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mmu_circRpap2_1339
Basic information of circular RNA
PanCircBase ID:
mmu_circRpap2_1339
mm39_Chr. Position ID:
chr5|107749596|107768621|+
Gene name:
Rpap2
Transcript:
ENSMUST00000112650.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
6
Exon/intron indexes:
3,4,5,6,7,8
Exon/intron offsets:
0,1795,2090,5174,16410,18091
Genomic length:
19025
Exon/intron sizes in nt:
1,15,99,66,89,36,934
Flanking exon/introns:
chr5:107746433-107749596|chr5:107768621-107771567
Splice length:
1339
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GCAAGCAGAACTGGAAGCTGCTATACAAAGGAAGGTGGAGTTTGAAAGGAAAGCTGTGCGCATCGTAGAGCAGCTCTTAGAGGAGAACATCACAGAAGAATTCCTGAAGGAGTGTGGCATGTTCATCACACCAGCTCACTACAGCGACGTTGTGGATGAGCGGTCCATCATCAAACTCTGTGGCTATCCTTTGTGTCAGAAGAAGCTAGGGGTTATCCCGAAACAGAAATATCGAATTTCTACTAAAACCAATAAAGTCTATGATATTACTGAAAGGAAGTCTTTCTGCAGCAATTTTTGTTACAGAGCATCTAAATTTTTTGAAACACAGATTCCCAAAACTCCAGTATGGGTTCGAGAGGAAGAGAGGCCTCCTGACTTTCAGCTGCTGAAGAAAGGACAAAGCGGCAGTTCTGGAGAAGTAGTACAGTTCTTCCGAGATGCCGTGACAGCAGCAGATGTTGACGGTTCCGGCGCCTTGGAGGCGCAGTGTGACCCTGCTTCTTCCAGCTCTTGGAGTGAGCGAGCCAGTGATGAGGAGGAGCAAGGCTTTGTTTCTTCTCTTCTACCAGGAAACAGACCAAAGGCAGTGGATACAAGACCGCAGCCGCACACAAAAAGCAGCATCATGAGAAAGAAGGCTGCTCAGAACGTGGACTCCAAGGAGGGAGAGCAGACCGTGTCAGAGGTTACCGAGCAGCTGGATAATTGCAGATTAGATAGTCAGGAGAAAGTGGCCACTTGTAAACGTCCTTTAAAGAAAGAAAGTACTCAGATTTCTTCACCTGGCCCTTTGTGTGACAGATTTAACACTTCAGCCATTTCTGAACATAAACACGGTGTATCACAAGTTACGCTTGTAGGCATAAGCAAGAAGAGTGCTGAGCATTTCAGGAGCAAATTTGCCAAGTCAAATCCAGGTTCTGGGTCAGCCTCTGGTTTGGTACACGTGCGTCCTGAGGTTGCGAAGGCAAATTTACTCCGAGTTCTGTCGGACACTCTGACTGAATGGAAGACAGAAGAAACACTGAAGTTTTTATATGGCCAGAACCACGATTCTGTGTGTCTGAAACCCTCTTCAGCCTCTGAGCCTGATGAAGAACTTGATGAAGATGACATAAGTTGTGACCCAGGTAGTTGTGGTCCTGCCCTGAGTCAAGCTCAGAACACCCTAGATGCAACACTGCCCTTTAGAGGCTCAGACACAGCCATTAAGCCACTGCCAAGTTATGAGAGCTTGAAAAAGGAAACGGAGATGCTGAACCTGAGGGTCAGGGAGTTCTACAGAGGGCGCTGTGTTTTAAATGAAGACACTACCAAGTCTCAGGACTCTAAAGAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CGGAGATGCTGAACCTGAGG
60.18
GCGCACAGCTTTCCTTTCAA
59.97
150
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GGAGATGCTGAACCTGAGGG
59.82
GCGCACAGCTTTCCTTTCAA
59.97
149
PCR template sequence:
GAAAAAGGAAACGGAGATGCTGAACCTGAGGGTCAGGGAGTTCTACAGAGGGCGCTGTGTTTTAAATGAAGACACTACCAAGTCTCAGGACTCTAAAGAGGCAAGCAGAACTGGAAGCTGCTATACAAAGGAAGGTGGAGTTTGAAAGGAAAGCTGTGCGCATCGTAGAGCAGCTCTTAGAGGAGAACATCACAGAAGAA
