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mmu_circRapgef6_1612
Basic information of circular RNA
PanCircBase ID:
mmu_circRapgef6_1612
mm39_Chr. Position ID:
chr11|54510711|54540165|+
Gene name:
Rapgef6
Transcript:
ENSMUST00000102743.10
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
10
Exon/intron indexes:
8,9,10,11,12,13,14,15,16,17
Exon/intron offsets:
0,2430,5975,6699,11306,14874,16126,19864,22825,29296
Genomic length:
29454
Exon/intron sizes in nt:
1,78,13,71,59,15,31,65,00,00,00,00,00,00,000
Flanking exon/introns:
chr11:54501745-54510711|chr11:54540165-54548071
Splice length:
1612
Other database IDs:
CIRCpedia: MMU_CIRCpedia_222530, circAtlas: mmu-Rapgef6_0054
Human Ortholog IDs:
Mature spliced Sequence:
GCTACAGAGAGTGAAGTAGGAGATGTAGATTTAACACGCCTTCCAGAAGGACCTGTTGATTCTGAGGATGAAGAGGAGGAGGAAGAAGAGATTGATAGAACAGATCCACTGCAGGGTCGAGATCTTGTTCGGGAGTGTCTTGAAAAGGAACCCGCAGACAAAACTGATGATGATGTTGAACAGTTACTTGAGTTCATGCACCAGCTGCCTGCCTTTGCGAACATGACCATGTCTGTAAGGAGAGAACTCTGCTCCGTCATGGTTTTTGAAGTAGTAGAGCAGGCTGGGGCTGTTATTCTTGAAGATGGGCAAGAGCTTGACTCATGGTATGTCATTTTAAATGGCACTGTAGAAATTAGTCATCCAGATGGGAAAATAGAAAATCTCTTCATGGGAAATAGTTTTGGGATTGTCCCCACGCTGGATAAGCAGCACATGCATGGAGCTGTCAGGACCAAAGTCGATGATTGTCAGTTTGTCTGCATAGCTCAACAAGACTATTGGAGAATTTTAAATCATGTGGAAAAAAATACTCACAAAGTTGAGGAAGAGGGAGAGATTGTCATGGTACATGAGCACCGTGAGCTAGACCGGAGCGGAACCAGGAAAGGACACATTGTAATCAAGGCAACACCTGAGCGTCTCATCATGCATTTGATAGAAGAACATTCTATTGTGGACCCAACATACATAGAAGATTTCCTCTTAACTTACAGGACATTTCTTGAAACTCCTTTGGATGTTGGGATCAAGCTTTTGGAATGGTTTAAGATTGACAACCTAAGGGATAAGGTGACACGGATTGTACTCTTATGGGTAAATAATCATTTTAATGATTTTGAAGGTGATCCTGCTATGACTCAATTTCTAGAAGAATTTGAAAGAAATTTGGAAGATACAAAAATGAATGGTCACCTCAGGTTATTGAATATTGCCTGTGCTGCAAAGGCTAAGTGGAGGCAAGTTGTACTGCAGAAGGCGTCCCGTGAGTCCCCGCTGCACTTCTGCCTTACTGGGGGCAGTGAGAAGGGATTTGGAGTCTTTGTTGAAGAAGTAGAATCTGGTAGCAAAGCTGCTGACGCAGGACTGAAAAGGGGTGATCAGGTAATGGAAGTCAATGGACAAAACTTTGAGAATATTACACTTGCTAAAGCCCTTGAAATTTTGAGAAATAATACTCATCTTGCACTTACTGTGAAGACCAACATTTTTGTGTTCAAAGAATTGCTCAGTAGGACTGAACAAGAGAAATCTGGTGTTCCTCATATTCCCAAAATTGCTGAAAAAAAAAGTAATCGCCATTCAATTCAAGATGTCCCAGGGGATATGGAGCAGGCACCACAGGAGAAAGGAAATAAGAAAATTAAAGCAAATACCGTTTCAGGTGGAAGAAACAAAATCAGGAAAATTTTGGATAAAACACGATTTAGTATCTTGCCTCCAAAACTATTTAGTGACGGAGGCCTGAGTCAATCACAAGATGACAGCATTGTGGGAACCAGGCACTGTAGGCACAGCCTGGCTATAATGCCAATTCCCGGAACACTTTCATCCAGCAGCCCAGATCTCTTACAGCCTACCACTAGCATGTTGGACTTTTCCAATCCTTCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CTTTCATCCAGCAGCCCAGA
60.03
TCCTCCTCCTCTTCATCCTCA
59.07
150
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
ATGCCAATTCCCGGAACACT
59.96
TCCTCCTCCTCTTCATCCTCA
59.07
168
PCR template sequence:
CACAGCCTGGCTATAATGCCAATTCCCGGAACACTTTCATCCAGCAGCCCAGATCTCTTACAGCCTACCACTAGCATGTTGGACTTTTCCAATCCTTCAGGCTACAGAGAGTGAAGTAGGAGATGTAGATTTAACACGCCTTCCAGAAGGACCTGTTGATTCTGAGGATGAAGAGGAGGAGGAAGAAGAGATTGATAGAA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
