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mmu_circRif1_1431
Basic information of circular RNA
PanCircBase ID:
mmu_circRif1_1431
mm39_Chr. Position ID:
chr2|51983514|51997769|+
Gene name:
Rif1
Transcript:
ENSMUST00000112693.10
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
11
Exon/intron indexes:
16,17,18,19,20,21,22,23,24,25,26
Exon/intron offsets:
0,1086,2319,4414,4854,5350,9930,11043,11932,13398,14135
Genomic length:
14255
Exon/intron sizes in nt:
8,77,41,81,10,81,50,10,00,00,00,00,00,00,000
Flanking exon/introns:
chr2:51982392-51983514|chr2:51997769-51998451
Splice length:
1431
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GTTCTCATGGAAATTACAGTTAAAGGACTTCCTCCGAAAGTACTAGGTTCACCAGCATATCAGGTTGCTAATATGGATATTCTTAATGGAACTCCAGCATTGTTTTTAATCCAGTTAATTTTCAACAACAATCTTTTAGAATGTGGTGTAGAAGATGAGAAGTTTTTTCTCAATCTAGAAACACTTGTAGGCTGTGTACTTTCTGGTCCAACATCACCACTGGCTTTTAGTGATTCTGTTCTAACTGTGATTAATCAGAATGCAAAGCAGTTGGTAAACAAGGAGCATCTCTGGAGAATGTGGAGTATGATAGTCAGTCCACTGACTGATGTGATTCACCAGACCAATGAAGTGAATCAAGGCGATGCCTTAGAACATAATTTTAGTGCCATCTATGGTGCATTGACTTTACCAATAAACCATATTTTTTCAGCTCAGACATTTCCCACGGGTACCATGAAAGCTTTACTTAAAACTTGGTCAGAATTGTATAGAGCATTTACTCGCTGTGCTTCTTTGGTGGCAACAGCAGAAGAGAATCTGTGCTGTGAAGAACTTTCTTCTAAAATAATGTGCAGTTTGGAAGATGAAGTCCTTTCAGATTTGCTATTCTTGGACAGGATCTCTCATATTATTATTGTAATGGTTGATTGTATCGACTTTTCACCATATAATAAGAAATACCAGCCAAAAATCAAATCACCGCAGAGATCTTCAGATTGGTCCAGAAAGAAGAAGGAGCCTCTAGGGAAATTGGCTTCTTTATTTAAGCTAATTGTGAAAGTCATCGATACTTTCCACACTCTAAGCCTCAAGGAAACATTCTCTGATACACTGCTTGCTATTGGTAACTCTATCATTAGCATGCTTTCCAATGTATTTGGACATATTTCCTTGCCCTCTATGATCCGAGAAATATTTGCAACTTTTACAAGACCTCTGGCTTTACTGTATGAAAACTCAAAGCTGGATGAGGCTCCTAAAGTGTATACTAGTCTGAACAACAAGTTAGAAAAGCTATTGGGAGAAATTGTTGCATGCCTACAGTTCAGCTATCTTGGAGCCTATGACAGTGAACTTCTTGAACATCTTTCTCCACTCCTGTGCGTAATATTTCTTCACAAGAATAAACAGATTCGGAAACAGAGTGCTCTGTTGTGGAATGCCACATTTGCTAAAGCGACAGCTCTGGTTTATCCTGAGGAATTAAAACCAATATTAAGACAAGCCAAACAGAAAATTTTGCTTCTGCTGCCTGGTTTGGAAAATGTTGAAATGATGGATGAGTCCAGTGAACCGTATTCAGAATCAACAGAGAATTCACAATTAAATGTCAAGATAAGTGGCATGGAAAGAAAATCAAGTGGAAAAAGAGATTCCATTTTGGCACATACAAAGGATAAAAAAAAAAAAGTGAAACTGTCGGCCAAA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TGTCAAGATAAGTGGCATGGA
57
GCAACCTGATATGCTGGTGA
57.96
168
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GGCATGGAAAGAAAATCAAGTGGA
60.02
GCAACCTGATATGCTGGTGA
57.96
155
PCR template sequence:
