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mmu_circRc3h2_2960
Basic information of circular RNA
PanCircBase ID:
mmu_circRc3h2_2960
mm39_Chr. Position ID:
chr2|37267862|37304824|-
Gene name:
Rc3h2
Transcript:
ENSMUST00000112934.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
15
Exon/intron indexes:
17,16,15,14,13,12,11,10,9,8,7,6,5,4,3
Exon/intron offsets:
0,457,1007,4019,4932,7395,11734,20393,21736,21970,22678,27393,31583,33289,36665
Genomic length:
36962
Exon/intron sizes in nt:
8,52,14,14,71,68,43,42,00,00,00,00,00,00,00,00,00,00,00,00,00,000
Flanking exon/introns:
chr2:37267448-37267862|chr2:37304824-37309443
Splice length:
2960
Other database IDs:
circAtlas: mmu-Rc3h2_0024
Human Ortholog IDs:
Mature spliced Sequence:
CTTAAAAAACACTACACATCAAAATAATGATCTGCTAGACTGCTAACCCGAGCATCAGCTTCCACAATGCCTGTGCAGGCAGCTCAATGGACAGAGTTTCTGTCCTGTCCAATCTGCTATAATGAATTTGATGAGAATGTGCACAAACCCATCAGTTTAGGTTGTTCACACACAGTTTGCAAGACCTGCTTGAATAAACTTCACCGAAAAGCGTGTCCTTTTGACCAGACTGCCATAAACACAGACATTGATGTGCTCCCTGTCAACTTTGCACTTCTTCAGTTAGTTGGAGCCCAGGTACCAGATCATCAGTCAATAAAGTTAAGTAATCTAGGTGAGAATAAACACTATGAAGTGGCAAAAAAATGCGTAGAGGACTTGGCACTCTACTTAAAACCACTAAGTGGAGGTAAAGGTGTAGCTAGTTTGAACCAGAGTGCCCTGAGCCGTCCAATGCAAAGGAAACTAGTTACACTTGTAAACTGTCAACTGGTGGAAGAAGAAGGTCGTGTCAGAGCTATGCGAGCGGCCCGTTCACTAGGAGAAAGAACTGTGACAGAACTGATACTGCAGCACCAGAACCCTCAGCAGCTGTCTGCCAACCTGTGGGCTGCTGTCAGGGCTCGAGGATGCCAGTTTCTAGGGCCAGCTATGCAAGAAGAAGCCTTGAAGTTGGTATTGCTGGCATTAGAAGATGGTTCTGCTCTCTCTAGGAAAGTTCTAGTACTTTTTGTTGTGCAAAGACTAGAACCAAGATTTCCTCAGGCATCAAAAACAAGTATTGGCCATGTTGTGCAGCTATTGTACCGAGCTTCTTGTTTTAAGGTTACTAAAAGGGATGAAGACTCTTCCCTGATGCAGCTAAAGGAGGAATTTCGGAGTTACGAGGCACTACGCAGAGAACATGATGCCCAGATTGTTCATATTGCCATGGAAGCAGGACTCCGTATTTCACCTGAGCAGTGGTCTTCACTGCTGTATGGGGACTTGGCTCATAAATCACACATGCAGTCTATCATTGATAAGCTACAGTCTCCAGAATCATTTGCAAAGAGTGTCCAGGAATTGACAATTGTTTTGCAGCGAACTGGTGACCCTGCTAATTTAAATAGGCTGAGACCTCATTTAGAGCTTCTTGCAAACATAGACCCTAATCCAGATGCTGTTTCACCAACTTGGGAGCAACTGGAAAATGCAATGGTAGCTGTTAAAACAGTTGTTCATGGTCTTGTGGACTTCATACAAAATTATAGTAGAAAAGGCCATGAGACACCTCAGCCACAGCCAAACAGCAAGTATAAAACTAGTATGTGCCGAGATTTACGACAACAAGGGGGTTGTCCACGAGGAACAAATTGTACATTTGCCCATTCTCAGGAAGAGCTTGAAAAGTACCGATTAAGGAACAAAAAGATGAGCGCGACTGTAAGAACATTTCCTCTTCTGAATAAAGTTGGTGTAAACAGCACTGTCACAACCACAGCCGGAAATGTCATTTCTGTCATAGGAAGTACTGAAACAACTGGGAAAATTGTTGCAAGTACAAATGGAATTTCAAATACAGAAAGCAGTGTTTCTCAGCTAATCCCACGAGGCACTGACAGTGCAGTAAGGACTTTGGAGACTGTGAAGAAAGTCGGGAAGGTTGGCACTAATGCTCAGAATGCTGGGCCCTCTGCAGAGTCCGTGTCTGAAAATAAAATTGGTTCTCCACCCAAGACTCCTGTAAGTAATGCAGCAGCTACCTCCGCTGGGCCCTCTAATTTTGGAACAGAGCTGAATTCCCTGCCTCCCAAATCCAGCCCATTTCTAACTAGAGTTCCAGTATATCCTCAGCATTCTGAAAGCATTCAGTATTTTCAAGATCCAAGGACTCAGATACCTTTTGAAGTCCCACAATACCCACAAACAGGATACTACCCACCACCTCCAACGGTACCAGCTGGTGTGACTCCCTGTGTTCCTCGCTTTGTGAGGTCCAGTAATGTTCCAGAGTCCTCCCTCCCACCTGCTTCCATGCCATATGCTGATCATTACAGTACATTCTCCCCTCGAGATCGAATGAATTCTTCTCCTTACCAACCTCCTCCTCCGCAGCAGTATGGACCAGTTCCTCCAGTACCCTCTGGAATGTATGCTCCGGTGTATGACAGCAGGCGCATCTGGCGCCCAGCTATGTACCAACGAGATGACATTATTAGAAGCAATTCTTTACCTCCAATGGATGTGATGCACTCATCTGTCTATCAGACATCTTTACGGGAAAGATACAACTCATTAGATGGATATTATTCAGTGGCTTGTCAGCCACCGAATGACCCAAGGACAACTGTGCCTTTACCAAGGGAACCTTGTGGTCATTTGAAGACCAGTTGTGAGGAACAGTTAAGAAGAAAGCCAGATCAGTGGACACAGTATCATACCCAGAAAACACCTGTCTCTTCAACTCTTCCTGTGGCCACACAGTCACCAACACCACCTTCTCCTCTATTCAGTGTAGACTTCCGATCGGATTTCTCTGAGAGTGTGAGTGGCGCAAAATTTGAGGAAGACCATCTTTCCCATTATTCTCCCTGGTCTTGTGGTACCATAGGCTCTTGTATAAATGCCATTGATTCGGAGCCCAAAGACGTAATTGCTAATTCAAATGCTGTATTGATGGACCTGGACAGTGGGGATGTAAAGAGAAGAGTGCATTTATTTGAAGCTCAGAGAAGGACAAAAGAAGAAGACCCAATTATTCCCTTTAGTGACGGACCCATTATCTCAAAATGGGGTGCAATTTCCCGATCCTCCCGAACAGGTTACCATACAACAGATCCCGTCCAGGCAACTGCTTCCCAAGGAAGTGCAACTAAGCCCATCAGCGTATCAGATTATGTCCCTTACGTGAATGCTGTCGATTCAAGGTGGAGTTCATATGGCAACGATGCTACATCATCAGCACACTATATTGAACG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TGCTGTCGATTCAAGGTGGA
59.32
ACTCTGTCCATTGAGCTGCC
60.04
163
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TGCTGTCGATTCAAGGTGGA
59.32
TCTGTCCATTGAGCTGCCTG
60.04
161
PCR template sequence:
CCATCAGCGTATCAGATTATGTCCCTTACGTGAATGCTGTCGATTCAAGGTGGAGTTCATATGGCAACGATGCTACATCATCAGCACACTATATTGAACGCTTAAAAAACACTACACATCAAAATAATGATCTGCTAGACTGCTAACCCGAGCATCAGCTTCCACAATGCCTGTGCAGGCAGCTCAATGGACAGAGTTTC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
30
Interacting miRNAs (#binding sites)
mmu-miR-9-5p(1), mmu-miR-140-5p(1), mmu-miR-134-5p(1), mmu-let-7a-5p(1), mmu-miR-27b-3p(1), mmu-miR-27a-3p(1), mmu-let-7e-5p(1), mmu-let-7b-5p(1), mmu-miR-135a-5p(1), mmu-let-7c-5p(1), mmu-miR-211-5p(1), mmu-miR-204-5p(1), mmu-miR-130a-3p(1), mmu-miR-138-5p(1), mmu-miR-381-3p(1), mmu-let-7d-5p(1), mmu-miR-431-5p(1), mmu-miR-501-3p(1), mmu-miR-130b-3p(1), mmu-miR-721(1), mmu-miR-125b-1-3p(1), mmu-miR-301a-3p(1), mmu-miR-98-5p(1), mmu-miR-705(1), mmu-miR-27a-5p(1), mmu-miR-1187(1), mmu-miR-3065-5p(1), mmu-miR-3470b(1), mmu-miR-350-3p(1), mmu-miR-338-3p(1)
