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mmu_circRapgef1_1823
Basic information of circular RNA
PanCircBase ID:
mmu_circRapgef1_1823
mm39_Chr. Position ID:
chr2|29569144|29597412|+
Gene name:
Rapgef1
Transcript:
ENSMUST00000095087.11
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
10
Exon/intron indexes:
2,3,4,5,6,7,8,9,10,11
Exon/intron offsets:
0,604,6972,9974,19864,20553,21053,21535,23060,28065
Genomic length:
28268
Exon/intron sizes in nt:
13,71,14,17,91,57,89,10,00,00,00,00,00,000
Flanking exon/introns:
chr2:29510075-29569144|chr2:29597412-29600164
Splice length:
1823
Other database IDs:
CIRCpedia: MMU_CIRCpedia_214532, circAtlas: mmu-Rapgef1_0010
circAtlas: hsa-SCAF8_0001
Human Ortholog IDs:
Mature spliced Sequence:
ACTCTCAGCGTTCTCATCTCTCCTCCTTCACCATGAAGCTGATGGACAAATTCCACTCTCCCAAAATCAAGAGAACACCATCCAAGAAGGGAAAGCCAGCCGAGGTGTCGAAGATTCCTGAGAAGCCTGTGAGCAAAGAGGCAAGAGACAGATTTCTACCAGAGGGCTACCCTATCCCCTTGGATCTGGAGCAGCAGGCAGTAGAATTTATGTCCACCAGTGCTGTGGCTTCCAGGTCTCAGAGGCAGAAGAACCTGTGCTGGCTGGAGGAGAAAGAGAAGGAGGTTGTCAGTGCCTTGCGCTACTTTAAGACCATTGTGGACAAAATGGCCATTGATAAGAAGGTTCTGGAGATGCTCCCGGGGTCAGCCAGCAAGGTGCTGGAGGCCATCTTACCCCTGGTGCAGACTGACCCTCGGATCCAGCACAGCTCAGCCCTCTCCTCCTGTTATAGCCGAGTATACCAGAGCCTCGCCAACCTTATCCGATGGTCTGACCAGGTGATGCTAGAGGGCGTGAACTCAGAAGATAAGGAGATGGTGACAACTGTGAAGGGCGTTATCAAAGCTGTCCTGGACGGAGTGAAGGAGCTAGTGAGGCTAACCATTGAGAAGCAGGGGCGGCCATCGCCAACAAGCCCAGTGAAGCCCAGTTCCCCAGCCAGCAAGCCTGATGGCCAGCCTGAGCTCCCTCTGACAGACCGAGAAATGGAGATTCTGAACAAGACGACAAGTGTGTCACCATCTGCTGAACTGCTCCCAGACTCCACCAGTGAAGAGGTCGCACCCCCCAAGCCCCCTTTACCTGGCATCCGGGTGGTTGATAACAGTCCACCAGCATTACCACCCAAGAAAAGGCAGTCTGCTCCATCCCCCACTCGGGTGGCTGTGGTAGCCCCAATGAGTCGGGCTACCAGTGGCTCCAGTTTGCCTGTTGGAATCAATAGGCAGGACTTTGATGTTGAATGTTACACCCAGAGGCGCCTGTCAGGAGGCAGCCGCTCCTGCGGTGGTGAGTCTCCTCGCCTGTCCCCCTGCAGCAGCACAGGCAAGCTCAGCCGCTCAGACGAGCAGCTGTCCTCCCTGGACAGGGATAGTGGGCAGTGCTCACGGAACACAAGCTGTGAAACACTAGATCACTACGACCCCGACTATGAATTCCTCCAGCAAGATCTCTCCAATGCAGACCAGATCCCTCCACAGGCAGCCTGTAACCTCAGCCCTCTGCCGGAGTCCCTGGGGGAATCTGGGCCTCCATTTCTTGGCCACCCTTTCCAGCTGCCTTTGGGCAGCTGTCTGCAGCAGGAGGGACAGCAGACAGACACTCCACCTGCCCTTCCGGAGAAGAAGCGTAGGAGCGCAGTCTCCCAGACCACGGACAGCTCTGGCTGCAGGGTGTCCTATGAGCGACACCCCTCACAGTATGACAACATCTCAGAGGGTGACCTGCAGAACCCAGTCCCAGTCCAGCCTGTGCCCTACCCACCCTTTGCTGCTGTCCTGCCCTTTCAGCAGGGAGCTTCCTCTGCCTCTGCTGAGTTTGTGGGTGATTTCAGTGTTCCTGAGTTGGCGGGTGACACAGAGAAGCCACCTCCTCTACCAGAGAAGAAGAACAAGCACATGCTGGCCTACATGCAACTGCTGGAGGACTACTCAGAGCCACAGCCCTCCATGTTCTACCAGACACCGCAGAGTGAGCACATCTACCAGCAGAAGAACAAGATGCTCATGGAGGTGTACGGCTTCAGCGAGTCCTTCTGCGGTAGTGATTCCACGCAGGAGCTGGCCCCTCCACCCGCTCTGCCCCCCAAGCAACGGCAGCTG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CGAGTCCTTCTGCGGTAGTG
60.18
GCTGGCTTTCCCTTCTTGGA
60.25
176
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GAGTCCTTCTGCGGTAGTGA
58.83
GCTGGCTTTCCCTTCTTGGA
60.25
175
PCR template sequence:
GCTCATGGAGGTGTACGGCTTCAGCGAGTCCTTCTGCGGTAGTGATTCCACGCAGGAGCTGGCCCCTCCACCCGCTCTGCCCCCCAAGCAACGGCAGCTGACTCTCAGCGTTCTCATCTCTCCTCCTTCACCATGAAGCTGATGGACAAATTCCACTCTCCCAAAATCAAGAGAACACCATCCAAGAAGGGAAAGCCAGC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
20
Interacting miRNAs (#binding sites)
mmu-miR-370-3p(2), mmu-miR-15a-5p(1), mmu-miR-27b-3p(1), mmu-miR-27a-3p(1), mmu-miR-181a-5p(1), mmu-miR-15b-5p(1), mmu-miR-33-5p(1), mmu-miR-298-5p(1), mmu-miR-709(1), mmu-miR-143-3p(1), mmu-miR-138-5p(1), mmu-miR-339-5p(1), mmu-miR-22-3p(1), mmu-miR-301b-3p(1), mmu-miR-218-5p(1), mmu-miR-342-5p(1), mmu-miR-673-5p(1), mmu-miR-3470b(1), mmu-miR-296-3p(1), mmu-miR-338-3p(1)
siRNAs for circular RNA silencing
Junction sequence
GCAACGGCAGCTGACTCTCAGCGTTC
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCRAPGEF1_1823_ORF_1
0.9501
0.381310655
0.999986074
1827
ORF sequence:
ATGAAGCTGATGGACAAATTCCACTCTCCCAAAATCAAGAGAACACCATCCAAGAAGGGAAAGCCAGCCGAGGTGTCGAAGATTCCTGAGAAGCCTGTGAGCAAAGAGGCAAGAGACAGATTTCTACCAGAGGGCTACCCTATCCCCTTGGATCTGGAGCAGCAGGCAGTAGAATTTATGTCCACCAGTGCTGTGGCTTCCAGGTCTCAGAGGCAGAAGAACCTGTGCTGGCTGGAGGAGAAAGAGAAGGAGGTTGTCAGTGCCTTGCGCTACTTTAAGACCATTGTGGACAAAATGGCCATTGATAAGAAGGTTCTGGAGATGCTCCCGGGGTCAGCCAGCAAGGTGCTGGAGGCCATCTTACCCCTGGTGCAGACTGACCCTCGGATCCAGCACAGCTCAGCCCTCTCCTCCTGTTATAGCCGAGTATACCAGAGCCTCGCCAACCTTATCCGATGGTCTGACCAGGTGATGCTAGAGGGCGTGAACTCAGAAGATAAGGAGATGGTGACAACTGTGAAGGGCGTTATCAAAGCTGTCCTGGACGGAGTGAAGGAGCTAGTGAGGCTAACCATTGAGAAGCAGGGGCGGCCATCGCCAACAAGCCCAGTGAAGCCCAGTTCCCCAGCCAGCAAGCCTGATGGCCAGCCTGAGCTCCCTCTGACAGACCGAGAAATGGAGATTCTGAACAAGACGACAAGTGTGTCACCATCTGCTGAACTGCTCCCAGACTCCACCAGTGAAGAGGTCGCACCCCCCAAGCCCCCTTTACCTGGCATCCGGGTGGTTGATAACAGTCCACCAGCATTACCACCCAAGAAAAGGCAGTCTGCTCCATCCCCCACTCGGGTGGCTGTGGTAGCCCCAATGAGTCGGGCTACCAGTGGCTCCAGTTTGCCTGTTGGAATCAATAGGCAGGACTTTGATGTTGAATGTTACACCCAGAGGCGCCTGTCAGGAGGCAGCCGCTCCTGCGGTGGTGAGTCTCCTCGCCTGTCCCCCTGCAGCAGCACAGGCAAGCTCAGCCGCTCAGACGAGCAGCTGTCCTCCCTGGACAGGGATAGTGGGCAGTGCTCACGGAACACAAGCTGTGAAACACTAGATCACTACGACCCCGACTATGAATTCCTCCAGCAAGATCTCTCCAATGCAGACCAGATCCCTCCACAGGCAGCCTGTAACCTCAGCCCTCTGCCGGAGTCCCTGGGGGAATCTGGGCCTCCATTTCTTGGCCACCCTTTCCAGCTGCCTTTGGGCAGCTGTCTGCAGCAGGAGGGACAGCAGACAGACACTCCACCTGCCCTTCCGGAGAAGAAGCGTAGGAGCGCAGTCTCCCAGACCACGGACAGCTCTGGCTGCAGGGTGTCCTATGAGCGACACCCCTCACAGTATGACAACATCTCAGAGGGTGACCTGCAGAACCCAGTCCCAGTCCAGCCTGTGCCCTACCCACCCTTTGCTGCTGTCCTGCCCTTTCAGCAGGGAGCTTCCTCTGCCTCTGCTGAGTTTGTGGGTGATTTCAGTGTTCCTGAGTTGGCGGGTGACACAGAGAAGCCACCTCCTCTACCAGAGAAGAAGAACAAGCACATGCTGGCCTACATGCAACTGCTGGAGGACTACTCAGAGCCACAGCCCTCCATGTTCTACCAGACACCGCAGAGTGAGCACATCTACCAGCAGAAGAACAAGATGCTCATGGAGGTGTACGGCTTCAGCGAGTCCTTCTGCGGTAGTGATTCCACGCAGGAGCTGGCCCCTCCACCCGCTCTGCCCCCCAAGCAACGGCAGCTGACTCTCAGCGTTCTCATCTCTCCTCCTTCACCATGA
Peptide sequence:
MKLMDKFHSPKIKRTPSKKGKPAEVSKIPEKPVSKEARDRFLPEGYPIPLDLEQQAVEFMSTSAVASRSQRQKNLCWLEEKEKEVVSALRYFKTIVDKMAIDKKVLEMLPGSASKVLEAILPLVQTDPRIQHSSALSSCYSRVYQSLANLIRWSDQVMLEGVNSEDKEMVTTVKGVIKAVLDGVKELVRLTIEKQGRPSPTSPVKPSSPASKPDGQPELPLTDREMEILNKTTSVSPSAELLPDSTSEEVAPPKPPLPGIRVVDNSPPALPPKKRQSAPSPTRVAVVAPMSRATSGSSLPVGINRQDFDVECYTQRRLSGGSRSCGGESPRLSPCSSTGKLSRSDEQLSSLDRDSGQCSRNTSCETLDHYDPDYEFLQQDLSNADQIPPQAACNLSPLPESLGESGPPFLGHPFQLPLGSCLQQEGQQTDTPPALPEKKRRSAVSQTTDSSGCRVSYERHPSQYDNISEGDLQNPVPVQPVPYPPFAAVLPFQQGASSASAEFVGDFSVPELAGDTEKPPPLPEKKNKHMLAYMQLLEDYSEPQPSMFYQTPQSEHIYQQKNKMLMEVYGFSESFCGSDSTQELAPPPALPPKQRQLTLSVLISPPSP
IRESfinder result
IRESfinder score
0.464159902
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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