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mmu_circSdk1_810
Basic information of circular RNA
PanCircBase ID:
mmu_circSdk1_810
mm39_Chr. Position ID:
chr5|142117778|142150343|+
Gene name:
Sdk1
Transcript:
ENSMUST00000085774.11
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
7
Exon/intron indexes:
32,33,34,35,36,37,38
Exon/intron offsets:
0,11748,12946,14236,26507,29751,32427
Genomic length:
32565
Exon/intron sizes in nt:
71,13,66,01,02,11,61,80,000
Flanking exon/introns:
chr5:142113629-142117778|chr5:142150343-142158196
Splice length:
810
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
TTCCAGGAGAGCCACCAGGGTCTGTCTCAGCCACACCGCACACCACGTCCTCCGTTCTGATCCAGTGGCAGCCTCCCCGGGATGAGAGCCTGAACGGTCTTCTGCAAGGCTACAGGATCTACTACCGTGAGCTGGAGTCTGAGACAGGCATGAGCCCTGAGCCCAAGACACTCAAGAGCCCCTCTGCCTTACGTGCTGAACTCACCGCTCAAAGCAGCTTCAAGACCGTGAACAGCAGCTCCTCGTTAACCACCTATGAATTAACACATCTGAAGAAGTACCGGCGCTATGAAGTCATCATGACTGCTTATAACATCATTGGTGAGAGCCCAGCCAGTGTACCAGTGGAAGTCTTCGTTGGTGAGGCTGCCCCAGCGATGGCCCCACAGAATGTCCAGGTGACCCCACTCACGGCCAGCCAGCTGGAGGTCACATGGGACCCACCGCCCCCAGAGAGCCAGAATGGGAACATCCAGGGTTATAAGGTTTACTACTGGGAGGCAGACAGTCGCAATGAGACAGAGAAAATGAAGGTCCTCTTCCTCCCCGAGCCTGTGGTGAAGATCAAGGATCTCACCAGCCACACAAAGTACCTGATCAGCATCTCAGCCTTCAATGCTGCTGGTGATGGGCCCAAGAGTGACCCGTGCCAAGGACGCACACATCAGGCGGCTCCAGGGCCCCCCAGCTTCTTGGCATTCTCAGAAATAACTTCTACCACACTCAACGTATCCTGGGGAGAGCCATCAGCTGCCAACGGCATCCTACAGGGCTATCGAGTGGTGTATGAGCCCTTAGCACCAGTGCAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CAACGTATCCTGGGGAGAGC
59.89
CTGGATCAGAACGGAGGACG
59.9
151
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CAACGTATCCTGGGGAGAGC
59.89
CCACTGGATCAGAACGGAGG
59.82
154
PCR template sequence:
ACTTCTACCACACTCAACGTATCCTGGGGAGAGCCATCAGCTGCCAACGGCATCCTACAGGGCTATCGAGTGGTGTATGAGCCCTTAGCACCAGTGCAAGTTCCAGGAGAGCCACCAGGGTCTGTCTCAGCCACACCGCACACCACGTCCTCCGTTCTGATCCAGTGGCAGCCTCCCCGGGATGAGAGCCTGAACGGTCT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
12
Interacting miRNAs (#binding sites)
mmu-miR-103-3p(1), mmu-miR-15b-5p(1), mmu-miR-298-5p(1), mmu-miR-433-3p(1), mmu-miR-96-5p(1), mmu-miR-125b-1-3p(1), mmu-miR-107-3p(1), mmu-miR-383-5p(1), mmu-miR-466a-5p(1), mmu-miR-1187(1), mmu-miR-466p-5p(1), mmu-miR-452-3p(1)
siRNAs for circular RNA silencing
Junction sequence
GCACCAGTGCAAGTTCCAGGAGAGCC
siRNA sets