siRNAs for circular RNA silencing
Junction sequence
ACTATATTGAACGCTTAAAAAACACT
siRNA sets
TTTTTAAGCGTTCAATATA, TTTAAGCGTTCAATATAGT, TTTTTTAAGCGTTCAATAT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCRC3H2_2960_ORF_1
0.9542
0.034902097
0.99999998
2940
ORF sequence:
ATGCCTGTGCAGGCAGCTCAATGGACAGAGTTTCTGTCCTGTCCAATCTGCTATAATGAATTTGATGAGAATGTGCACAAACCCATCAGTTTAGGTTGTTCACACACAGTTTGCAAGACCTGCTTGAATAAACTTCACCGAAAAGCGTGTCCTTTTGACCAGACTGCCATAAACACAGACATTGATGTGCTCCCTGTCAACTTTGCACTTCTTCAGTTAGTTGGAGCCCAGGTACCAGATCATCAGTCAATAAAGTTAAGTAATCTAGGTGAGAATAAACACTATGAAGTGGCAAAAAAATGCGTAGAGGACTTGGCACTCTACTTAAAACCACTAAGTGGAGGTAAAGGTGTAGCTAGTTTGAACCAGAGTGCCCTGAGCCGTCCAATGCAAAGGAAACTAGTTACACTTGTAAACTGTCAACTGGTGGAAGAAGAAGGTCGTGTCAGAGCTATGCGAGCGGCCCGTTCACTAGGAGAAAGAACTGTGACAGAACTGATACTGCAGCACCAGAACCCTCAGCAGCTGTCTGCCAACCTGTGGGCTGCTGTCAGGGCTCGAGGATGCCAGTTTCTAGGGCCAGCTATGCAAGAAGAAGCCTTGAAGTTGGTATTGCTGGCATTAGAAGATGGTTCTGCTCTCTCTAGGAAAGTTCTAGTACTTTTTGTTGTGCAAAGACTAGAACCAAGATTTCCTCAGGCATCAAAAACAAGTATTGGCCATGTTGTGCAGCTATTGTACCGAGCTTCTTGTTTTAAGGTTACTAAAAGGGATGAAGACTCTTCCCTGATGCAGCTAAAGGAGGAATTTCGGAGTTACGAGGCACTACGCAGAGAACATGATGCCCAGATTGTTCATATTGCCATGGAAGCAGGACTCCGTATTTCACCTGAGCAGTGGTCTTCACTGCTGTATGGGGACTTGGCTCATAAATCACACATGCAGTCTATCATTGATAAGCTACAGTCTCCAGAATCATTTGCAAAGAGTGTCCAGGAATTGACAATTGTTTTGCAGCGAACTGGTGACCCTGCTAATTTAAATAGGCTGAGACCTCATTTAGAGCTTCTTGCAAACATAGACCCTAATCCAGATGCTGTTTCACCAACTTGGGAGCAACTGGAAAATGCAATGGTAGCTGTTAAAACAGTTGTTCATGGTCTTGTGGACTTCATACAAAATTATAGTAGAAAAGGCCATGAGACACCTCAGCCACAGCCAAACAGCAAGTATAAAACTAGTATGTGCCGAGATTTACGACAACAAGGGGGTTGTCCACGAGGAACAAATTGTACATTTGCCCATTCTCAGGAAGAGCTTGAAAAGTACCGATTAAGGAACAAAAAGATGAGCGCGACTGTAAGAACATTTCCTCTTCTGAATAAAGTTGGTGTAAACAGCACTGTCACAACCACAGCCGGAAATGTCATTTCTGTCATAGGAAGTACTGAAACAACTGGGAAAATTGTTGCAAGTACAAATGGAATTTCAAATACAGAAAGCAGTGTTTCTCAGCTAATCCCACGAGGCACTGACAGTGCAGTAAGGACTTTGGAGACTGTGAAGAAAGTCGGGAAGGTTGGCACTAATGCTCAGAATGCTGGGCCCTCTGCAGAGTCCGTGTCTGAAAATAAAATTGGTTCTCCACCCAAGACTCCTGTAAGTAATGCAGCAGCTACCTCCGCTGGGCCCTCTAATTTTGGAACAGAGCTGAATTCCCTGCCTCCCAAATCCAGCCCATTTCTAACTAGAGTTCCAGTATATCCTCAGCATTCTGAAAGCATTCAGTATTTTCAAGATCCAAGGACTCAGATACCTTTTGAAGTCCCACAATACCCACAAACAGGATACTACCCACCACCTCCAACGGTACCAGCTGGTGTGACTCCCTGTGTTCCTCGCTTTGTGAGGTCCAGTAATGTTCCAGAGTCCTCCCTCCCACCTGCTTCCATGCCATATGCTGATCATTACAGTACATTCTCCCCTCGAGATCGAATGAATTCTTCTCCTTACCAACCTCCTCCTCCGCAGCAGTATGGACCAGTTCCTCCAGTACCCTCTGGAATGTATGCTCCGGTGTATGACAGCAGGCGCATCTGGCGCCCAGCTATGTACCAACGAGATGACATTATTAGAAGCAATTCTTTACCTCCAATGGATGTGATGCACTCATCTGTCTATCAGACATCTTTACGGGAAAGATACAACTCATTAGATGGATATTATTCAGTGGCTTGTCAGCCACCGAATGACCCAAGGACAACTGTGCCTTTACCAAGGGAACCTTGTGGTCATTTGAAGACCAGTTGTGAGGAACAGTTAAGAAGAAAGCCAGATCAGTGGACACAGTATCATACCCAGAAAACACCTGTCTCTTCAACTCTTCCTGTGGCCACACAGTCACCAACACCACCTTCTCCTCTATTCAGTGTAGACTTCCGATCGGATTTCTCTGAGAGTGTGAGTGGCGCAAAATTTGAGGAAGACCATCTTTCCCATTATTCTCCCTGGTCTTGTGGTACCATAGGCTCTTGTATAAATGCCATTGATTCGGAGCCCAAAGACGTAATTGCTAATTCAAATGCTGTATTGATGGACCTGGACAGTGGGGATGTAAAGAGAAGAGTGCATTTATTTGAAGCTCAGAGAAGGACAAAAGAAGAAGACCCAATTATTCCCTTTAGTGACGGACCCATTATCTCAAAATGGGGTGCAATTTCCCGATCCTCCCGAACAGGTTACCATACAACAGATCCCGTCCAGGCAACTGCTTCCCAAGGAAGTGCAACTAAGCCCATCAGCGTATCAGATTATGTCCCTTACGTGAATGCTGTCGATTCAAGGTGGAGTTCATATGGCAACGATGCTACATCATCAGCACACTATATTGAACGCTTAAAAAACACTACACATCAAAATAATGATCTGCTAGACTGCTAA
Peptide sequence:
MPVQAAQWTEFLSCPICYNEFDENVHKPISLGCSHTVCKTCLNKLHRKACPFDQTAINTDIDVLPVNFALLQLVGAQVPDHQSIKLSNLGENKHYEVAKKCVEDLALYLKPLSGGKGVASLNQSALSRPMQRKLVTLVNCQLVEEEGRVRAMRAARSLGERTVTELILQHQNPQQLSANLWAAVRARGCQFLGPAMQEEALKLVLLALEDGSALSRKVLVLFVVQRLEPRFPQASKTSIGHVVQLLYRASCFKVTKRDEDSSLMQLKEEFRSYEALRREHDAQIVHIAMEAGLRISPEQWSSLLYGDLAHKSHMQSIIDKLQSPESFAKSVQELTIVLQRTGDPANLNRLRPHLELLANIDPNPDAVSPTWEQLENAMVAVKTVVHGLVDFIQNYSRKGHETPQPQPNSKYKTSMCRDLRQQGGCPRGTNCTFAHSQEELEKYRLRNKKMSATVRTFPLLNKVGVNSTVTTTAGNVISVIGSTETTGKIVASTNGISNTESSVSQLIPRGTDSAVRTLETVKKVGKVGTNAQNAGPSAESVSENKIGSPPKTPVSNAAATSAGPSNFGTELNSLPPKSSPFLTRVPVYPQHSESIQYFQDPRTQIPFEVPQYPQTGYYPPPPTVPAGVTPCVPRFVRSSNVPESSLPPASMPYADHYSTFSPRDRMNSSPYQPPPPQQYGPVPPVPSGMYAPVYDSRRIWRPAMYQRDDIIRSNSLPPMDVMHSSVYQTSLRERYNSLDGYYSVACQPPNDPRTTVPLPREPCGHLKTSCEEQLRRKPDQWTQYHTQKTPVSSTLPVATQSPTPPSPLFSVDFRSDFSESVSGAKFEEDHLSHYSPWSCGTIGSCINAIDSEPKDVIANSNAVLMDLDSGDVKRRVHLFEAQRRTKEEDPIIPFSDGPIISKWGAISRSSRTGYHTTDPVQATASQGSATKPISVSDYVPYVNAVDSRWSSYGNDATSSAHYIERLKNTTHQNNDLLDC
IRESfinder result
IRESfinder score
0.650521578
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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