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mmu_circSpats2_1280
Basic information of circular RNA
PanCircBase ID:
mmu_circSpats2_1280
mm39_Chr. Position ID:
chr15|99047514|99103588|+
Gene name:
Spats2
Transcript:
ENSMUST00000063517.6
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
9
Exon/intron indexes:
2,3,4,5,6,7,8,9,10
Exon/intron offsets:
0,17446,23768,24768,28673,30947,36325,49574,55964
Genomic length:
56074
Exon/intron sizes in nt:
2,97,80,10,95,02,59,18,00,00,00,000
Flanking exon/introns:
chr15:99024768-99047514|chr15:99103588-99106713
Splice length:
1280
Other database IDs:
CIRCpedia: MMU_CIRCpedia_36066, circAtlas: mmu-Spats2_0021
Human Ortholog IDs:
Mature spliced Sequence:
GATCTCCCTGGGGAAAGACATGACTGTCTGCGGAGATTCATCCTGACAAGAAGTTGATACCAGAGAAGGAAAAGAAATTGACAGCTAGAGAACAGAATCTTAAACAACCAGGATTTTGGATTTATCACTTCCAACTATAGACTTCTATTGCCACTTTTAAATTAGCAGGATTCCCAGAACTTGGACGAAGATAATTTCTTCTGGTTTTTGCTTGTTTTCTCTCTTTCTTTTCTTTTTTCTTTCTTTTTTAATTTGATCGTGAGGAAACTGCAATGTCTAGGAAACAAAGCCAGAAAGATTCATCAGGATTCATTTTTGATTTGCAGTCCAATACTGTCCTGGCCCAGGGAGGAACCTTTGAGAATATGAAGGAGAAGATAAACGCGGTACGTGCGATAGTTCCCAATAAGAGCAACAATGAGATCATCCTGGTCTTGCAGCACTTTGACAACTGTGTGGACAAAACAGTGCAAGCGTTCATGGAAGGTAGTGCCAGTGAAGTGCTCAAAGAATGGATAGTAACTGGCAAAAAAAAGAACAAAAAGAAGAAGAGCAAGCCAAAGCCTGCATCAGAAGCAAGTGGCAGTGCCCCAGACTCCAGTAAGTCGGCCCCCATTCAAGAGGAGCAGCCTGCATCTTCAGAGAAAGGCAGCATCAATGGTTACCACGTAAACGGTGCCATCAACGATGCCGAGTCTGTGGACTCGCTCAGTGAAGGGCTGGAGACGCTGTCAATAGATGCCAGAGAGCTGGAGGATCCCGAGTTTGCCGCAGCAGAGACGCTGGACAGAACTGGATCTGTGCTGGAGAATGGTGTCTCTGACTTTGAGCCCAAATCTTTGACTGCGCACTCTATCTCGAATGTCCAGCAATCCCGGAACGCTGCCAAATCTCTGTCCAGAACCACCCCAGGAGCACAGGTTTCAAATCTGGGAATGGAGAACGTTCCACTCTCTTCCACCAATAAAAAGCTAGGTTCTAATATTGAGAAATCGGTGAAAGACCTCCAGCGCTGCACTGTTTCTCTTGCACGGTACCGAGTTGTCGTTAAAGAAGAGATGGATGCGTCCATTAAGAAAATGAAACAAGCGTTTGCCGAATTGCAAAGCTGTTTAATGGATCGAGAAGTGGCACTGCTTGCTGAGATGGATAAAGTGAAAGCTGAAGCAATGGAAATCTTGCTCAGCCGGCAGAAGAAAGCGGAGCTTCTAAAGAAGATGACAGATGTGGCCGTTCGCATGTCAGAGGAGCAGTTGGTTGAACTCAGGGCTGATATCAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CTCAGCCGGCAGAAGAAAGC
61.64
CAGGATGAATCTCCGCAGACA
59.86
144
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GCTCAGCCGGCAGAAGAAAG
61.64
CAGGATGAATCTCCGCAGACA
59.86
145
PCR template sequence:
GCTCAGCCGGCAGAAGAAAGCGGAGCTTCTAAAGAAGATGACAGATGTGGCCGTTCGCATGTCAGAGGAGCAGTTGGTTGAACTCAGGGCTGATATCAAGGATCTCCCTGGGGAAAGACATGACTGTCTGCGGAGATTCATCCTGACAAGAAGTTGATACCAGAGAAGGAAAAGAAATTGACAGCTAGAGAACAGAATCT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
15
Interacting miRNAs (#binding sites)
mmu-miR-20b-5p(1), mmu-miR-106a-5p(1), mmu-miR-93-5p(1), mmu-miR-20a-5p(1), mmu-miR-17-5p(1), mmu-miR-106b-5p(1), mmu-miR-148b-3p(1), mmu-miR-148a-3p(1), mmu-miR-125b-5p(1), mmu-miR-136-5p(1), mmu-miR-125a-5p(1), mmu-miR-680(1), mmu-miR-384-3p(1), mmu-miR-207(1), mmu-miR-539-5p(1)
siRNAs for circular RNA silencing
Junction sequence
GGCTGATATCAAGGATCTCCCTGGGG
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSPATS2_1280_ORF_1
1.0899
0.301815617
0.996471232
1065
ORF sequence:
ATGTCTAGGAAACAAAGCCAGAAAGATTCATCAGGATTCATTTTTGATTTGCAGTCCAATACTGTCCTGGCCCAGGGAGGAACCTTTGAGAATATGAAGGAGAAGATAAACGCGGTACGTGCGATAGTTCCCAATAAGAGCAACAATGAGATCATCCTGGTCTTGCAGCACTTTGACAACTGTGTGGACAAAACAGTGCAAGCGTTCATGGAAGGTAGTGCCAGTGAAGTGCTCAAAGAATGGATAGTAACTGGCAAAAAAAAGAACAAAAAGAAGAAGAGCAAGCCAAAGCCTGCATCAGAAGCAAGTGGCAGTGCCCCAGACTCCAGTAAGTCGGCCCCCATTCAAGAGGAGCAGCCTGCATCTTCAGAGAAAGGCAGCATCAATGGTTACCACGTAAACGGTGCCATCAACGATGCCGAGTCTGTGGACTCGCTCAGTGAAGGGCTGGAGACGCTGTCAATAGATGCCAGAGAGCTGGAGGATCCCGAGTTTGCCGCAGCAGAGACGCTGGACAGAACTGGATCTGTGCTGGAGAATGGTGTCTCTGACTTTGAGCCCAAATCTTTGACTGCGCACTCTATCTCGAATGTCCAGCAATCCCGGAACGCTGCCAAATCTCTGTCCAGAACCACCCCAGGAGCACAGGTTTCAAATCTGGGAATGGAGAACGTTCCACTCTCTTCCACCAATAAAAAGCTAGGTTCTAATATTGAGAAATCGGTGAAAGACCTCCAGCGCTGCACTGTTTCTCTTGCACGGTACCGAGTTGTCGTTAAAGAAGAGATGGATGCGTCCATTAAGAAAATGAAACAAGCGTTTGCCGAATTGCAAAGCTGTTTAATGGATCGAGAAGTGGCACTGCTTGCTGAGATGGATAAAGTGAAAGCTGAAGCAATGGAAATCTTGCTCAGCCGGCAGAAGAAAGCGGAGCTTCTAAAGAAGATGACAGATGTGGCCGTTCGCATGTCAGAGGAGCAGTTGGTTGAACTCAGGGCTGATATCAAGGATCTCCCTGGGGAAAGACATGACTGTCTGCGGAGATTCATCCTGACAAGAAGTTGA
Peptide sequence:
MSRKQSQKDSSGFIFDLQSNTVLAQGGTFENMKEKINAVRAIVPNKSNNEIILVLQHFDNCVDKTVQAFMEGSASEVLKEWIVTGKKKNKKKKSKPKPASEASGSAPDSSKSAPIQEEQPASSEKGSINGYHVNGAINDAESVDSLSEGLETLSIDARELEDPEFAAAETLDRTGSVLENGVSDFEPKSLTAHSISNVQQSRNAAKSLSRTTPGAQVSNLGMENVPLSSTNKKLGSNIEKSVKDLQRCTVSLARYRVVVKEEMDASIKKMKQAFAELQSCLMDREVALLAEMDKVKAEAMEILLSRQKKAELLKKMTDVAVRMSEEQLVELRADIKDLPGERHDCLRRFILTRS
IRESfinder result
IRESfinder score
0.61922059
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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