CTCCTGGAACTTGCACTGG, TCTCCTGGAACTTGCACTG, CTGGAACTTGCACTGGTGC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSDK1_810_ORF_1
1.0597
0.392656937
0.99986405
1470
ORF sequence:
ATGAGCCCTGAGCCCAAGACACTCAAGAGCCCCTCTGCCTTACGTGCTGAACTCACCGCTCAAAGCAGCTTCAAGACCGTGAACAGCAGCTCCTCGTTAACCACCTATGAATTAACACATCTGAAGAAGTACCGGCGCTATGAAGTCATCATGACTGCTTATAACATCATTGGTGAGAGCCCAGCCAGTGTACCAGTGGAAGTCTTCGTTGGTGAGGCTGCCCCAGCGATGGCCCCACAGAATGTCCAGGTGACCCCACTCACGGCCAGCCAGCTGGAGGTCACATGGGACCCACCGCCCCCAGAGAGCCAGAATGGGAACATCCAGGGTTATAAGGTTTACTACTGGGAGGCAGACAGTCGCAATGAGACAGAGAAAATGAAGGTCCTCTTCCTCCCCGAGCCTGTGGTGAAGATCAAGGATCTCACCAGCCACACAAAGTACCTGATCAGCATCTCAGCCTTCAATGCTGCTGGTGATGGGCCCAAGAGTGACCCGTGCCAAGGACGCACACATCAGGCGGCTCCAGGGCCCCCCAGCTTCTTGGCATTCTCAGAAATAACTTCTACCACACTCAACGTATCCTGGGGAGAGCCATCAGCTGCCAACGGCATCCTACAGGGCTATCGAGTGGTGTATGAGCCCTTAGCACCAGTGCAAGTTCCAGGAGAGCCACCAGGGTCTGTCTCAGCCACACCGCACACCACGTCCTCCGTTCTGATCCAGTGGCAGCCTCCCCGGGATGAGAGCCTGAACGGTCTTCTGCAAGGCTACAGGATCTACTACCGTGAGCTGGAGTCTGAGACAGGCATGAGCCCTGAGCCCAAGACACTCAAGAGCCCCTCTGCCTTACGTGCTGAACTCACCGCTCAAAGCAGCTTCAAGACCGTGAACAGCAGCTCCTCGTTAACCACCTATGAATTAACACATCTGAAGAAGTACCGGCGCTATGAAGTCATCATGACTGCTTATAACATCATTGGTGAGAGCCCAGCCAGTGTACCAGTGGAAGTCTTCGTTGGTGAGGCTGCCCCAGCGATGGCCCCACAGAATGTCCAGGTGACCCCACTCACGGCCAGCCAGCTGGAGGTCACATGGGACCCACCGCCCCCAGAGAGCCAGAATGGGAACATCCAGGGTTATAAGGTTTACTACTGGGAGGCAGACAGTCGCAATGAGACAGAGAAAATGAAGGTCCTCTTCCTCCCCGAGCCTGTGGTGAAGATCAAGGATCTCACCAGCCACACAAAGTACCTGATCAGCATCTCAGCCTTCAATGCTGCTGGTGATGGGCCCAAGAGTGACCCGTGCCAAGGACGCACACATCAGGCGGCTCCAGGGCCCCCCAGCTTCTTGGCATTCTCAGAAATAACTTCTACCACACTCAACGTATCCTGGGGAGAGCCATCAGCTGCCAACGGCATCCTACAGGGCTATCGAGTGGTGTATGAGCCCTTAGCACCAGTGCAA
Peptide sequence:
MSPEPKTLKSPSALRAELTAQSSFKTVNSSSSLTTYELTHLKKYRRYEVIMTAYNIIGESPASVPVEVFVGEAAPAMAPQNVQVTPLTASQLEVTWDPPPPESQNGNIQGYKVYYWEADSRNETEKMKVLFLPEPVVKIKDLTSHTKYLISISAFNAAGDGPKSDPCQGRTHQAAPGPPSFLAFSEITSTTLNVSWGEPSAANGILQGYRVVYEPLAPVQVPGEPPGSVSATPHTTSSVLIQWQPPRDESLNGLLQGYRIYYRELESETGMSPEPKTLKSPSALRAELTAQSSFKTVNSSSSLTTYELTHLKKYRRYEVIMTAYNIIGESPASVPVEVFVGEAAPAMAPQNVQVTPLTASQLEVTWDPPPPESQNGNIQGYKVYYWEADSRNETEKMKVLFLPEPVVKIKDLTSHTKYLISISAFNAAGDGPKSDPCQGRTHQAAPGPPSFLAFSEITSTTLNVSWGEPSAANGILQGYRVVYEPLAPVQ
IRESfinder result
IRESfinder score
0.365973283
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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