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mmu_circThumpd2_1061
Basic information of circular RNA
PanCircBase ID:
mmu_circThumpd2_1061
mm39_Chr. Position ID:
chr17|81340060|81363339|-
Gene name:
Thumpd2
Transcript:
ENSMUST00000025093.6
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
8
Exon/intron indexes:
9,8,7,6,5,4,3,2
Exon/intron offsets:
0,4866,5473,11468,17305,20263,21492,23143
Genomic length:
23279
Exon/intron sizes in nt:
1,09,11,57,28,85,37,84,00,000
Flanking exon/introns:
chr17:81334399-81340060|chr17:81363339-81372363
Splice length:
1061
Other database IDs:
circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_145855
Human Ortholog IDs:
Mature spliced Sequence:
GTTGAATACATTTCAGGAAAAGTGTTTTTCACCACCTGTTCAGATTTGCCCTCTATGAAGAAGTTGAAGTCAGCGGAAAGACTGTTTGTGTTGATTAAGAAGCAGCTTCCCATTGCAGTCTCTTCTCTGCACAAAGGAAAAATACTTAATGAGATGCAAAGATTTGTAAATGATGATCCAGGAAGTTGGCTGGAGGCCATTTCACTTTGGAAAAAACTTCTCGAACATGACCCAAAAAGAGAAAAAGTTTCTCAAAGGGATGCTAACCCACTAAAACGGAAAGCGGGAGAAAATGAAACTATCATTGCTAAGAAATTAAAAGTGGAGGAGAAACAAGAGGTTGCCAAGGATCACGGAGAAAGCCAGGAGGACAAACTTCTGCAAGGCTCCCCGGAGCAAGGAGAAGCTGTCACTAGAACAGAGCTGCAAGACCATAGACTCAATAGTACCACAGAGAAGGCAGCTGATGCTCAGGACCAGGAGGACTTGACCTTCAGGGTTTCCTGCCGCTGCACCGGGAATGTCAGAAAGGTCATCACGGGACAGGAGGCAGGAAGAGTGATTGGACTTGCTCTCATGAGGCAGTTTGGATGGAAAGCTGACTTGAGGAATCCAAATATAGAGATCTTCATGCACCTGAGTGATGCTTACTCCGTGGTGGGGATTCCTCTGCTCAGAATGCCCTTGGCCAGCAGAACTTACATCCAGACAGCTGGGCTGCGGTCAACCATAGCGTGGGCCATGGCGTCCATTGCAGAAATTAAGGCTGGAGCACTGGTTTTAGATCCGATGTGTGGCCTTGGGACTATACTTGTGGAAGCAGCCGAAGAGTGGCCAGATGTATTTTACATGGGTGCTGATATGAGTGACGCACAGTTACTTGGCGCATGTGACAATCTGAAGGCTGCAGGCCTTACAGACAGGATTGAGTTACTTAAAAGCTCTGTTACAGATTTACCACTGCCATCACAAAGTACGGATGTTATTATTTCTGACATTCCATTTGGGAAAAAATTTAAGTTAGGAAAAGACATCAAAAGCATTCTACAAGAAATGGAAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TGCCATCACAAAGTACGGATGT
60.29
GGGCAAATCTGAACAGGTGG
59.11
151
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TGCCATCACAAAGTACGGATG
58.64
GGGCAAATCTGAACAGGTGG
59.11
151
PCR template sequence:
TGCCATCACAAAGTACGGATGTTATTATTTCTGACATTCCATTTGGGAAAAAATTTAAGTTAGGAAAAGACATCAAAAGCATTCTACAAGAAATGGAAAGGTTGAATACATTTCAGGAAAAGTGTTTTTCACCACCTGTTCAGATTTGCCCTCTATGAAGAAGTTGAAGTCAGCGGAAAGACTGTTTGTGTTGATTAAGA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
