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mmu_circSlf2_1433
Basic information of circular RNA
PanCircBase ID:
mmu_circSlf2_1433
mm39_Chr. Position ID:
chr19|44929897|44940610|+
Gene name:
Slf2
Transcript:
ENSMUST00000096053.5
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
5,6,7,8,9
Exon/intron offsets:
0,1990,6471,7513,10610
Genomic length:
10713
Exon/intron sizes in nt:
9,68,71,12,31,68,103
Flanking exon/introns:
chr19:44926858-44929897|chr19:44940610-44947443
Splice length:
1433
Other database IDs:
CIRCpedia: MMU_CIRCpedia_20444, circAtlas: mmu-Fam178a_0006
circBase: hsa_circ_0092402, circAtlas: hsa-SCAF8_0001
Human Ortholog IDs:
Mature spliced Sequence:
GCTCTAAACAGAATAAATTCTCCGACAAAAGAAAGAGGAACTCTGTGGACTCAGACCTGAAAAGCACAAAAGAACCTATCATACCAAAAGCAAGAGAGTCCTTTCTAGAGAAGCGCCCAGACACATCCCATCAGAGAGAAAAGTTTATCAGACACATTGCACTGAAGACTCCTGGTGGTGTTCTGCGCTTGGAAGACATAGCCAAGGAGCCTGAGGACGAGACAGATCGCTCTTCTGCAGACTCGGCACCTTCAAATGCTGGCCACCATTCTTCCAGGAATAGTGACCAAGTCCACTCAGCAAGTACCAAAGAGACTAAAATACAGAAACCCCACTTACCTTTACCTCAGGAAAAATCTACAATTAAAAGAGCTAGCAACCTTCAGAAAAACAAACCGGCTGGCTCTGTGACATCAAAAGAGACAAAGCTACCTTTACTTTCCCATGTTCCAAGTGCTGTTTCCTCTCGAGTACCACTAAATGCTAAAAATTGCACTCTTCCAGTTCCTAAAAAAGATAAAGAGCGTTCCTCCTCAAAAGAACGTTCTGGGCATTCTACAGAATCCTCCAAACACAAGGAACACAGAGCAAAGACTATTAAGGCTGTTTCTAATGAATCGTCAGGGAAAAATTCTGGGGGATCTTTGCATTCAGAGTATGCCCCTCCAACAGCATCTCCCCCAGCTGCCTTGGAAGTCGTGCCGAGTGTCCCAAGCCCTGCAGCACCTTCAGATAAAGAGAGTTCAGGAAATTCCAATGCAGGTAGCAATGCACTGAAAAGGAAATTCAGGGGTGATTTTGATAGTGATGAAGAAAGTTTAGGTTACACCTTAGAGAGTGATGAGGAAGAGGAAACACTAAAATCACTGGAAGAAATAATGGCTCTGAACTTCAGTCGGACTCCTACAACTTCAGGAAAGCCTCCTGCGGTTTCCAAGGGGCTTAGATCCCAGTCGTCAGACTACATGGAATATGCTCAGAGCGGAACTTACACAAATACCTTAGAGCGACTAGTAAAGGAGATGGAAGACACGCAGAGGCTAGATGAACTACAGAAGAAGCTACAGGAAGACATAAGACAAGGCCGTGGCATTAAATCTCCTCTCAGAACTGGCGATCAGGATAGTACAGATGATGGTGATGGCCTCTTGGAAGAACACAGGGAATTTCTAAAGAAATTTTCAGTTACAGTTGATGCTATTCCTGATCATCATCCAGGTGAAGAAATATTTAATTTCCTCAATTCTGGAAAAATTTTCAATCAGTATACCTTAGATTTAAGAGACTCTGGTTTTATTGGAGAAAGTGCTGTGGAAAAGCTTATTCTCAAATCAGGAAAAACAGATCAGATTTTTTTGACAACACAAGGCTTCCTTACCACTGCATATCACTACGTCCAATGTCCTGTACCTGTGTTAAAGTGGCTGTTTCGG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
ACAACACAAGGCTTCCTTACCA
60.09
TGCTTTTCAGGTCTGAGTCCA
59.23
141
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CAACACAAGGCTTCCTTACCAC
59.71
TGCTTTTCAGGTCTGAGTCCA
59.23
140
PCR template sequence:
AGGAAAAACAGATCAGATTTTTTTGACAACACAAGGCTTCCTTACCACTGCATATCACTACGTCCAATGTCCTGTACCTGTGTTAAAGTGGCTGTTTCGGGCTCTAAACAGAATAAATTCTCCGACAAAAGAAAGAGGAACTCTGTGGACTCAGACCTGAAAAGCACAAAAGAACCTATCATACCAAAAGCAAGAGAGTC
