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mmu_circSt18_848
Basic information of circular RNA
PanCircBase ID:
mmu_circSt18_848
mm39_Chr. Position ID:
chr1|6879500|6898245|+
Gene name:
St18
Transcript:
ENSMUST00000140079.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
10,11,12,13,14
Exon/intron offsets:
0,1297,8326,10657,18499
Genomic length:
18745
Exon/intron sizes in nt:
9,11,05,19,42,12,246
Flanking exon/introns:
chr1:6877901-6879500|chr1:6898245-6903786
Splice length:
848
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
TTCTCGCCATGCATGAGAACGTGCTCAAGTGTCCCACGCCAGGATGCACAGGAAGGGGACATGTGAACAGCAATCGCAACACTCACAGAAGTCTTTCTGGTTGTCCGATTGCTGCAGCTGAAAAGCTGGCAATGACCCAGGACAAAAGTCAACTTGATTCTTCTCAGACGGGGCAGTGTCCTGAGCAGGCACACAGGGTGAATTTGGTGAAGCAAATTGAATTTAATTTCCGCTCACATGCCATCACTTCTCCAAGAGCCTCTGCATCAAAAGAACAAGAGAAGTTTGGGAAAGTACCGTTTGATTATGCCAGTTTTGATGCACAAGTATTTGGGAAACGTCCTCTCCTACAAACAGGGCAAGGACAAAAAGCACCACCATTTCCTGAATCAAAGCATTTTTCAAATCCAGTGAAATTTCCTAATGGACTGCCTAGTGCTGGCGCCCACACACAGAGCACAGTCCGTGCCAGCTCTTATGGCCATGGTCAGTACAGTGAAGACACCCACATAGCAGCAGCTGCTGCCATCCTGAACCTTTCCACCCGCTGCAGGGAAGCCACAGACATCCTCTCCAACAAACCACAAAGCCTGCGTGCCAAGGGAGCTGAGATAGAAGTAGATGAAAACGGCACATTGGACTTAAGCATGAAAAAAAATCGAATCCACGACAAGTCTATACCCCCAACTTCCTCACCTACTACAATTACAACCCCATCCTCATCCCCATTCAACGCAAGCAGCCTTCTGGTCAATGCTGCCTTCTATCAGGCCCTCTCTGATCAAGAAGGCTGGAATGTGCCCATCAACTATAGCAAATCCCATGGGAAGACAGAGGAGGAGAAAGAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GCTGGAATGTGCCCATCAAC
59.83
TGTGAGTGTTGCGATTGCTG
59.41
146
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GCTGGAATGTGCCCATCAAC
59.83
GTGAGTGTTGCGATTGCTGT
59.41
145
PCR template sequence:
GGTCAATGCTGCCTTCTATCAGGCCCTCTCTGATCAAGAAGGCTGGAATGTGCCCATCAACTATAGCAAATCCCATGGGAAGACAGAGGAGGAGAAAGAGTTCTCGCCATGCATGAGAACGTGCTCAAGTGTCCCACGCCAGGATGCACAGGAAGGGGACATGTGAACAGCAATCGCAACACTCACAGAAGTCTTTCTGG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
10
Interacting miRNAs (#binding sites)
mmu-miR-383-5p(2), mmu-miR-93-5p(1), mmu-miR-20a-5p(1), mmu-miR-7b-5p(1), mmu-miR-103-3p(1), mmu-miR-96-5p(1), mmu-miR-324-3p(1), mmu-miR-107-3p(1), mmu-miR-207(1), mmu-miR-335-3p(1)
siRNAs for circular RNA silencing
Junction sequence
GGAGGAGAAAGAGTTCTCGCCATGCA
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCST18_848_ORF_1
0.7807
0.155350432
0.965848747
906
ORF sequence:
ATGCATGAGAACGTGCTCAAGTGTCCCACGCCAGGATGCACAGGAAGGGGACATGTGAACAGCAATCGCAACACTCACAGAAGTCTTTCTGGTTGTCCGATTGCTGCAGCTGAAAAGCTGGCAATGACCCAGGACAAAAGTCAACTTGATTCTTCTCAGACGGGGCAGTGTCCTGAGCAGGCACACAGGGTGAATTTGGTGAAGCAAATTGAATTTAATTTCCGCTCACATGCCATCACTTCTCCAAGAGCCTCTGCATCAAAAGAACAAGAGAAGTTTGGGAAAGTACCGTTTGATTATGCCAGTTTTGATGCACAAGTATTTGGGAAACGTCCTCTCCTACAAACAGGGCAAGGACAAAAAGCACCACCATTTCCTGAATCAAAGCATTTTTCAAATCCAGTGAAATTTCCTAATGGACTGCCTAGTGCTGGCGCCCACACACAGAGCACAGTCCGTGCCAGCTCTTATGGCCATGGTCAGTACAGTGAAGACACCCACATAGCAGCAGCTGCTGCCATCCTGAACCTTTCCACCCGCTGCAGGGAAGCCACAGACATCCTCTCCAACAAACCACAAAGCCTGCGTGCCAAGGGAGCTGAGATAGAAGTAGATGAAAACGGCACATTGGACTTAAGCATGAAAAAAAATCGAATCCACGACAAGTCTATACCCCCAACTTCCTCACCTACTACAATTACAACCCCATCCTCATCCCCATTCAACGCAAGCAGCCTTCTGGTCAATGCTGCCTTCTATCAGGCCCTCTCTGATCAAGAAGGCTGGAATGTGCCCATCAACTATAGCAAATCCCATGGGAAGACAGAGGAGGAGAAAGAGTTCTCGCCATGCATGAGAACGTGCTCAAGTGTCCCACGCCAGGATGCACAGGAAGGGGACATGTGA
Peptide sequence:
MHENVLKCPTPGCTGRGHVNSNRNTHRSLSGCPIAAAEKLAMTQDKSQLDSSQTGQCPEQAHRVNLVKQIEFNFRSHAITSPRASASKEQEKFGKVPFDYASFDAQVFGKRPLLQTGQGQKAPPFPESKHFSNPVKFPNGLPSAGAHTQSTVRASSYGHGQYSEDTHIAAAAAILNLSTRCREATDILSNKPQSLRAKGAEIEVDENGTLDLSMKKNRIHDKSIPPTSSPTTITTPSSSPFNASSLLVNAAFYQALSDQEGWNVPINYSKSHGKTEEEKEFSPCMRTCSSVPRQDAQEGDM
IRESfinder result
IRESfinder score
0.48552184
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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