TGTCAAGATAAGTGGCATGGAAAGAAAATCAAGTGGAAAAAGAGATTCCATTTTGGCACATACAAAGGATAAAAAAAAAAAAGTGAAACTGTCGGCCAAAGTTCTCATGGAAATTACAGTTAAAGGACTTCCTCCGAAAGTACTAGGTTCACCAGCATATCAGGTTGCTAATATGGATATTCTTAATGGAACTCCAGCAT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
6
Interacting miRNAs (#binding sites)
mmu-miR-17-5p(1), mmu-miR-191-5p(1), mmu-miR-183-5p(1), mmu-miR-297a-5p(1), mmu-miR-673-5p(1), mmu-miR-3470b(1)
siRNAs for circular RNA silencing
Junction sequence
ACTGTCGGCCAAAGTTCTCATGGAAA
siRNA sets
TGAGAACTTTGGCCGACAG, CATGAGAACTTTGGCCGAC, ATGAGAACTTTGGCCGACA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCRIF1_1431_ORF_1
0.9292
-0.031399611
0.999999954
2856
ORF sequence:
ATGGAAATTACAGTTAAAGGACTTCCTCCGAAAGTACTAGGTTCACCAGCATATCAGGTTGCTAATATGGATATTCTTAATGGAACTCCAGCATTGTTTTTAATCCAGTTAATTTTCAACAACAATCTTTTAGAATGTGGTGTAGAAGATGAGAAGTTTTTTCTCAATCTAGAAACACTTGTAGGCTGTGTACTTTCTGGTCCAACATCACCACTGGCTTTTAGTGATTCTGTTCTAACTGTGATTAATCAGAATGCAAAGCAGTTGGTAAACAAGGAGCATCTCTGGAGAATGTGGAGTATGATAGTCAGTCCACTGACTGATGTGATTCACCAGACCAATGAAGTGAATCAAGGCGATGCCTTAGAACATAATTTTAGTGCCATCTATGGTGCATTGACTTTACCAATAAACCATATTTTTTCAGCTCAGACATTTCCCACGGGTACCATGAAAGCTTTACTTAAAACTTGGTCAGAATTGTATAGAGCATTTACTCGCTGTGCTTCTTTGGTGGCAACAGCAGAAGAGAATCTGTGCTGTGAAGAACTTTCTTCTAAAATAATGTGCAGTTTGGAAGATGAAGTCCTTTCAGATTTGCTATTCTTGGACAGGATCTCTCATATTATTATTGTAATGGTTGATTGTATCGACTTTTCACCATATAATAAGAAATACCAGCCAAAAATCAAATCACCGCAGAGATCTTCAGATTGGTCCAGAAAGAAGAAGGAGCCTCTAGGGAAATTGGCTTCTTTATTTAAGCTAATTGTGAAAGTCATCGATACTTTCCACACTCTAAGCCTCAAGGAAACATTCTCTGATACACTGCTTGCTATTGGTAACTCTATCATTAGCATGCTTTCCAATGTATTTGGACATATTTCCTTGCCCTCTATGATCCGAGAAATATTTGCAACTTTTACAAGACCTCTGGCTTTACTGTATGAAAACTCAAAGCTGGATGAGGCTCCTAAAGTGTATACTAGTCTGAACAACAAGTTAGAAAAGCTATTGGGAGAAATTGTTGCATGCCTACAGTTCAGCTATCTTGGAGCCTATGACAGTGAACTTCTTGAACATCTTTCTCCACTCCTGTGCGTAATATTTCTTCACAAGAATAAACAGATTCGGAAACAGAGTGCTCTGTTGTGGAATGCCACATTTGCTAAAGCGACAGCTCTGGTTTATCCTGAGGAATTAAAACCAATATTAAGACAAGCCAAACAGAAAATTTTGCTTCTGCTGCCTGGTTTGGAAAATGTTGAAATGATGGATGAGTCCAGTGAACCGTATTCAGAATCAACAGAGAATTCACAATTAAATGTCAAGATAAGTGGCATGGAAAGAAAATCAAGTGGAAAAAGAGATTCCATTTTGGCACATACAAAGGATAAAAAAAAAAAAGTGAAACTGTCGGCCAAAGTTCTCATGGAAATTACAGTTAAAGGACTTCCTCCGAAAGTACTAGGTTCACCAGCATATCAGGTTGCTAATATGGATATTCTTAATGGAACTCCAGCATTGTTTTTAATCCAGTTAATTTTCAACAACAATCTTTTAGAATGTGGTGTAGAAGATGAGAAGTTTTTTCTCAATCTAGAAACACTTGTAGGCTGTGTACTTTCTGGTCCAACATCACCACTGGCTTTTAGTGATTCTGTTCTAACTGTGATTAATCAGAATGCAAAGCAGTTGGTAAACAAGGAGCATCTCTGGAGAATGTGGAGTATGATAGTCAGTCCACTGACTGATGTGATTCACCAGACCAATGAAGTGAATCAAGGCGATGCCTTAGAACATAATTTTAGTGCCATCTATGGTGCATTGACTTTACCAATAAACCATATTTTTTCAGCTCAGACATTTCCCACGGGTACCATGAAAGCTTTACTTAAAACTTGGTCAGAATTGTATAGAGCATTTACTCGCTGTGCTTCTTTGGTGGCAACAGCAGAAGAGAATCTGTGCTGTGAAGAACTTTCTTCTAAAATAATGTGCAGTTTGGAAGATGAAGTCCTTTCAGATTTGCTATTCTTGGACAGGATCTCTCATATTATTATTGTAATGGTTGATTGTATCGACTTTTCACCATATAATAAGAAATACCAGCCAAAAATCAAATCACCGCAGAGATCTTCAGATTGGTCCAGAAAGAAGAAGGAGCCTCTAGGGAAATTGGCTTCTTTATTTAAGCTAATTGTGAAAGTCATCGATACTTTCCACACTCTAAGCCTCAAGGAAACATTCTCTGATACACTGCTTGCTATTGGTAACTCTATCATTAGCATGCTTTCCAATGTATTTGGACATATTTCCTTGCCCTCTATGATCCGAGAAATATTTGCAACTTTTACAAGACCTCTGGCTTTACTGTATGAAAACTCAAAGCTGGATGAGGCTCCTAAAGTGTATACTAGTCTGAACAACAAGTTAGAAAAGCTATTGGGAGAAATTGTTGCATGCCTACAGTTCAGCTATCTTGGAGCCTATGACAGTGAACTTCTTGAACATCTTTCTCCACTCCTGTGCGTAATATTTCTTCACAAGAATAAACAGATTCGGAAACAGAGTGCTCTGTTGTGGAATGCCACATTTGCTAAAGCGACAGCTCTGGTTTATCCTGAGGAATTAAAACCAATATTAAGACAAGCCAAACAGAAAATTTTGCTTCTGCTGCCTGGTTTGGAAAATGTTGAAATGATGGATGAGTCCAGTGAACCGTATTCAGAATCAACAGAGAATTCACAATTAAATGTCAAGATAAGTGGCATGGAAAGAAAATCAAGTGGAAAAAGAGATTCCATTTTGGCACATACAAAGGATAAAAAAAAAAAAGTGAAACTGTCGGCCAAA
Peptide sequence:
MEITVKGLPPKVLGSPAYQVANMDILNGTPALFLIQLIFNNNLLECGVEDEKFFLNLETLVGCVLSGPTSPLAFSDSVLTVINQNAKQLVNKEHLWRMWSMIVSPLTDVIHQTNEVNQGDALEHNFSAIYGALTLPINHIFSAQTFPTGTMKALLKTWSELYRAFTRCASLVATAEENLCCEELSSKIMCSLEDEVLSDLLFLDRISHIIIVMVDCIDFSPYNKKYQPKIKSPQRSSDWSRKKKEPLGKLASLFKLIVKVIDTFHTLSLKETFSDTLLAIGNSIISMLSNVFGHISLPSMIREIFATFTRPLALLYENSKLDEAPKVYTSLNNKLEKLLGEIVACLQFSYLGAYDSELLEHLSPLLCVIFLHKNKQIRKQSALLWNATFAKATALVYPEELKPILRQAKQKILLLLPGLENVEMMDESSEPYSESTENSQLNVKISGMERKSSGKRDSILAHTKDKKKKVKLSAKVLMEITVKGLPPKVLGSPAYQVANMDILNGTPALFLIQLIFNNNLLECGVEDEKFFLNLETLVGCVLSGPTSPLAFSDSVLTVINQNAKQLVNKEHLWRMWSMIVSPLTDVIHQTNEVNQGDALEHNFSAIYGALTLPINHIFSAQTFPTGTMKALLKTWSELYRAFTRCASLVATAEENLCCEELSSKIMCSLEDEVLSDLLFLDRISHIIIVMVDCIDFSPYNKKYQPKIKSPQRSSDWSRKKKEPLGKLASLFKLIVKVIDTFHTLSLKETFSDTLLAIGNSIISMLSNVFGHISLPSMIREIFATFTRPLALLYENSKLDEAPKVYTSLNNKLEKLLGEIVACLQFSYLGAYDSELLEHLSPLLCVIFLHKNKQIRKQSALLWNATFAKATALVYPEELKPILRQAKQKILLLLPGLENVEMMDESSEPYSESTENSQLNVKISGMERKSSGKRDSILAHTKDKKKKVKLSAK
IRESfinder result
IRESfinder score
0.806729687
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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