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-130a-3p(2), mmu-miR-18a-5p(2), mmu-miR-301b-3p(2), mmu-miR-301a-3p(2), mmu-miR-9-5p(1), mmu-miR-33-5p(1), mmu-miR-298-5p(1), mmu-miR-130b-3p(1), mmu-miR-721(1), mmu-miR-382-5p(1), mmu-miR-669d-5p(1)
siRNAs for circular RNA silencing
Junction sequence
GTGGCTGTTTCGGGCTCTAAACAGAA
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSLF2_1433_ORF_1
1.026
0.086008207
0.999466714
1467
ORF sequence:
ATGTCCTGTACCTGTGTTAAAGTGGCTGTTTCGGGCTCTAAACAGAATAAATTCTCCGACAAAAGAAAGAGGAACTCTGTGGACTCAGACCTGAAAAGCACAAAAGAACCTATCATACCAAAAGCAAGAGAGTCCTTTCTAGAGAAGCGCCCAGACACATCCCATCAGAGAGAAAAGTTTATCAGACACATTGCACTGAAGACTCCTGGTGGTGTTCTGCGCTTGGAAGACATAGCCAAGGAGCCTGAGGACGAGACAGATCGCTCTTCTGCAGACTCGGCACCTTCAAATGCTGGCCACCATTCTTCCAGGAATAGTGACCAAGTCCACTCAGCAAGTACCAAAGAGACTAAAATACAGAAACCCCACTTACCTTTACCTCAGGAAAAATCTACAATTAAAAGAGCTAGCAACCTTCAGAAAAACAAACCGGCTGGCTCTGTGACATCAAAAGAGACAAAGCTACCTTTACTTTCCCATGTTCCAAGTGCTGTTTCCTCTCGAGTACCACTAAATGCTAAAAATTGCACTCTTCCAGTTCCTAAAAAAGATAAAGAGCGTTCCTCCTCAAAAGAACGTTCTGGGCATTCTACAGAATCCTCCAAACACAAGGAACACAGAGCAAAGACTATTAAGGCTGTTTCTAATGAATCGTCAGGGAAAAATTCTGGGGGATCTTTGCATTCAGAGTATGCCCCTCCAACAGCATCTCCCCCAGCTGCCTTGGAAGTCGTGCCGAGTGTCCCAAGCCCTGCAGCACCTTCAGATAAAGAGAGTTCAGGAAATTCCAATGCAGGTAGCAATGCACTGAAAAGGAAATTCAGGGGTGATTTTGATAGTGATGAAGAAAGTTTAGGTTACACCTTAGAGAGTGATGAGGAAGAGGAAACACTAAAATCACTGGAAGAAATAATGGCTCTGAACTTCAGTCGGACTCCTACAACTTCAGGAAAGCCTCCTGCGGTTTCCAAGGGGCTTAGATCCCAGTCGTCAGACTACATGGAATATGCTCAGAGCGGAACTTACACAAATACCTTAGAGCGACTAGTAAAGGAGATGGAAGACACGCAGAGGCTAGATGAACTACAGAAGAAGCTACAGGAAGACATAAGACAAGGCCGTGGCATTAAATCTCCTCTCAGAACTGGCGATCAGGATAGTACAGATGATGGTGATGGCCTCTTGGAAGAACACAGGGAATTTCTAAAGAAATTTTCAGTTACAGTTGATGCTATTCCTGATCATCATCCAGGTGAAGAAATATTTAATTTCCTCAATTCTGGAAAAATTTTCAATCAGTATACCTTAGATTTAAGAGACTCTGGTTTTATTGGAGAAAGTGCTGTGGAAAAGCTTATTCTCAAATCAGGAAAAACAGATCAGATTTTTTTGACAACACAAGGCTTCCTTACCACTGCATATCACTACGTCCAATGTCCTGTACCTGTGTTAAAGTGGCTGTTTCGG
Peptide sequence:
MSCTCVKVAVSGSKQNKFSDKRKRNSVDSDLKSTKEPIIPKARESFLEKRPDTSHQREKFIRHIALKTPGGVLRLEDIAKEPEDETDRSSADSAPSNAGHHSSRNSDQVHSASTKETKIQKPHLPLPQEKSTIKRASNLQKNKPAGSVTSKETKLPLLSHVPSAVSSRVPLNAKNCTLPVPKKDKERSSSKERSGHSTESSKHKEHRAKTIKAVSNESSGKNSGGSLHSEYAPPTASPPAALEVVPSVPSPAAPSDKESSGNSNAGSNALKRKFRGDFDSDEESLGYTLESDEEEETLKSLEEIMALNFSRTPTTSGKPPAVSKGLRSQSSDYMEYAQSGTYTNTLERLVKEMEDTQRLDELQKKLQEDIRQGRGIKSPLRTGDQDSTDDGDGLLEEHREFLKKFSVTVDAIPDHHPGEEIFNFLNSGKIFNQYTLDLRDSGFIGESAVEKLILKSGKTDQIFLTTQGFLTTAYHYVQCPVPVLKWLFR
IRESfinder result
IRESfinder score
0.624156003
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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