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mmu_circRps6ka3_1890
Basic information of circular RNA
PanCircBase ID:
mmu_circRps6ka3_1890
mm39_Chr. Position ID:
chrX|158068261|158135429|+
Gene name:
Rps6ka3
Transcript:
ENSMUST00000112493.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
19
Exon/intron indexes:
5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23
Exon/intron offsets:
0,26198,32655,41575,42506,43105,45292,45521,46885,51429,51697,51920,52652,57319,60074,61750,63986,66098,67050
Genomic length:
67168
Exon/intron sizes in nt:
57,11,78,28,18,01,07,30,00,00,00,00,00,00,00,00,00,00,00,00,00,00,000
Flanking exon/introns:
chrX:158062199-158068261|chrX:158135429-158145637
Splice length:
1890
Other database IDs:
circAtlas: mmu-Rps6ka3_0029
Human Ortholog IDs:
Mature spliced Sequence:
AATGGACAGCAAATTATGGATGAACCTATGGGAGAGGAGGAGATTAACCCACAAACTGAAGAAGGCAGTATCAAAGAAATTGCAATCACACATCATGTGAAGGAAGGACATGAAAAGGCAGATCCTTCCCAGTTTGAACTTTTAAAAGTATTAGGGCAGGGATCATTTGGAAAGGTTTTCTTAGTTAAAAAAATCTCAGGCTCTGATGCTAGACAGCTTTATGCCATGAAAGTATTAAAGAAGGCCACGCTGAAAGTTCGAGACCGTGTTCGGACAAAAATGGAACGTGATATCTTGGTAGAAGTCAATCACCCTTTCATTGTCAAATTGCATTACGCTTTTCAAACGGAAGGGAAGTTGTATCTTATTTTGGATTTTCTCAGGGGCGGAGACTTGTTTACACGCTTATCCAAAGAGGTGATGTTCACAGAGGAAGATGTCAAATTCTACTTGGCTGAACTTGCACTTGCTTTAGACCATCTTCATAGCCTGGGAATAATCTATAGAGACTTAAAACCAGAAAACATACTTCTTGATGAAGAAGGTCACATCAAGTTAACTGATTTTGGCTTAAGTAAGGAATCTATTGATCATGAGAAGAAGGCTTATTCTTTTTGTGGCACTGTGGAATACATGGCTCCAGAAGTAGTTAACCGCAGAGGTCACACTCAGAGTGCGGACTGGTGGTCCTTTGGTGTGTTGATGTTTGAAATGCTCACTGGTACACTACCTTTCCAAGGAAAAGATCGTAAAGAAACAATGACTATGATTCTTAAAGCCAAACTCGGGATGCCACAGTTTCTGAGTCCTGAAGCCCAGAGTCTTTTACGAATGCTTTTCAAACGGAATCCTGCAAACAGATTAGGTGCTGGACCAGATGGAGTTGAAGAAATTAAAAGACATTCATTTTTCTCAACAATAGACTGGAATAAACTATATAGAAGAGAGATTCACCCACCTTTTAAGCCTGCAACTGGCAGACCTGAAGATACATTTTATTTTGATCCTGAGTTTACTGCAAAAACTCCCAAAGATTCACCGGGCATTCCACCTAGTGCTAACGCACATCAGCTTTTTCGGGGGTTTAGTTTTGTTGCTATTACCTCAGATGATGAAAGCCAAGCTATGCAGACAGTTGGTGTGCATTCAATTGTTCAGCAATTACACAGAAACAGTATTCAGTTTACTGATGGATATGAAGTAAAAGAGGATATTGGCGTTGGCTCATACTCCGTTTGTAAGAGATGTATACATAAAGCTACAAACATGGAGTTTGCCGTGAAGATTATTGATAAAAGCAAGAGAGACCCAACAGAAGAGATTGAAATTCTTCTTCGCTATGGACAGCATCCAAACATCATTACCCTAAAGGATGTGTATGATGATGGAAAATATGTGTATGTAGTAACAGAACTTATGAAAGGAGGTGAATTGCTGGATAAGATTCTTAGACAGAAGTTTTTCTCAGAGCGAGAGGCCAGCGCTGTCCTGTTTACTATAACCAAAACTGTTGAGTATCTTCATGCACAAGGGGTGGTTCACAGAGACTTGAAACCTAGCAACATTCTTTATGTGGATGAGTCTGGTAATCCAGAATCTATTCGAATTTGTGATTTTGGCTTTGCAAAACAACTGAGAGCAGAAAATGGTCTTCTCATGACTCCTTGTTATACTGCAAATTTTGTTGCACCAGAGGTTTTAAAACGGCAAGGTTATGATGCTGCCTGTGATATATGGAGTCTTGGCGTCCTCCTTTATACAATGCTTACTGGTTACACTCCATTTGCAAATGGCCCTGATGATACTCCAGAGGAAATACTGGCACGAATAGGTAGTGGAAAATTCTCACTCAGTGGTGGTTACTGGAATTCTGTTTCAGACACAGCAAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TGGCCCTGATGATACTCCAGA
60.06
TGCCTTCTTCAGTTTGTGGGT
60.06
167
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CCAGAGGAAATACTGGCACGA
59.79
TGCCTTCTTCAGTTTGTGGGT
60.06
151
PCR template sequence:
TGGCCCTGATGATACTCCAGAGGAAATACTGGCACGAATAGGTAGTGGAAAATTCTCACTCAGTGGTGGTTACTGGAATTCTGTTTCAGACACAGCAAAGAATGGACAGCAAATTATGGATGAACCTATGGGAGAGGAGGAGATTAACCCACAAACTGAAGAAGGCAGTATCAAAGAAATTGCAATCACACATCATGTGA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
18
Interacting miRNAs (#binding sites)
mmu-miR-429-3p(1), mmu-miR-200b-3p(1), mmu-miR-103-3p(1), mmu-miR-200c-3p(1), mmu-miR-122-5p(1), mmu-miR-320-3p(1), mmu-miR-30d-5p(1), mmu-miR-125a-5p(1), mmu-miR-130b-3p(1), mmu-miR-301b-3p(1), mmu-miR-107-3p(1), mmu-miR-301a-3p(1), mmu-miR-1187(1), mmu-miR-129-5p(1), mmu-miR-3065-5p(1), mmu-miR-466b-3p(1), mmu-miR-338-3p(1), mmu-miR-7a-2-3p(1)
siRNAs for circular RNA silencing
Junction sequence
AGACACAGCAAAGAATGGACAGCAAA
siRNA sets
TTTGCTGTCCATTCTTTGC,TTGCTGTCCATTCTTTGCT,GTCCATTCTTTGCTGTGTC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCRPS6KA3_1890_ORF_1
0.9671
0.051095006
1
3765
ORF sequence:
ATGGATGAACCTATGGGAGAGGAGGAGATTAACCCACAAACTGAAGAAGGCAGTATCAAAGAAATTGCAATCACACATCATGTGAAGGAAGGACATGAAAAGGCAGATCCTTCCCAGTTTGAACTTTTAAAAGTATTAGGGCAGGGATCATTTGGAAAGGTTTTCTTAGTTAAAAAAATCTCAGGCTCTGATGCTAGACAGCTTTATGCCATGAAAGTATTAAAGAAGGCCACGCTGAAAGTTCGAGACCGTGTTCGGACAAAAATGGAACGTGATATCTTGGTAGAAGTCAATCACCCTTTCATTGTCAAATTGCATTACGCTTTTCAAACGGAAGGGAAGTTGTATCTTATTTTGGATTTTCTCAGGGGCGGAGACTTGTTTACACGCTTATCCAAAGAGGTGATGTTCACAGAGGAAGATGTCAAATTCTACTTGGCTGAACTTGCACTTGCTTTAGACCATCTTCATAGCCTGGGAATAATCTATAGAGACTTAAAACCAGAAAACATACTTCTTGATGAAGAAGGTCACATCAAGTTAACTGATTTTGGCTTAAGTAAGGAATCTATTGATCATGAGAAGAAGGCTTATTCTTTTTGTGGCACTGTGGAATACATGGCTCCAGAAGTAGTTAACCGCAGAGGTCACACTCAGAGTGCGGACTGGTGGTCCTTTGGTGTGTTGATGTTTGAAATGCTCACTGGTACACTACCTTTCCAAGGAAAAGATCGTAAAGAAACAATGACTATGATTCTTAAAGCCAAACTCGGGATGCCACAGTTTCTGAGTCCTGAAGCCCAGAGTCTTTTACGAATGCTTTTCAAACGGAATCCTGCAAACAGATTAGGTGCTGGACCAGATGGAGTTGAAGAAATTAAAAGACATTCATTTTTCTCAACAATAGACTGGAATAAACTATATAGAAGAGAGATTCACCCACCTTTTAAGCCTGCAACTGGCAGACCTGAAGATACATTTTATTTTGATCCTGAGTTTACTGCAAAAACTCCCAAAGATTCACCGGGCATTCCACCTAGTGCTAACGCACATCAGCTTTTTCGGGGGTTTAGTTTTGTTGCTATTACCTCAGATGATGAAAGCCAAGCTATGCAGACAGTTGGTGTGCATTCAATTGTTCAGCAATTACACAGAAACAGTATTCAGTTTACTGATGGATATGAAGTAAAAGAGGATATTGGCGTTGGCTCATACTCCGTTTGTAAGAGATGTATACATAAAGCTACAAACATGGAGTTTGCCGTGAAGATTATTGATAAAAGCAAGAGAGACCCAACAGAAGAGATTGAAATTCTTCTTCGCTATGGACAGCATCCAAACATCATTACCCTAAAGGATGTGTATGATGATGGAAAATATGTGTATGTAGTAACAGAACTTATGAAAGGAGGTGAATTGCTGGATAAGATTCTTAGACAGAAGTTTTTCTCAGAGCGAGAGGCCAGCGCTGTCCTGTTTACTATAACCAAAACTGTTGAGTATCTTCATGCACAAGGGGTGGTTCACAGAGACTTGAAACCTAGCAACATTCTTTATGTGGATGAGTCTGGTAATCCAGAATCTATTCGAATTTGTGATTTTGGCTTTGCAAAACAACTGAGAGCAGAAAATGGTCTTCTCATGACTCCTTGTTATACTGCAAATTTTGTTGCACCAGAGGTTTTAAAACGGCAAGGTTATGATGCTGCCTGTGATATATGGAGTCTTGGCGTCCTCCTTTATACAATGCTTACTGGTTACACTCCATTTGCAAATGGCCCTGATGATACTCCAGAGGAAATACTGGCACGAATAGGTAGTGGAAAATTCTCACTCAGTGGTGGTTACTGGAATTCTGTTTCAGACACAGCAAAGAATGGACAGCAAATTATGGATGAACCTATGGGAGAGGAGGAGATTAACCCACAAACTGAAGAAGGCAGTATCAAAGAAATTGCAATCACACATCATGTGAAGGAAGGACATGAAAAGGCAGATCCTTCCCAGTTTGAACTTTTAAAAGTATTAGGGCAGGGATCATTTGGAAAGGTTTTCTTAGTTAAAAAAATCTCAGGCTCTGATGCTAGACAGCTTTATGCCATGAAAGTATTAAAGAAGGCCACGCTGAAAGTTCGAGACCGTGTTCGGACAAAAATGGAACGTGATATCTTGGTAGAAGTCAATCACCCTTTCATTGTCAAATTGCATTACGCTTTTCAAACGGAAGGGAAGTTGTATCTTATTTTGGATTTTCTCAGGGGCGGAGACTTGTTTACACGCTTATCCAAAGAGGTGATGTTCACAGAGGAAGATGTCAAATTCTACTTGGCTGAACTTGCACTTGCTTTAGACCATCTTCATAGCCTGGGAATAATCTATAGAGACTTAAAACCAGAAAACATACTTCTTGATGAAGAAGGTCACATCAAGTTAACTGATTTTGGCTTAAGTAAGGAATCTATTGATCATGAGAAGAAGGCTTATTCTTTTTGTGGCACTGTGGAATACATGGCTCCAGAAGTAGTTAACCGCAGAGGTCACACTCAGAGTGCGGACTGGTGGTCCTTTGGTGTGTTGATGTTTGAAATGCTCACTGGTACACTACCTTTCCAAGGAAAAGATCGTAAAGAAACAATGACTATGATTCTTAAAGCCAAACTCGGGATGCCACAGTTTCTGAGTCCTGAAGCCCAGAGTCTTTTACGAATGCTTTTCAAACGGAATCCTGCAAACAGATTAGGTGCTGGACCAGATGGAGTTGAAGAAATTAAAAGACATTCATTTTTCTCAACAATAGACTGGAATAAACTATATAGAAGAGAGATTCACCCACCTTTTAAGCCTGCAACTGGCAGACCTGAAGATACATTTTATTTTGATCCTGAGTTTACTGCAAAAACTCCCAAAGATTCACCGGGCATTCCACCTAGTGCTAACGCACATCAGCTTTTTCGGGGGTTTAGTTTTGTTGCTATTACCTCAGATGATGAAAGCCAAGCTATGCAGACAGTTGGTGTGCATTCAATTGTTCAGCAATTACACAGAAACAGTATTCAGTTTACTGATGGATATGAAGTAAAAGAGGATATTGGCGTTGGCTCATACTCCGTTTGTAAGAGATGTATACATAAAGCTACAAACATGGAGTTTGCCGTGAAGATTATTGATAAAAGCAAGAGAGACCCAACAGAAGAGATTGAAATTCTTCTTCGCTATGGACAGCATCCAAACATCATTACCCTAAAGGATGTGTATGATGATGGAAAATATGTGTATGTAGTAACAGAACTTATGAAAGGAGGTGAATTGCTGGATAAGATTCTTAGACAGAAGTTTTTCTCAGAGCGAGAGGCCAGCGCTGTCCTGTTTACTATAACCAAAACTGTTGAGTATCTTCATGCACAAGGGGTGGTTCACAGAGACTTGAAACCTAGCAACATTCTTTATGTGGATGAGTCTGGTAATCCAGAATCTATTCGAATTTGTGATTTTGGCTTTGCAAAACAACTGAGAGCAGAAAATGGTCTTCTCATGACTCCTTGTTATACTGCAAATTTTGTTGCACCAGAGGTTTTAAAACGGCAAGGTTATGATGCTGCCTGTGATATATGGAGTCTTGGCGTCCTCCTTTATACAATGCTTACTGGTTACACTCCATTTGCAAATGGCCCTGATGATACTCCAGAGGAAATACTGGCACGAATAGGTAGTGGAAAATTCTCACTCAGTGGTGGTTACTGGAATTCTGTTTCAGACACAGCAAAG
Peptide sequence:
MDEPMGEEEINPQTEEGSIKEIAITHHVKEGHEKADPSQFELLKVLGQGSFGKVFLVKKISGSDARQLYAMKVLKKATLKVRDRVRTKMERDILVEVNHPFIVKLHYAFQTEGKLYLILDFLRGGDLFTRLSKEVMFTEEDVKFYLAELALALDHLHSLGIIYRDLKPENILLDEEGHIKLTDFGLSKESIDHEKKAYSFCGTVEYMAPEVVNRRGHTQSADWWSFGVLMFEMLTGTLPFQGKDRKETMTMILKAKLGMPQFLSPEAQSLLRMLFKRNPANRLGAGPDGVEEIKRHSFFSTIDWNKLYRREIHPPFKPATGRPEDTFYFDPEFTAKTPKDSPGIPPSANAHQLFRGFSFVAITSDDESQAMQTVGVHSIVQQLHRNSIQFTDGYEVKEDIGVGSYSVCKRCIHKATNMEFAVKIIDKSKRDPTEEIEILLRYGQHPNIITLKDVYDDGKYVYVVTELMKGGELLDKILRQKFFSEREASAVLFTITKTVEYLHAQGVVHRDLKPSNILYVDESGNPESIRICDFGFAKQLRAENGLLMTPCYTANFVAPEVLKRQGYDAACDIWSLGVLLYTMLTGYTPFANGPDDTPEEILARIGSGKFSLSGGYWNSVSDTAKNGQQIMDEPMGEEEINPQTEEGSIKEIAITHHVKEGHEKADPSQFELLKVLGQGSFGKVFLVKKISGSDARQLYAMKVLKKATLKVRDRVRTKMERDILVEVNHPFIVKLHYAFQTEGKLYLILDFLRGGDLFTRLSKEVMFTEEDVKFYLAELALALDHLHSLGIIYRDLKPENILLDEEGHIKLTDFGLSKESIDHEKKAYSFCGTVEYMAPEVVNRRGHTQSADWWSFGVLMFEMLTGTLPFQGKDRKETMTMILKAKLGMPQFLSPEAQSLLRMLFKRNPANRLGAGPDGVEEIKRHSFFSTIDWNKLYRREIHPPFKPATGRPEDTFYFDPEFTAKTPKDSPGIPPSANAHQLFRGFSFVAITSDDESQAMQTVGVHSIVQQLHRNSIQFTDGYEVKEDIGVGSYSVCKRCIHKATNMEFAVKIIDKSKRDPTEEIEILLRYGQHPNIITLKDVYDDGKYVYVVTELMKGGELLDKILRQKFFSEREASAVLFTITKTVEYLHAQGVVHRDLKPSNILYVDESGNPESIRICDFGFAKQLRAENGLLMTPCYTANFVAPEVLKRQGYDAACDIWSLGVLLYTMLTGYTPFANGPDDTPEEILARIGSGKFSLSGGYWNSVSDTAK
IRESfinder result
IRESfinder score
0.663585494
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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