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mmu_circRad50_696
Basic information of circular RNA
PanCircBase ID:
mmu_circRad50_696
mm39_Chr. Position ID:
chr11|53582939|53586238|-
Gene name:
Rad50
Transcript:
ENSMUST00000020649.14
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
9,8,7,6
Exon/intron offsets:
0,595,2788,3170
Genomic length:
3299
Exon/intron sizes in nt:
2,07,19,41,66,129
Flanking exon/introns:
chr11:53579104-53582939|chr11:53586238-53588940
Splice length:
696
Other database IDs:
circBase: hsa_circ_0127923, circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_136884
Human Ortholog IDs:
Mature spliced Sequence:
AATCGCCTGAAAGAGATTGAACACAACCTGTCTAAAATAATGAAACTTGATAATGAAATTAAAGCCTTGGAGAGCCGAAAGAAACAAATGGAGAAAGATAACAGTGAATTAGAACAGAAAATGGAAAAGGTTTTTCAAGGGACTGATGAGCAGCTAAATGACTTGTATCACAATCACCAGAGAACAGTAAGGGAGAAAGAAAGGCGCCTGGTAGACTGCCAGCGAGAACTGGAGAAGCTGAATAAAGAAGCACGGCTCCTCAACCAGGAAAAAGCAGAGCTGCTTGTGGAGCAGGGTCGTCTACAGCTACAGGCAGATCGCCATCAAGAGCACATCCGAGCCAGAGACTCATTAATTCAGTCTTTGGCAACACATCTTGAATTGGATGGTTTTGAGCGTGGACCATTCAGTGAAAGACAGATTAAAAATTTTCATGAACTTGTGAAAGAGAGACAGGAAAGAGAAGCTAAAACTGCCAGCCAGCTCTTGAGCGACCTGACAGACAAAGAAGCTCTGAAGCAGAGGCAGCTTGATGAGCTGAGGGACAGGAAGAGCGGACTGGGGAGGACGATTGAGCTGAAGACAGAGATCCTCACGAAGAAGCAGAGCGAGCTGCGGCACGTGAGGAGTGAGCTGCAGCAGCTGGAGGGCTCCTCCGACAGGATTCTGGAACTGGACCAGGAGCTCACGAAAGCT
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CGTGAGGAGTGAGCTGCAG
60.45
TTCTTTCGGCTCTCCAAGGC
60.32
159
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GAGGAGTGAGCTGCAGCAG
60.45
TTCTTTCGGCTCTCCAAGGC
60.32
156
PCR template sequence:
GAAGAAGCAGAGCGAGCTGCGGCACGTGAGGAGTGAGCTGCAGCAGCTGGAGGGCTCCTCCGACAGGATTCTGGAACTGGACCAGGAGCTCACGAAAGCTAATCGCCTGAAAGAGATTGAACACAACCTGTCTAAAATAATGAAACTTGATAATGAAATTAAAGCCTTGGAGAGCCGAAAGAAACAAATGGAGAAAGATA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
6
Interacting miRNAs (#binding sites)
mmu-miR-138-5p(1), mmu-miR-149-5p(1), mmu-miR-136-5p(1), mmu-miR-22-3p(1), mmu-miR-1198-5p(1), mmu-miR-207(1)
siRNAs for circular RNA silencing
Junction sequence
GCTCACGAAAGCTAATCGCCTGAAAG
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCRAD50_696_ORF_1
1.2377
0.344576576
0.999725027
1353
ORF sequence:
ATGAAACTTGATAATGAAATTAAAGCCTTGGAGAGCCGAAAGAAACAAATGGAGAAAGATAACAGTGAATTAGAACAGAAAATGGAAAAGGTTTTTCAAGGGACTGATGAGCAGCTAAATGACTTGTATCACAATCACCAGAGAACAGTAAGGGAGAAAGAAAGGCGCCTGGTAGACTGCCAGCGAGAACTGGAGAAGCTGAATAAAGAAGCACGGCTCCTCAACCAGGAAAAAGCAGAGCTGCTTGTGGAGCAGGGTCGTCTACAGCTACAGGCAGATCGCCATCAAGAGCACATCCGAGCCAGAGACTCATTAATTCAGTCTTTGGCAACACATCTTGAATTGGATGGTTTTGAGCGTGGACCATTCAGTGAAAGACAGATTAAAAATTTTCATGAACTTGTGAAAGAGAGACAGGAAAGAGAAGCTAAAACTGCCAGCCAGCTCTTGAGCGACCTGACAGACAAAGAAGCTCTGAAGCAGAGGCAGCTTGATGAGCTGAGGGACAGGAAGAGCGGACTGGGGAGGACGATTGAGCTGAAGACAGAGATCCTCACGAAGAAGCAGAGCGAGCTGCGGCACGTGAGGAGTGAGCTGCAGCAGCTGGAGGGCTCCTCCGACAGGATTCTGGAACTGGACCAGGAGCTCACGAAAGCTAATCGCCTGAAAGAGATTGAACACAACCTGTCTAAAATAATGAAACTTGATAATGAAATTAAAGCCTTGGAGAGCCGAAAGAAACAAATGGAGAAAGATAACAGTGAATTAGAACAGAAAATGGAAAAGGTTTTTCAAGGGACTGATGAGCAGCTAAATGACTTGTATCACAATCACCAGAGAACAGTAAGGGAGAAAGAAAGGCGCCTGGTAGACTGCCAGCGAGAACTGGAGAAGCTGAATAAAGAAGCACGGCTCCTCAACCAGGAAAAAGCAGAGCTGCTTGTGGAGCAGGGTCGTCTACAGCTACAGGCAGATCGCCATCAAGAGCACATCCGAGCCAGAGACTCATTAATTCAGTCTTTGGCAACACATCTTGAATTGGATGGTTTTGAGCGTGGACCATTCAGTGAAAGACAGATTAAAAATTTTCATGAACTTGTGAAAGAGAGACAGGAAAGAGAAGCTAAAACTGCCAGCCAGCTCTTGAGCGACCTGACAGACAAAGAAGCTCTGAAGCAGAGGCAGCTTGATGAGCTGAGGGACAGGAAGAGCGGACTGGGGAGGACGATTGAGCTGAAGACAGAGATCCTCACGAAGAAGCAGAGCGAGCTGCGGCACGTGAGGAGTGAGCTGCAGCAGCTGGAGGGCTCCTCCGACAGGATTCTGGAACTGGACCAGGAGCTCACGAAAGCT
Peptide sequence:
MKLDNEIKALESRKKQMEKDNSELEQKMEKVFQGTDEQLNDLYHNHQRTVREKERRLVDCQRELEKLNKEARLLNQEKAELLVEQGRLQLQADRHQEHIRARDSLIQSLATHLELDGFERGPFSERQIKNFHELVKERQEREAKTASQLLSDLTDKEALKQRQLDELRDRKSGLGRTIELKTEILTKKQSELRHVRSELQQLEGSSDRILELDQELTKANRLKEIEHNLSKIMKLDNEIKALESRKKQMEKDNSELEQKMEKVFQGTDEQLNDLYHNHQRTVREKERRLVDCQRELEKLNKEARLLNQEKAELLVEQGRLQLQADRHQEHIRARDSLIQSLATHLELDGFERGPFSERQIKNFHELVKERQEREAKTASQLLSDLTDKEALKQRQLDELRDRKSGLGRTIELKTEILTKKQSELRHVRSELQQLEGSSDRILELDQELTKA
IRESfinder result
IRESfinder score
0.467802726
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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