCGCTAAGTGCGCAGACCGCGAGGCTCTGATCACCTCGTTGAAGGTGGAGTTGCAGAACGTGCTGCACTGCTGGGAGAAGGAGAAGGCCTGTGCCGCCCAGTGTGAGAGCGAGCTGCAGAAGCTGTCGCAGGCCTTCCAGAAGGACTCCGAGGAGAAGCTAACCTTCCTTCACACCTTGTATCAGCACTTGGTAGCAGGCTGTGTGCTCATAAAACAACCAGAAGGCATGTTGGATAAATTCTCTTGGTCTGAGCTTTGTGCAGTCTTGCAGGAGAATGTTGATGCCCTCATTGCAGACCTTAACAGGGCTAATGAGAAGATAAGCCATCTGGAGTATATCTGTAAAAACAAGTCCGATACGATGAGAGAGCTTCAGCAGACGCAGGAAGACACCTTCAACAAGGTGGCGGAACAGATCAAGGCCCAGGAGAGCTGCTGGCAGAAGCAGAAGAAGGAGCTGGAGTTCCAGTACTCTGAACTTCTCCTGGAGGTGCAGAGGAGGGCACAGAAATTTCAAGAAATTGCAGAAAAAAACTCAGAAAAATTGAACCGCATTGAGACCTCCCATGAACAACTGGTTCGTGAGAATTCGCACTTCAAAACCACATTGTCCAGGACGCAGAGGGAACAGACGTGCTTGCTGGCGGCCTGTGCGCTGATGGCCGGTGCGCTGTGTCCCCTCTACAGCAGGTCATGTGCCTTATCCACACAGAGGGACTTTCTCCAGGAACAAGTCAACAGCTTGGAACTGTTCAAACTGGAAATTAGAACCCTGGCCCAGGCGTTGTCAGCGGTAGATGAGAAGAAACAAGAAGAAGCCAAAACGAAGAAAAAAACATTCAAAGGATTGGTCCGTGTCTTCCGGAAAGGCGTGATTGCAATCTTGGCAGCAAACAGACTCAAGCTTTTGGGCCAATCCTGTGCCTTTCTTTTCACCTGGATGGAGAGTTGTAAAGAAGGCATAGGCATGCTAGTGTGTACCGGGGAGCCCAAAGACAAGCGCCAATTCCCAAAACATCAGAGGGAACAGTTACGCTGTTTACAGGCACTCGCGTGGCTCACCAGTTCTGACCTTCTAGGTACGGTTATCAGTTCTATGACAGAGCTGCAAGAAGTCATTAGTAAAACAGATCCAAATTCCAGGATTTGTGGACATTTACTCATAGGTGCAGCCAAGAATTCTTTTGCAAAACTAATGGATAAACTTAGCTCGGCAATGGCAAGCATCCCTCTGCATAGCAGCCGGAGCATAACGTATGTAGAAAAGGATTCTCTGGTTCAGAGGCTGGCCCGGGGGCTTCACAAAGTGAACACGCTGGCCCTGAAGTATGGTTTATGCAGCCATATTCCCATCATGAAAAGCACTGCAGCGTTACAAAAGCAAATATTTGGGTTTACGCAAAGGCTGCACGCAGCTGAGGTTGAGCGCCGCTCCCTGCGCCTCGAGGTGACAGAATACAAACGGACCGTGCACGAGATGAAAAAGGAGCTGGACAAGTCACAGAGTCTGCAAACACAATTAAATGAATTCAAGCACTCTAAATTGATCACCCACGAGAAGTTTGAAAGTGCATGTGAAGAACTAAATAACGCATTGCTTCGGGAACAGCAGGCACAAATGTTGCTGAATGAACAGGCCCAGCAGCTGCAGGAGCTGAACTATAGACTTGAATTGCACTCCAGCGAGGAAGCTGACAAAAACCAGACTCTTGGAGAAGCTGTTAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
ACTTGAATTGCACTCCAGCG
59.12
TGGTAATCTGTCAAGGTCCGC
60.07
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GAATGAACAGGCCCAGCAGC
61.94
GGTCCGCCTCAAAGTCTCAA
59.97
165
PCR template sequence:
GAATGAACAGGCCCAGCAGCTGCAGGAGCTGAACTATAGACTTGAATTGCACTCCAGCGAGGAAGCTGACAAAAACCAGACTCTTGGAGAAGCTGTTAAGGCGTCCACAAGGACAAAGATAAGCCTCCCAGCTTCTCCGTCGTCCTTGAGACTTTGAGGCGGACCTTGACAGATTACCAGAACAAGCTGGAAGATGCATC
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-7b-5p(1), mmu-miR-135a-5p(1), mmu-miR-30e-5p(1), mmu-miR-30a-5p(1), mmu-miR-130a-3p(1), mmu-miR-148b-3p(1), mmu-miR-30c-5p(1), mmu-miR-298-5p(1), mmu-miR-128-3p(1), mmu-miR-30b-5p(1), mmu-miR-433-3p(1), mmu-miR-721(1), mmu-miR-382-5p(1), mmu-miR-370-3p(1), mmu-miR-207(1), mmu-miR-1904(1)