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-34c-5p(1), mmu-miR-34a-5p(1), mmu-miR-203-3p(1), mmu-miR-138-5p(1), mmu-miR-149-5p(1), mmu-miR-433-3p(1), mmu-miR-511-3p(1), mmu-miR-324-3p(1), mmu-miR-34b-5p(1), mmu-miR-377-3p(1), mmu-miR-484(1)
siRNAs for circular RNA silencing
Junction sequence
GGACTCTAAAGAGGCAAGCAGAACTG
siRNA sets
TTCTGCTTGCCTCTTTAGA, GTTCTGCTTGCCTCTTTAG, TCTGCTTGCCTCTTTAGAG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCRPAP2_1339_ORF_1
0.9079
0.197282566
0.999179278
1374
ORF sequence:
ATGAAGACACTACCAAGTCTCAGGACTCTAAAGAGGCAAGCAGAACTGGAAGCTGCTATACAAAGGAAGGTGGAGTTTGAAAGGAAAGCTGTGCGCATCGTAGAGCAGCTCTTAGAGGAGAACATCACAGAAGAATTCCTGAAGGAGTGTGGCATGTTCATCACACCAGCTCACTACAGCGACGTTGTGGATGAGCGGTCCATCATCAAACTCTGTGGCTATCCTTTGTGTCAGAAGAAGCTAGGGGTTATCCCGAAACAGAAATATCGAATTTCTACTAAAACCAATAAAGTCTATGATATTACTGAAAGGAAGTCTTTCTGCAGCAATTTTTGTTACAGAGCATCTAAATTTTTTGAAACACAGATTCCCAAAACTCCAGTATGGGTTCGAGAGGAAGAGAGGCCTCCTGACTTTCAGCTGCTGAAGAAAGGACAAAGCGGCAGTTCTGGAGAAGTAGTACAGTTCTTCCGAGATGCCGTGACAGCAGCAGATGTTGACGGTTCCGGCGCCTTGGAGGCGCAGTGTGACCCTGCTTCTTCCAGCTCTTGGAGTGAGCGAGCCAGTGATGAGGAGGAGCAAGGCTTTGTTTCTTCTCTTCTACCAGGAAACAGACCAAAGGCAGTGGATACAAGACCGCAGCCGCACACAAAAAGCAGCATCATGAGAAAGAAGGCTGCTCAGAACGTGGACTCCAAGGAGGGAGAGCAGACCGTGTCAGAGGTTACCGAGCAGCTGGATAATTGCAGATTAGATAGTCAGGAGAAAGTGGCCACTTGTAAACGTCCTTTAAAGAAAGAAAGTACTCAGATTTCTTCACCTGGCCCTTTGTGTGACAGATTTAACACTTCAGCCATTTCTGAACATAAACACGGTGTATCACAAGTTACGCTTGTAGGCATAAGCAAGAAGAGTGCTGAGCATTTCAGGAGCAAATTTGCCAAGTCAAATCCAGGTTCTGGGTCAGCCTCTGGTTTGGTACACGTGCGTCCTGAGGTTGCGAAGGCAAATTTACTCCGAGTTCTGTCGGACACTCTGACTGAATGGAAGACAGAAGAAACACTGAAGTTTTTATATGGCCAGAACCACGATTCTGTGTGTCTGAAACCCTCTTCAGCCTCTGAGCCTGATGAAGAACTTGATGAAGATGACATAAGTTGTGACCCAGGTAGTTGTGGTCCTGCCCTGAGTCAAGCTCAGAACACCCTAGATGCAACACTGCCCTTTAGAGGCTCAGACACAGCCATTAAGCCACTGCCAAGTTATGAGAGCTTGAAAAAGGAAACGGAGATGCTGAACCTGAGGGTCAGGGAGTTCTACAGAGGGCGCTGTGTTTTAAATGAAGACACTACCAAGTCTCAGGACTCTAAAGAG
Peptide sequence:
MKTLPSLRTLKRQAELEAAIQRKVEFERKAVRIVEQLLEENITEEFLKECGMFITPAHYSDVVDERSIIKLCGYPLCQKKLGVIPKQKYRISTKTNKVYDITERKSFCSNFCYRASKFFETQIPKTPVWVREEERPPDFQLLKKGQSGSSGEVVQFFRDAVTAADVDGSGALEAQCDPASSSSWSERASDEEEQGFVSSLLPGNRPKAVDTRPQPHTKSSIMRKKAAQNVDSKEGEQTVSEVTEQLDNCRLDSQEKVATCKRPLKKESTQISSPGPLCDRFNTSAISEHKHGVSQVTLVGISKKSAEHFRSKFAKSNPGSGSASGLVHVRPEVAKANLLRVLSDTLTEWKTEETLKFLYGQNHDSVCLKPSSASEPDEELDEDDISCDPGSCGPALSQAQNTLDATLPFRGSDTAIKPLPSYESLKKETEMLNLRVREFYRGRCVLNEDTTKSQDSKE
IRESfinder result
IRESfinder score
0.536682191
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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