11
Interacting miRNAs (#binding sites)
mmu-miR-203-3p(2), mmu-miR-1a-3p(1), mmu-miR-206-3p(1), mmu-miR-211-5p(1), mmu-miR-204-5p(1), mmu-miR-324-5p(1), mmu-miR-431-5p(1), mmu-miR-182-5p(1), mmu-miR-362-5p(1), mmu-miR-34b-5p(1), mmu-miR-207(1)
siRNAs for circular RNA silencing
Junction sequence
AAGAAATGGAAAGGTTGAATACATTT
siRNA sets
TATTCAACCTTTCCATTTC, AAATGTATTCAACCTTTCC, ATTCAACCTTTCCATTTCT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCTHUMPD2_1061_ORF_1
1.0182
0.102244632
0.991024266
1065
ORF sequence:
ATGAAGAAGTTGAAGTCAGCGGAAAGACTGTTTGTGTTGATTAAGAAGCAGCTTCCCATTGCAGTCTCTTCTCTGCACAAAGGAAAAATACTTAATGAGATGCAAAGATTTGTAAATGATGATCCAGGAAGTTGGCTGGAGGCCATTTCACTTTGGAAAAAACTTCTCGAACATGACCCAAAAAGAGAAAAAGTTTCTCAAAGGGATGCTAACCCACTAAAACGGAAAGCGGGAGAAAATGAAACTATCATTGCTAAGAAATTAAAAGTGGAGGAGAAACAAGAGGTTGCCAAGGATCACGGAGAAAGCCAGGAGGACAAACTTCTGCAAGGCTCCCCGGAGCAAGGAGAAGCTGTCACTAGAACAGAGCTGCAAGACCATAGACTCAATAGTACCACAGAGAAGGCAGCTGATGCTCAGGACCAGGAGGACTTGACCTTCAGGGTTTCCTGCCGCTGCACCGGGAATGTCAGAAAGGTCATCACGGGACAGGAGGCAGGAAGAGTGATTGGACTTGCTCTCATGAGGCAGTTTGGATGGAAAGCTGACTTGAGGAATCCAAATATAGAGATCTTCATGCACCTGAGTGATGCTTACTCCGTGGTGGGGATTCCTCTGCTCAGAATGCCCTTGGCCAGCAGAACTTACATCCAGACAGCTGGGCTGCGGTCAACCATAGCGTGGGCCATGGCGTCCATTGCAGAAATTAAGGCTGGAGCACTGGTTTTAGATCCGATGTGTGGCCTTGGGACTATACTTGTGGAAGCAGCCGAAGAGTGGCCAGATGTATTTTACATGGGTGCTGATATGAGTGACGCACAGTTACTTGGCGCATGTGACAATCTGAAGGCTGCAGGCCTTACAGACAGGATTGAGTTACTTAAAAGCTCTGTTACAGATTTACCACTGCCATCACAAAGTACGGATGTTATTATTTCTGACATTCCATTTGGGAAAAAATTTAAGTTAGGAAAAGACATCAAAAGCATTCTACAAGAAATGGAAAGGTTGAATACATTTCAGGAAAAGTGTTTTTCACCACCTGTTCAGATTTGCCCTCTATGA
Peptide sequence:
MKKLKSAERLFVLIKKQLPIAVSSLHKGKILNEMQRFVNDDPGSWLEAISLWKKLLEHDPKREKVSQRDANPLKRKAGENETIIAKKLKVEEKQEVAKDHGESQEDKLLQGSPEQGEAVTRTELQDHRLNSTTEKAADAQDQEDLTFRVSCRCTGNVRKVITGQEAGRVIGLALMRQFGWKADLRNPNIEIFMHLSDAYSVVGIPLLRMPLASRTYIQTAGLRSTIAWAMASIAEIKAGALVLDPMCGLGTILVEAAEEWPDVFYMGADMSDAQLLGACDNLKAAGLTDRIELLKSSVTDLPLPSQSTDVIISDIPFGKKFKLGKDIKSILQEMERLNTFQEKCFSPPVQICPL
IRESfinder result
IRESfinder score
0.564348339
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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