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mmu_ciSugp1_2677
Basic information of circular RNA
PanCircBase ID:
mmu_ciSugp1_2677
mm39_Chr. Position ID:
chr8|70509254|70511931|+
Gene name:
Sugp1
Transcript:
ENSMUST00000011450.8
CircRNA type:
Circular intronic (ci)RNA
Exon/Intron count:
1
Exon/intron indexes:
4
Exon/intron offsets:
0
Genomic length:
2677
Exon/intron sizes in nt:
2677
Flanking exon/introns:
chr8:70509254-70511931
Splice length:
2677
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GTAAGTTATGGGGCCGCTGTGGCTGGGTCAGTAGCTCACATTTGCCTAGGTGAAACTGTGGAGTTTGGGCAGAGTTAGCCATCAAGGCATGTTGGAGAAGCCCTTTCAAGAAGCCTGAGAACAGTTACTGTTGTCCCAGTCCAGCATAGAAGACTTTCCTGGACAGGGCTTCATGTAAACTGAGGCAGGAGCTGCTTTGACTGTCTCCACAGTTTGGGCCAGAGGTTTGGAATGTTGAAGATTGGAGGATGCACTCCAACATGGGGGAGGTGGTCTCTGGTCTCAGGCTGAGAGTGCTGAGGCTCATCTAGTAACCCATTCCAGGTCATTAAGAACAAGGCCCTGTGACAGACAGCAAGACCCTATGGAGAACTGTCTGTGCATCCTGACACAGAGGACAGAGTGATCGTTAGCTGTGACATGTCAACCCATTCTGAATTAGGGTCCCTAGAGTAGGTTGCACTTCTTAGGTGCTCTGTCCTTTTTCATGGCTATGCTCATACGCTACAAGGGGCCTCCTGGCTCATCTCAAGGCCTTAGCACCTGTTTTGGGCATTGATATGGCCTTAAACACACCTGCTTCAGTACGCAGTAATCAGATAGTATTCTAACTATACACGTGGAAGGAAGATAAACTGGAAGAAAATTCAGCGCAGAATGCCCCGGGACTCACTGGGCCCTGCTTCGGTCGTGTGTGCCTTTGGACTCTATCCCATTCCTGTGCTTCCTGGCCATCAAACAACAAGGAATATAAGATGAGCCACAGGCTCAGCATCTACCCTAATGGCCACACACCAGCTGACAGACAGCTGTTTTCCTGTGATGCTCATAAAAGGACATGACCCATTACTGTGACTAACAGACTCAGCCTTAGGACTAGGCCAAAGAGAATTACAAAAGCAAGTTATACTTGCCTCATACAGGCAGCTAATCCTCCTGTAAAGAGATATCTTGGGCTGTGGATGCAGCTCAGATGGTATAGTACTTGCCTAGCAGGTACAAAATCCTGGGTCCCATTCCCAGAACAGCATAGGCCCAGGCATGGTGGTACAAGTCTGTTATCCCAGCACTCAGAAGCTTGAAGCAAGAGGATGGGAAATTTAGGCCAGCCTTAAATAAACTAGTCCAAGGACCTATATGTGTCTTAAAACAAAACAAACAAACAAAAAGTTAACATTGTGTCTGTGAGGTAGTGCTTGAGCTTGAGTGGGTGTCCCAGTGCCCAGAGCTCAGGCTGCCAGCATACTCTCCCAGCACAGACACAGACTGACTGCCAGACAGCTGGCTGTGAGTGTATGGGGGTGCAAGAGATTACAGGGGATTATCCTAGAGAGCTGTATGACGGGATCAAGGGGGAGTCCAGCAGAAATACCTGGAATCATGTCCAGAGTGCTTGGGATCCAGCTTCAAGATAGTGAACTGAAGTCCATCCAGTCTTCAGATCAGAGTGTGTAATCATTTGTAAAGGAGACATTGTTAGAGCTGGAAATATAGCTTAGTCAGGAAAGTGCTTGGCTTTCTCACGGCTCCTAAGCCTGGGGACCAGCTGGGTTTGATTGCAAATCCCACGTTGAAGAGCAGAAGAAAATACCGGATGTGGTGACATTGCTGTAATCACAGTGCTGGCACTGTAGAGACAGGTAGGACTTATGATCCAGCCAGCTTAGTAAACTTGACAAATTCCAGGGGAGATCCAAAATCAGAAATTAATATTTAAAAAAGGAAATAAAAAAGTTGGAGAGATGGTTCAGCAATTAAAAGCACTTGCTGCTCTTTCAGAGAATTTTGGTTCCTAGTACCCACGTGATGGCTCACAACCATTTGCAACCAACATTTACATGACACCCAGACATACATACTGGCAAAACACTCAAAATCTTTTAAAAAGACAAAATGAAAGAAAAAAGGTGGAAGAACTACTTTGGCCACATCTTCACCTGCTCACACATGCATTTGCGTACACATACAAAAGAAGTCGCCATTTTTTAAAAGCACCAGTACTCTGCAGGCAGGTAGAGTTCAAGGTTATCATCATCTCCAAGTCTTTCCAGGACAGCCAAGGCTACACAGAGAAATAAAACAAAATCCCCAGGTGGATGGGGGAGACCTAGAAGGAAAAGGAACCAATGCATTATGCTGAAAACCAATAAATTAAAAAAACAAACGAAAAAAAAATGTAGAGCTAGCAAGGTTGCTTAATGTTTTGAGCACCAGCTGATCTTACAGGTTTGGTTCAAAGGACCTACATGGTATCTCACACCTTTAACTCCAGTTCCAGGGGATCCAACACCCTTTCTTGGCTTCTATTGTCACTGTATACACTTACATACACGCAGGTAAAATACTCATACACAAAAGCTTAAAAATAATTTTTGTAAAGAACATTAACCCACACATACACAACACACACACAATACAGGGGTGGGGGGAGGCACTTCCTAGTGGCCTTTTTTAGCTTGAAGATGGTTCTCCCGCTACAGGTCCTGACACCCATTCCCTGCCAGATTGTCTGACTGTGGAGACCAAGCACCCCTCCACAGAGCCATGTGTATGGGTGGTCAGCAGCCTCCTGCATCTCCCAATCCTCTCCCCTCTGTCGTTGCGGTCTATAGAGAGAGTGTACCTAGTTACTGTTGGGTGTGTGAGTTGGAGCCCTGTACTGACAGCCTCCTTAAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CCCAATCCTCTCCCCTCTGT
60.33
CTCTGCCCAAACTCCACAGT
59.89
174
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CCCAATCCTCTCCCCTCTGT
60.33
ACTCTGCCCAAACTCCACAG
59.89
175
PCR template sequence:
CCCAATCCTCTCCCCTCTGTCGTTGCGGTCTATAGAGAGAGTGTACCTAGTTACTGTTGGGTGTGTGAGTTGGAGCCCTGTACTGACAGCCTCCTTAAAGGTAAGTTATGGGGCCGCTGTGGCTGGGTCAGTAGCTCACATTTGCCTAGGTGAAACTGTGGAGTTTGGGCAGAGTTAGCCATCAAGGCATGTTGGAGAAG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
27
Interacting miRNAs (#binding sites)
mmu-miR-297a-5p(5), mmu-miR-1187(5), mmu-miR-466a-5p(3), mmu-miR-466p-5p(3), mmu-miR-138-5p(2), mmu-miR-673-5p(2), mmu-miR-5101(2), mmu-miR-124-3p(1), mmu-miR-27b-3p(1), mmu-miR-429-3p(1), mmu-miR-322-5p(1), mmu-miR-33-5p(1), mmu-miR-130a-3p(1), mmu-miR-184-3p(1), mmu-miR-326-3p(1), mmu-miR-139-5p(1), mmu-miR-434-3p(1), mmu-miR-431-5p(1), mmu-miR-22-3p(1), mmu-miR-127-5p(1), mmu-miR-511-3p(1), mmu-miR-27a-5p(1), mmu-miR-499-5p(1), mmu-miR-802-5p(1), mmu-miR-532-5p(1), mmu-miR-1904(1), mmu-miR-574-5p(1)
siRNAs for circular RNA silencing
Junction sequence
AGCCTCCTTAAAGGTAAGTTATGGGG
siRNA sets
CATAACTTACCTTTAAGGA,ATAACTTACCTTTAAGGAG,CCATAACTTACCTTTAAGG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CISUGP1_2677_ORF_3
0.8246
-0.180623119
0.038015401
186
ORF sequence:
ATGTGTATGGGTGGTCAGCAGCCTCCTGCATCTCCCAATCCTCTCCCCTCTGTCGTTGCGGTCTATAGAGAGAGTGTACCTAGTTACTGTTGGGTGTGTGAGTTGGAGCCCTGTACTGACAGCCTCCTTAAAGGTAAGTTATGGGGCCGCTGTGGCTGGGTCAGTAGCTCACATTTGCCTAGGTGA
Peptide sequence:
MCMGGQQPPASPNPLPSVVAVYRESVPSYCWVCELEPCTDSLLKGKLWGRCGWVSSSHLPR
IRESfinder result
IRESfinder score
0.664422982
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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