12
Interacting miRNAs (#binding sites)
mmu-miR-139-5p(2), mmu-miR-9-5p(1), mmu-miR-31-5p(1), mmu-miR-138-5p(1), mmu-miR-26b-5p(1), mmu-miR-182-5p(1), mmu-miR-130b-3p(1), mmu-miR-301b-3p(1), mmu-miR-324-3p(1), mmu-miR-297a-5p(1), mmu-miR-301a-3p(1), mmu-miR-3105-3p(1)
siRNAs for circular RNA silencing
Junction sequence
TCCAATCCTTCAGGCTACAGAGAGTG
siRNA sets
ACTCTCTGTAGCCTGAAGG,TGTAGCCTGAAGGATTGGA,CTGTAGCCTGAAGGATTGG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCRAPGEF6_1612_ORF_1
1.0285
0.042330589
0.999170485
1431
ORF sequence:
ATGCACCAGCTGCCTGCCTTTGCGAACATGACCATGTCTGTAAGGAGAGAACTCTGCTCCGTCATGGTTTTTGAAGTAGTAGAGCAGGCTGGGGCTGTTATTCTTGAAGATGGGCAAGAGCTTGACTCATGGTATGTCATTTTAAATGGCACTGTAGAAATTAGTCATCCAGATGGGAAAATAGAAAATCTCTTCATGGGAAATAGTTTTGGGATTGTCCCCACGCTGGATAAGCAGCACATGCATGGAGCTGTCAGGACCAAAGTCGATGATTGTCAGTTTGTCTGCATAGCTCAACAAGACTATTGGAGAATTTTAAATCATGTGGAAAAAAATACTCACAAAGTTGAGGAAGAGGGAGAGATTGTCATGGTACATGAGCACCGTGAGCTAGACCGGAGCGGAACCAGGAAAGGACACATTGTAATCAAGGCAACACCTGAGCGTCTCATCATGCATTTGATAGAAGAACATTCTATTGTGGACCCAACATACATAGAAGATTTCCTCTTAACTTACAGGACATTTCTTGAAACTCCTTTGGATGTTGGGATCAAGCTTTTGGAATGGTTTAAGATTGACAACCTAAGGGATAAGGTGACACGGATTGTACTCTTATGGGTAAATAATCATTTTAATGATTTTGAAGGTGATCCTGCTATGACTCAATTTCTAGAAGAATTTGAAAGAAATTTGGAAGATACAAAAATGAATGGTCACCTCAGGTTATTGAATATTGCCTGTGCTGCAAAGGCTAAGTGGAGGCAAGTTGTACTGCAGAAGGCGTCCCGTGAGTCCCCGCTGCACTTCTGCCTTACTGGGGGCAGTGAGAAGGGATTTGGAGTCTTTGTTGAAGAAGTAGAATCTGGTAGCAAAGCTGCTGACGCAGGACTGAAAAGGGGTGATCAGGTAATGGAAGTCAATGGACAAAACTTTGAGAATATTACACTTGCTAAAGCCCTTGAAATTTTGAGAAATAATACTCATCTTGCACTTACTGTGAAGACCAACATTTTTGTGTTCAAAGAATTGCTCAGTAGGACTGAACAAGAGAAATCTGGTGTTCCTCATATTCCCAAAATTGCTGAAAAAAAAAGTAATCGCCATTCAATTCAAGATGTCCCAGGGGATATGGAGCAGGCACCACAGGAGAAAGGAAATAAGAAAATTAAAGCAAATACCGTTTCAGGTGGAAGAAACAAAATCAGGAAAATTTTGGATAAAACACGATTTAGTATCTTGCCTCCAAAACTATTTAGTGACGGAGGCCTGAGTCAATCACAAGATGACAGCATTGTGGGAACCAGGCACTGTAGGCACAGCCTGGCTATAATGCCAATTCCCGGAACACTTTCATCCAGCAGCCCAGATCTCTTACAGCCTACCACTAGCATGTTGGACTTTTCCAATCCTTCAGGCTACAGAGAGTGA
Peptide sequence:
MHQLPAFANMTMSVRRELCSVMVFEVVEQAGAVILEDGQELDSWYVILNGTVEISHPDGKIENLFMGNSFGIVPTLDKQHMHGAVRTKVDDCQFVCIAQQDYWRILNHVEKNTHKVEEEGEIVMVHEHRELDRSGTRKGHIVIKATPERLIMHLIEEHSIVDPTYIEDFLLTYRTFLETPLDVGIKLLEWFKIDNLRDKVTRIVLLWVNNHFNDFEGDPAMTQFLEEFERNLEDTKMNGHLRLLNIACAAKAKWRQVVLQKASRESPLHFCLTGGSEKGFGVFVEEVESGSKAADAGLKRGDQVMEVNGQNFENITLAKALEILRNNTHLALTVKTNIFVFKELLSRTEQEKSGVPHIPKIAEKKSNRHSIQDVPGDMEQAPQEKGNKKIKANTVSGGRNKIRKILDKTRFSILPPKLFSDGGLSQSQDDSIVGTRHCRHSLAIMPIPGTLSSSSPDLLQPTTSMLDFSNPSGYRE
IRESfinder result
IRESfinder score
0.598364091
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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