siRNAs for circular RNA silencing
Junction sequence
AGAAGCTGTTAAGGCGTCCACAAGGA
siRNA sets
CTTGTGGACGCCTTAACAG, TTGTGGACGCCTTAACAGC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCCCDC171_1949_ORF_1
1.0119
0.202937326
0.999818327
1557
ORF sequence:
ATGTTGGATAAATTCTCTTGGTCTGAGCTTTGTGCAGTCTTGCAGGAGAATGTTGATGCCCTCATTGCAGACCTTAACAGGGCTAATGAGAAGATAAGCCATCTGGAGTATATCTGTAAAAACAAGTCCGATACGATGAGAGAGCTTCAGCAGACGCAGGAAGACACCTTCAACAAGGTGGCGGAACAGATCAAGGCCCAGGAGAGCTGCTGGCAGAAGCAGAAGAAGGAGCTGGAGTTCCAGTACTCTGAACTTCTCCTGGAGGTGCAGAGGAGGGCACAGAAATTTCAAGAAATTGCAGAAAAAAACTCAGAAAAATTGAACCGCATTGAGACCTCCCATGAACAACTGGTTCGTGAGAATTCGCACTTCAAAACCACATTGTCCAGGACGCAGAGGGAACAGACGTGCTTGCTGGCGGCCTGTGCGCTGATGGCCGGTGCGCTGTGTCCCCTCTACAGCAGGTCATGTGCCTTATCCACACAGAGGGACTTTCTCCAGGAACAAGTCAACAGCTTGGAACTGTTCAAACTGGAAATTAGAACCCTGGCCCAGGCGTTGTCAGCGGTAGATGAGAAGAAACAAGAAGAAGCCAAAACGAAGAAAAAAACATTCAAAGGATTGGTCCGTGTCTTCCGGAAAGGCGTGATTGCAATCTTGGCAGCAAACAGACTCAAGCTTTTGGGCCAATCCTGTGCCTTTCTTTTCACCTGGATGGAGAGTTGTAAAGAAGGCATAGGCATGCTAGTGTGTACCGGGGAGCCCAAAGACAAGCGCCAATTCCCAAAACATCAGAGGGAACAGTTACGCTGTTTACAGGCACTCGCGTGGCTCACCAGTTCTGACCTTCTAGGTACGGTTATCAGTTCTATGACAGAGCTGCAAGAAGTCATTAGTAAAACAGATCCAAATTCCAGGATTTGTGGACATTTACTCATAGGTGCAGCCAAGAATTCTTTTGCAAAACTAATGGATAAACTTAGCTCGGCAATGGCAAGCATCCCTCTGCATAGCAGCCGGAGCATAACGTATGTAGAAAAGGATTCTCTGGTTCAGAGGCTGGCCCGGGGGCTTCACAAAGTGAACACGCTGGCCCTGAAGTATGGTTTATGCAGCCATATTCCCATCATGAAAAGCACTGCAGCGTTACAAAAGCAAATATTTGGGTTTACGCAAAGGCTGCACGCAGCTGAGGTTGAGCGCCGCTCCCTGCGCCTCGAGGTGACAGAATACAAACGGACCGTGCACGAGATGAAAAAGGAGCTGGACAAGTCACAGAGTCTGCAAACACAATTAAATGAATTCAAGCACTCTAAATTGATCACCCACGAGAAGTTTGAAAGTGCATGTGAAGAACTAAATAACGCATTGCTTCGGGAACAGCAGGCACAAATGTTGCTGAATGAACAGGCCCAGCAGCTGCAGGAGCTGAACTATAGACTTGAATTGCACTCCAGCGAGGAAGCTGACAAAAACCAGACTCTTGGAGAAGCTGTTAAGGCGTCCACAAGGACAAAGATAAGCCTCCCAGCTTCTCCGTCGTCCTTGAGACTTTGA
Peptide sequence:
MLDKFSWSELCAVLQENVDALIADLNRANEKISHLEYICKNKSDTMRELQQTQEDTFNKVAEQIKAQESCWQKQKKELEFQYSELLLEVQRRAQKFQEIAEKNSEKLNRIETSHEQLVRENSHFKTTLSRTQREQTCLLAACALMAGALCPLYSRSCALSTQRDFLQEQVNSLELFKLEIRTLAQALSAVDEKKQEEAKTKKKTFKGLVRVFRKGVIAILAANRLKLLGQSCAFLFTWMESCKEGIGMLVCTGEPKDKRQFPKHQREQLRCLQALAWLTSSDLLGTVISSMTELQEVISKTDPNSRICGHLLIGAAKNSFAKLMDKLSSAMASIPLHSSRSITYVEKDSLVQRLARGLHKVNTLALKYGLCSHIPIMKSTAALQKQIFGFTQRLHAAEVERRSLRLEVTEYKRTVHEMKKELDKSQSLQTQLNEFKHSKLITHEKFESACEELNNALLREQQAQMLLNEQAQQLQELNYRLELHSSEEADKNQTLGEAVKASTRTKISLPASPSSLRL
IRESfinder result
IRESfinder score
0.453821257
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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