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mmu_circStk25_1211
Basic information of circular RNA
PanCircBase ID:
mmu_circStk25_1211
mm39_Chr. Position ID:
chr1|93551117|93556986|-
Gene name:
Stk25
Transcript:
ENSMUST00000027498.14
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
9
Exon/intron indexes:
11,10,9,8,7,6,5,4,3
Exon/intron offsets:
0,1157,1638,2065,2385,2655,3629,4258,5638
Genomic length:
5869
Exon/intron sizes in nt:
13,77,21,15,14,61,86,10,00,00,00,000
Flanking exon/introns:
chr1:93550248-93551117|chr1:93556986-93563019
Splice length:
1211
Other database IDs:
circBase: mmu_circ_0009098, CIRCpedia: MMU_CIRCpedia_34554, circAtlas: mmu-Stk25_0002
circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_40375
Human Ortholog IDs:
Mature spliced Sequence:
CATTCTCGTGTGGACCCAGAGGAACTCTTCACCAAGCTTGACCGCATTGGCAAAGGCTCATTTGGGGAGGTGTACAAGGGGATCGACAACCACACCAAGGAAGTGGTGGCCATCAAGATCATTGACTTGGAAGAGGCCGAGGATGAAATTGAGGACATCCAACAGGAGATCACTGTGCTCAGCCAATGTGACAGTCCTTATATCACCCGCTACTTCGGCTCCTACCTGAAGAGCACCAAGCTGTGGATTATCATGGAGTACCTGGGTGGTGGCTCTGCACTGGACTTGCTGAAACCTGGTCCCCTGGAAGAGACCTATATTGCCACCATCTTGCGGGAGATCCTGAAAGGCCTGGATTATCTGCACTCAGAGCGCAAGATCCACCGAGATATCAAAGCTGCCAACGTGCTGCTCTCGGAGCAGGGTGATGTGAAGCTGGCAGACTTCGGTGTGGCTGGGCAGCTCACAGACACACAAATCAAGAGGAACACATTTGTGGGTACACCCTTCTGGATGGCACCTGAGGTTATCAAGCAGTCGGCCTATGACTTCAAGGCTGACATCTGGTCCCTGGGCATCACAGCCATTGAGCTGGCCAAGGGGGAGCCGCCAAACTCTGATCTCCACCCTATGCGAGTCCTGTTCCTGATTCCCAAGAACAACCCACCCACATTGGAGGGCCACCACAGCAAACCCTTCAAGGAGTTTGTAGAGGCCTGCCTCAATAAGGACCCACGATTCCGACCCACTGCCAAGGAGCTCCTGAAGCACAAATTCATCACACGATACACCAAGAAGACCTCCTTTCTCACTGAACTTATTGACCGATATAAGCGCTGGAAGTCTGAGGGGCATGGAGAGGAGTCCAGTTCTGAGGATTCTGACATTGATGGCGAGGCTGAGGATGGGGAGCAGGGTCCCATCTGGACGTTTCCTCCAACCATCCGGCCAAGTCCACATAGCAAGCTGCACAAGGGAACTGCTCTGCACAGCTCACAGAAGCCTGCAGAGCCTATCAAGAGACAGCCAAGGTCCCAGTGCTTGTCCACACTAGTCCGTCCTGTCTTTGGAGAGCTCAAAGAGAAGCACAAGCAGAGCGGTGGGAGCGTGGGTGCCCTGGAGGAGCTAGAGAATGCCTTCAGCCTGGCTGAGGAATCCTGTCCTGGCATCTCAGACAAGCTGATGGTGCACCTGGTGGAGCGTGTGCAGAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TCCTGTCCTGGCATCTCAGA
59.96
TGTGGTTGTCGATCCCCTTG
59.96
150
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TCCTGTCCTGGCATCTCAGA
59.96
GTGGTTGTCGATCCCCTTGT
59.96
149
PCR template sequence:
GTGCCCTGGAGGAGCTAGAGAATGCCTTCAGCCTGGCTGAGGAATCCTGTCCTGGCATCTCAGACAAGCTGATGGTGCACCTGGTGGAGCGTGTGCAGAGCATTCTCGTGTGGACCCAGAGGAACTCTTCACCAAGCTTGACCGCATTGGCAAAGGCTCATTTGGGGAGGTGTACAAGGGGATCGACAACCACACCAAGG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
