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mmu_circSdk1_722
Basic information of circular RNA
PanCircBase ID:
mmu_circSdk1_722
mm39_Chr. Position ID:
chr5|142017334|142037038|+
Gene name:
Sdk1
Transcript:
ENSMUST00000085774.11
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
18,19,20,21,22
Exon/intron offsets:
0,2773,6654,14548,19582
Genomic length:
19704
Exon/intron sizes in nt:
116,193,99,192,122
Flanking exon/introns:
chr5:141992560-142017334|chr5:142037038-142067371
Splice length:
722
Other database IDs:
circAtlas: mmu-Sdk1_0021
circBase: hsa_circ_0134302, circAtlas: hsa-SDK1_0003, CIRCpedia: HSA_CIRCpedia_121464
Human Ortholog IDs:
Mature spliced Sequence:
TGCCCACTGCACCTCCCCAGAACGTGCAGGCAGAGGCTGTGAATTCCACCACTGTGCACTTCCTGTGGAACCCGCCACCCCAGCAGTTCATCAACGGCATCAACCAGGGATACAAGCTCCTAGCATGGCCGGCAGATGCTCCTGAGACTGTCACTGTAGTCACTATTGCTCCTGACTTCCATGGAATCCATCATGGGTACATAACAAACTTGAAGAAGTTCACTGCCTACTTCACATCCGTCCTGTGTTTTACCACCCCGGGGGATGGGCCTCCAAGTTCACCTCAGCTCGTGTGGACCCATGAGGACAAGCCGGGAGCTGTGGGGCACCTGAGCTTCACGGAGATTTTGGACACCTCTCTCAAGGTCAGCTGGCAGGAGCCCCTGGAGAGAAACGGCATCATTATGGGCTATCAGATTTCCTGGGAGGTGTATGGGAGGAATGACTCTCGACTCACGCACACCCTCAACAGCACGATGCACGAGTATAAGATCCAAGGACTGTCATCACTCACCACCTATACCATCGATGTGGCTGCCTTGACCGCCGCAGGCGTGGGCGTGACCACATCATCCACCATCTCTTCAGGTGTACCCCCAGATCTTCCTGGCGCTCCATCCAATCTGGTCATTTCCAACATCAGCCCTCGCTCAGCCACACTCCAGTTCCGACCTGGCTATGATGGGAAGACGGCCATCTGCAGGTGGATTGTGGAGGGGCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CCAGTTCCGACCTGGCTATG
60.18
TTGATGAACTGCTGGGGTGG
60.25
155
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CACACTCCAGTTCCGACCTG
60.32
TTGATGAACTGCTGGGGTGG
60.25
161
PCR template sequence:
TCTGGTCATTTCCAACATCAGCCCTCGCTCAGCCACACTCCAGTTCCGACCTGGCTATGATGGGAAGACGGCCATCTGCAGGTGGATTGTGGAGGGGCAGTGCCCACTGCACCTCCCCAGAACGTGCAGGCAGAGGCTGTGAATTCCACCACTGTGCACTTCCTGTGGAACCCGCCACCCCAGCAGTTCATCAACGGCAT
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-210-3p(1), mmu-miR-34a-5p(1), mmu-miR-138-5p(1), mmu-miR-139-5p(1), mmu-miR-433-3p(1), mmu-miR-127-5p(1), mmu-miR-370-3p(1), mmu-miR-673-5p(1), mmu-miR-452-3p(1), mmu-miR-574-5p(1)
siRNAs for circular RNA silencing
Junction sequence
TGTGGAGGGGCAGTGCCCACTGCACC
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSDK1_722_ORF_1
0.7543
0.303661743
0.491314514
360
ORF sequence:
ATGGGCTATCAGATTTCCTGGGAGGTGTATGGGAGGAATGACTCTCGACTCACGCACACCCTCAACAGCACGATGCACGAGTATAAGATCCAAGGACTGTCATCACTCACCACCTATACCATCGATGTGGCTGCCTTGACCGCCGCAGGCGTGGGCGTGACCACATCATCCACCATCTCTTCAGGTGTACCCCCAGATCTTCCTGGCGCTCCATCCAATCTGGTCATTTCCAACATCAGCCCTCGCTCAGCCACACTCCAGTTCCGACCTGGCTATGATGGGAAGACGGCCATCTGCAGGTGGATTGTGGAGGGGCAGTGCCCACTGCACCTCCCCAGAACGTGCAGGCAGAGGCTGTGA
Peptide sequence:
MGYQISWEVYGRNDSRLTHTLNSTMHEYKIQGLSSLTTYTIDVAALTAAGVGVTTSSTISSGVPPDLPGAPSNLVISNISPRSATLQFRPGYDGKTAICRWIVEGQCPLHLPRTCRQRL
IRESfinder result
IRESfinder score
0.571044859
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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