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mmu_circSocs6_1188
Basic information of circular RNA
PanCircBase ID:
mmu_circSocs6_1188
mm39_Chr. Position ID:
chr18|88776473|88780292|-
Gene name:
Socs6
Transcript:
ENSMUST00000136173.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
6,5,4
Exon/intron offsets:
0,2296,3602
Genomic length:
3819
Exon/intron sizes in nt:
16,18,10,217
Flanking exon/introns:
chr18:88706321-88776473|chr18:88780292-88810794
Splice length:
1188
Other database IDs:
circAtlas: mmu-Socs6_0001
Human Ortholog IDs:
Mature spliced Sequence:
ATGGAAAATGATTTTACACCTCAGTATGAGAACTTTTCATGATGACGCATTATGTATGACATGGGCCATTCAAGTTTAAAGAACCAGAGGACTATGAGGGTTACTGCAAAATGGTGCCTCCTGGATATGGCAGGGATACTGCCAAAGTGAACTCACAGCAGCTGTGGATGCCTGACTTGACCTGCAGAAGATCAAACCAGTCATCGATGAAGCACAGTGAGTGAGACCAATAAGGAATTTCTCATCATTGCTGGGATCCCTTGCAGATGTTAGAGGGATCCTGTCAGGTGTCTGCATGGTGTCCTTGTTATCAGAATGTCAAAGCTCTCTCATGCTTGGCCATCTTCCTTACGCTTGAGGAATGGTACATATGAACCTGTAAGTAAACTAAGACCTTTACTTACTGAGATACTAGGTTGCTGTAGCTTTGAAAGAGAGTTTGTGTGAATAAGATTATGAGGTCAAGAATAGCATACTGACTGTGAGTAATAGTGTATTAGTCGGGGTTCTCTAGAGTCACAGAACTTATGGAATGTCTTTACACATTAAAAAAATTTATTGTAATGATTTATAGTCTGTAGTCCAACTAAACCAACAATGGAGAGCTGTGAATGGGAAATGAATGGGAAAAATCTAGCAGTAGTTAAGTCCCACTAGGCTAGTTGTTTCACCTGCTCTTCTGTATAAGCTGGGATTCTGAAGAAGTAGGCACCAACAGATGTTCTGGCAAGTAAGTTTAAGCAGATGAAGAAGAATGAGTCCTCCTCCTTCCAATGTCCTTAAGTACGTTGTGAGCAGAAAGGTGTGGCCCAGGTTAAAGGTGTGTACCACCACACTTGGATCTGGAACTTGCTTTTTCCCAGGCTGGCCTTGAACTCAGAGATCTGCTTGCCTCAGTCTGCTTGGATTAAAGGCATATACTACCTTGCCTGAGCCTAAGATTTTCATGGCCATTGTGCCTCAGGACTCTCATGTCAAGATCCATGTCAGAAGCCCGTGTCTTTCAGCTTCAAGATCTAGATCACAGACAGTCTATTCATGAATGCCTAGCTCCCAAGACCAAATTACCTCTTCAAGGTGGGAACATGCCAGCATCCAGGCAGACATGGTACAAGAGGAGCTGAGAGTTCTACATCTTCATCTGAAGGCTGCTGGCAGAATACTGGCTCCCAGGCAGCTAGGAAAAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GCATCCAGGCAGACATGGTA
59.82
GGCCCATGTCATACATAATGCG
59.84
164
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GCATCCAGGCAGACATGGTA
59.82
AACTTGAATGGCCCATGTCA
57.69
173
PCR template sequence:
CCAGCATCCAGGCAGACATGGTACAAGAGGAGCTGAGAGTTCTACATCTTCATCTGAAGGCTGCTGGCAGAATACTGGCTCCCAGGCAGCTAGGAAAAAGATGGAAAATGATTTTACACCTCAGTATGAGAACTTTTCATGATGACGCATTATGTATGACATGGGCCATTCAAGTTTAAAGAACCAGAGGACTATGAGGG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
16
Interacting miRNAs (#binding sites)
mmu-miR-20b-5p(1), mmu-miR-27b-3p(1), mmu-miR-27a-3p(1), mmu-miR-196a-5p(1), mmu-miR-136-5p(1), mmu-miR-29b-1-5p(1), mmu-miR-127-5p(1), mmu-miR-218-5p(1), mmu-miR-27a-5p(1), mmu-miR-29b-2-5p(1), mmu-miR-377-3p(1), mmu-miR-673-5p(1), mmu-miR-539-5p(1), mmu-miR-532-5p(1), mmu-miR-490-3p(1), mmu-miR-3105-3p(1)
siRNAs for circular RNA silencing
Junction sequence
AGCTAGGAAAAAGATGGAAAATGATT
siRNA sets
TTTTCCATCTTTTTCCTAG, TTTCCATCTTTTTCCTAGC, ATTTTCCATCTTTTTCCTA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSOCS6_1188_ORF_1
0.8139
-0.14295683
0.060319173
225
ORF sequence:
ATGCCTAGCTCCCAAGACCAAATTACCTCTTCAAGGTGGGAACATGCCAGCATCCAGGCAGACATGGTACAAGAGGAGCTGAGAGTTCTACATCTTCATCTGAAGGCTGCTGGCAGAATACTGGCTCCCAGGCAGCTAGGAAAAAGATGGAAAATGATTTTACACCTCAGTATGAGAACTTTTCATGATGACGCATTATGTATGACATGGGCCATTCAAGTTTAA
Peptide sequence:
MPSSQDQITSSRWEHASIQADMVQEELRVLHLHLKAAGRILAPRQLGKRWKMILHLSMRTFHDDALCMTWAIQV
IRESfinder result
IRESfinder score
0.607800269
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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