15
Interacting miRNAs (#binding sites)
mmu-miR-9-5p(1), mmu-miR-23b-3p(1), mmu-let-7a-5p(1), mmu-miR-16-5p(1), mmu-miR-15a-5p(1), mmu-let-7e-5p(1), mmu-miR-31-5p(1), mmu-let-7c-5p(1), mmu-miR-322-5p(1), mmu-miR-15b-5p(1), mmu-miR-184-3p(1), mmu-miR-23a-3p(1), mmu-miR-22-3p(1), mmu-miR-325-3p(1), mmu-miR-1198-5p(1)
siRNAs for circular RNA silencing
Junction sequence
AGCGTGTGCAGAGCATTCTCGTGTGG
siRNA sets
ACACGAGAATGCTCTGCAC, ACGAGAATGCTCTGCACAC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSTK25_1211_ORF_1
1.055
0.338160734
0.998665412
1188
ORF sequence:
ATGGAGTACCTGGGTGGTGGCTCTGCACTGGACTTGCTGAAACCTGGTCCCCTGGAAGAGACCTATATTGCCACCATCTTGCGGGAGATCCTGAAAGGCCTGGATTATCTGCACTCAGAGCGCAAGATCCACCGAGATATCAAAGCTGCCAACGTGCTGCTCTCGGAGCAGGGTGATGTGAAGCTGGCAGACTTCGGTGTGGCTGGGCAGCTCACAGACACACAAATCAAGAGGAACACATTTGTGGGTACACCCTTCTGGATGGCACCTGAGGTTATCAAGCAGTCGGCCTATGACTTCAAGGCTGACATCTGGTCCCTGGGCATCACAGCCATTGAGCTGGCCAAGGGGGAGCCGCCAAACTCTGATCTCCACCCTATGCGAGTCCTGTTCCTGATTCCCAAGAACAACCCACCCACATTGGAGGGCCACCACAGCAAACCCTTCAAGGAGTTTGTAGAGGCCTGCCTCAATAAGGACCCACGATTCCGACCCACTGCCAAGGAGCTCCTGAAGCACAAATTCATCACACGATACACCAAGAAGACCTCCTTTCTCACTGAACTTATTGACCGATATAAGCGCTGGAAGTCTGAGGGGCATGGAGAGGAGTCCAGTTCTGAGGATTCTGACATTGATGGCGAGGCTGAGGATGGGGAGCAGGGTCCCATCTGGACGTTTCCTCCAACCATCCGGCCAAGTCCACATAGCAAGCTGCACAAGGGAACTGCTCTGCACAGCTCACAGAAGCCTGCAGAGCCTATCAAGAGACAGCCAAGGTCCCAGTGCTTGTCCACACTAGTCCGTCCTGTCTTTGGAGAGCTCAAAGAGAAGCACAAGCAGAGCGGTGGGAGCGTGGGTGCCCTGGAGGAGCTAGAGAATGCCTTCAGCCTGGCTGAGGAATCCTGTCCTGGCATCTCAGACAAGCTGATGGTGCACCTGGTGGAGCGTGTGCAGAGCATTCTCGTGTGGACCCAGAGGAACTCTTCACCAAGCTTGACCGCATTGGCAAAGGCTCATTTGGGGAGGTGTACAAGGGGATCGACAACCACACCAAGGAAGTGGTGGCCATCAAGATCATTGACTTGGAAGAGGCCGAGGATGAAATTGAGGACATCCAACAGGAGATCACTGTGCTCAGCCAATGTGACAGTCCTTATATCACCCGCTACTTCGGCTCCTACCTGA
Peptide sequence:
MEYLGGGSALDLLKPGPLEETYIATILREILKGLDYLHSERKIHRDIKAANVLLSEQGDVKLADFGVAGQLTDTQIKRNTFVGTPFWMAPEVIKQSAYDFKADIWSLGITAIELAKGEPPNSDLHPMRVLFLIPKNNPPTLEGHHSKPFKEFVEACLNKDPRFRPTAKELLKHKFITRYTKKTSFLTELIDRYKRWKSEGHGEESSSEDSDIDGEAEDGEQGPIWTFPPTIRPSPHSKLHKGTALHSSQKPAEPIKRQPRSQCLSTLVRPVFGELKEKHKQSGGSVGALEELENAFSLAEESCPGISDKLMVHLVERVQSILVWTQRNSSPSLTALAKAHLGRCTRGSTTTPRKWWPSRSLTWKRPRMKLRTSNRRSLCSANVTVLISPATSAPT
IRESfinder result
IRESfinder score
0.417549016
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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