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mmu_circSlk_1829
Basic information of circular RNA
PanCircBase ID:
mmu_circSlk_1829
mm39_Chr. Position ID:
chr19|47603634|47609391|+
Gene name:
Slk
Transcript:
ENSMUST00000026043.12
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
5,6,7,8,9
Exon/intron offsets:
0,210,1326,3995,4407
Genomic length:
5757
Exon/intron sizes in nt:
7,31,95,82,12,91,350
Flanking exon/introns:
chr19:47600490-47603634|chr19:47609391-47610674
Splice length:
1829
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
CGGATTTTGGAGTATCAGCTAAAAATACCAGGACAATTCAAAGGAGGGATTCATTTATTGGCACACCATATTGGATGGCTCCTGAAGTAGTCATGTGTGAGACATCAAAGGACAGACCTTATGACTACAAAGCTGATGTTTGGTCCCTGGGTATTACTTTAATAGAAATGGCTGAGATAGAGCCACCTCATCATGAGTTAAATCCAATGCGCGTGCTGCTGAAAATTGCAAAATCTGAGCCCCCAACATTAGCACAGCCATCAAAATGGTCTTCAAATTTTAAGGACTTTCTAAGGAAATGCTTGGAAAAGAATGTGGATGCGCGGTGGACCACGTCTCAGCTGTTGCAGCATCCCTTTGTTACCGTTGATTCCAACAAACCAGTCCGAGAGTTGATTGCTGAGGCAAAGGCTGAAGTAACAGAAGAAGTTGAAGATGGCAAGGAAGAAGATGAGGAGGAGGAAGCAGAGAATGCTCTGCCAATACCTGCAAATAAACGTGCCTCCTCTGACCTCAGCATTGCCAGCTCTGAAGAAGATAAACTTTCACAAAATGCTTGTATTTTGGAATCTGTGTCAGAAAGAACAGAACAAAGTACTTCTGAGGATAAATTTAGCAACAAAATTCTTAATGAGAAACCTACGACTGACGGTCCTGAGAAGGCTGTGGATGAGCATGCAAGTGATGTGAACTTAGAAACTGGGGCTGAACTAAATGACCAAACAGTAGGAATCCATGAGAATGGGAGAGAGAAGAAAAGACCCAAGCTGGAAAATCTGCCAGATACACAAGACCAGCAAACTGTGGATGTTAATTCAGTCAGTGAAGAAAATGAGAATAATAGAGTAACTTTAGAAACGAACACTGATTGTCTGAAACCAGAGGAAGACAGAAATAAAGAAAACCAAGAGACACTTGAGAGTAAACTTATACAATCTGAAGAAATTAATGACACACATATTCAAACAATGGACTTAGTTTCTCAAGAGACTGGAGAAAAAGAAGCAGATTTTCAGGCAGTTGACAATGAAGTTGGGCTTACAAAGGAAGAAACCCAAGAGAAATTAGGAAAAGATGGTACAGCTCAAAAAGTTATAACCAGTGATAGAAGCAGTGAGGTGGGGACAGACGAGGCTCTAGATGACACTCAGAAGGCTGCTGAGCTCAGTAAGGCAGCACAGAGTGGGGAAGGGGACGAAGCCCTGGCGCCTACCCAGACACTAGCAGAGAAGCCCACAGAGGGCCCTGAGGCCGGTGGGGCTGAGGAAGAGCCTCCTGGTGGAGAGAGAGTTGAGGATAAACAGCCAGAGCAGCAGCCTGCAGTGTGTGAAGCTGAGGGACAGTTAACCAGCACGTCAGAGACCACACGGGCAACCCTGGAGCAACCGGAGACGGATGAAGTTGAGCAGGTCAGCGAGTCCAATAGCATTGAGGAGCTAGAGAGACTTGTAGTTACTGGTGCTGAGGCACGGGCTCTCGGGAGTGAAGGTGAGGCAGCTGCTACTGAGGTAGATTTGGAGAGAAAAGAAAACGCACAGAAAGTGCCCGTTAAAGCAGAGTCCCAAGCTCCTGCAGCATCGCAGCCCAGCGAGCCTCACCCTGTCTTAATACCCAGTATTAATATTAATTCTGAAACCACAGAAAATAAAGAAGAAATGGGTGCTTTGCCAAAACCTGAAACCATACTGCCACCAGAGCCTGAACATGAAAAGGGAAATGACACCGACTCAGGGACTGGGTCCACTGTGGAGAATAGCAGTGGTGACCTGAACTTGTCCATCTCTAGCTTCCTAAGCAAAGCTAAGGACAGCGGCTCAGTGTCTCTGCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AGCAGTGGTGACCTGAACTT
59.16
GCCATCCAATATGGTGTGCC
59.32
154
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GCAGTGGTGACCTGAACTTG
59.05
GCCATCCAATATGGTGTGCC
59.32
153
PCR template sequence:
AGGGACTGGGTCCACTGTGGAGAATAGCAGTGGTGACCTGAACTTGTCCATCTCTAGCTTCCTAAGCAAAGCTAAGGACAGCGGCTCAGTGTCTCTGCAGCGGATTTTGGAGTATCAGCTAAAAATACCAGGACAATTCAAAGGAGGGATTCATTTATTGGCACACCATATTGGATGGCTCCTGAAGTAGTCATGTGTGA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
26
Interacting miRNAs (#binding sites)
mmu-miR-29b-2-5p(3), mmu-miR-16-5p(1), mmu-miR-15a-5p(1), mmu-miR-27b-3p(1), mmu-miR-27a-3p(1), mmu-miR-429-3p(1), mmu-miR-200b-3p(1), mmu-miR-200c-3p(1), mmu-miR-205-5p(1), mmu-miR-211-5p(1), mmu-miR-204-5p(1), mmu-miR-15b-5p(1), mmu-miR-29b-3p(1), mmu-miR-328-3p(1), mmu-miR-138-5p(1), mmu-miR-128-3p(1), mmu-miR-24-3p(1), mmu-miR-433-3p(1), mmu-miR-29b-1-5p(1), mmu-miR-802-5p(1), mmu-miR-377-3p(1), mmu-miR-1187(1), mmu-miR-669d-5p(1), mmu-miR-540-3p(1), mmu-miR-670-5p(1), mmu-miR-296-3p(1)
siRNAs for circular RNA silencing
Junction sequence
AGTGTCTCTGCAGCGGATTTTGGAGT
siRNA sets
AAATCCGCTGCAGAGACAC, AATCCGCTGCAGAGACACT, CAAAATCCGCTGCAGAGAC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSLK_1829_ORF_1
1.1183
0.191702159
0.999980576
1845
ORF sequence:
ATGGCTCCTGAAGTAGTCATGTGTGAGACATCAAAGGACAGACCTTATGACTACAAAGCTGATGTTTGGTCCCTGGGTATTACTTTAATAGAAATGGCTGAGATAGAGCCACCTCATCATGAGTTAAATCCAATGCGCGTGCTGCTGAAAATTGCAAAATCTGAGCCCCCAACATTAGCACAGCCATCAAAATGGTCTTCAAATTTTAAGGACTTTCTAAGGAAATGCTTGGAAAAGAATGTGGATGCGCGGTGGACCACGTCTCAGCTGTTGCAGCATCCCTTTGTTACCGTTGATTCCAACAAACCAGTCCGAGAGTTGATTGCTGAGGCAAAGGCTGAAGTAACAGAAGAAGTTGAAGATGGCAAGGAAGAAGATGAGGAGGAGGAAGCAGAGAATGCTCTGCCAATACCTGCAAATAAACGTGCCTCCTCTGACCTCAGCATTGCCAGCTCTGAAGAAGATAAACTTTCACAAAATGCTTGTATTTTGGAATCTGTGTCAGAAAGAACAGAACAAAGTACTTCTGAGGATAAATTTAGCAACAAAATTCTTAATGAGAAACCTACGACTGACGGTCCTGAGAAGGCTGTGGATGAGCATGCAAGTGATGTGAACTTAGAAACTGGGGCTGAACTAAATGACCAAACAGTAGGAATCCATGAGAATGGGAGAGAGAAGAAAAGACCCAAGCTGGAAAATCTGCCAGATACACAAGACCAGCAAACTGTGGATGTTAATTCAGTCAGTGAAGAAAATGAGAATAATAGAGTAACTTTAGAAACGAACACTGATTGTCTGAAACCAGAGGAAGACAGAAATAAAGAAAACCAAGAGACACTTGAGAGTAAACTTATACAATCTGAAGAAATTAATGACACACATATTCAAACAATGGACTTAGTTTCTCAAGAGACTGGAGAAAAAGAAGCAGATTTTCAGGCAGTTGACAATGAAGTTGGGCTTACAAAGGAAGAAACCCAAGAGAAATTAGGAAAAGATGGTACAGCTCAAAAAGTTATAACCAGTGATAGAAGCAGTGAGGTGGGGACAGACGAGGCTCTAGATGACACTCAGAAGGCTGCTGAGCTCAGTAAGGCAGCACAGAGTGGGGAAGGGGACGAAGCCCTGGCGCCTACCCAGACACTAGCAGAGAAGCCCACAGAGGGCCCTGAGGCCGGTGGGGCTGAGGAAGAGCCTCCTGGTGGAGAGAGAGTTGAGGATAAACAGCCAGAGCAGCAGCCTGCAGTGTGTGAAGCTGAGGGACAGTTAACCAGCACGTCAGAGACCACACGGGCAACCCTGGAGCAACCGGAGACGGATGAAGTTGAGCAGGTCAGCGAGTCCAATAGCATTGAGGAGCTAGAGAGACTTGTAGTTACTGGTGCTGAGGCACGGGCTCTCGGGAGTGAAGGTGAGGCAGCTGCTACTGAGGTAGATTTGGAGAGAAAAGAAAACGCACAGAAAGTGCCCGTTAAAGCAGAGTCCCAAGCTCCTGCAGCATCGCAGCCCAGCGAGCCTCACCCTGTCTTAATACCCAGTATTAATATTAATTCTGAAACCACAGAAAATAAAGAAGAAATGGGTGCTTTGCCAAAACCTGAAACCATACTGCCACCAGAGCCTGAACATGAAAAGGGAAATGACACCGACTCAGGGACTGGGTCCACTGTGGAGAATAGCAGTGGTGACCTGAACTTGTCCATCTCTAGCTTCCTAAGCAAAGCTAAGGACAGCGGCTCAGTGTCTCTGCAGCGGATTTTGGAGTATCAGCTAAAAATACCAGGACAATTCAAAGGAGGGATTCATTTATTGGCACACCATATTGGATGGCTCCTGAAGTAG
Peptide sequence:
MAPEVVMCETSKDRPYDYKADVWSLGITLIEMAEIEPPHHELNPMRVLLKIAKSEPPTLAQPSKWSSNFKDFLRKCLEKNVDARWTTSQLLQHPFVTVDSNKPVRELIAEAKAEVTEEVEDGKEEDEEEEAENALPIPANKRASSDLSIASSEEDKLSQNACILESVSERTEQSTSEDKFSNKILNEKPTTDGPEKAVDEHASDVNLETGAELNDQTVGIHENGREKKRPKLENLPDTQDQQTVDVNSVSEENENNRVTLETNTDCLKPEEDRNKENQETLESKLIQSEEINDTHIQTMDLVSQETGEKEADFQAVDNEVGLTKEETQEKLGKDGTAQKVITSDRSSEVGTDEALDDTQKAAELSKAAQSGEGDEALAPTQTLAEKPTEGPEAGGAEEEPPGGERVEDKQPEQQPAVCEAEGQLTSTSETTRATLEQPETDEVEQVSESNSIEELERLVVTGAEARALGSEGEAAATEVDLERKENAQKVPVKAESQAPAASQPSEPHPVLIPSININSETTENKEEMGALPKPETILPPEPEHEKGNDTDSGTGSTVENSSGDLNLSISSFLSKAKDSGSVSLQRILEYQLKIPGQFKGGIHLLAHHIGWLLK
IRESfinder result
IRESfinder score
0.483358848
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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