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mmu_ciCsde1_698
Basic information of circular RNA
PanCircBase ID:
mmu_ciCsde1_698
mm39_Chr. Position ID:
chr3|102951247|102951945|+
Gene name:
Csde1
Transcript:
ENSMUST00000198174.2
CircRNA type:
Circular intronic (ci)RNA
Exon/Intron count:
1
Exon/intron indexes:
3
Exon/intron offsets:
0
Genomic length:
698
Exon/intron sizes in nt:
698
Flanking exon/introns:
chr3:102951247-102952074
Splice length:
698
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GTAAATTGTCTTTATCAGCAATGTCTTCTTCTGACCAATCAGTACAATATTATGATGATACACTAAAGGTGGAGTCTGTTTGATTGATGTAGTTGTGTGTAGTGGGGTGTATCTTTTAATAGGTATTTTAATTAAAAAAAAAAAAAAAACAAAAAACAAAATAGATGCTGATGGTGTGGTTCAGTGGCAGAGGGCTGACCTAGCATGCAAAAGGCCCCCAGTACTGCAGAAAGAAAAGAGACACTAATGAACGGTAGGTTGATGGGTATGTTTTTGCTTATTTGATTTTCACTGAGTGATTAAGATTAAAAGAAACTGTTACCTGAACTGGGGAAGGTCCTACTGAATTGGACTGCATGTGCTACTTCTCTGTTCCCCCGTCTTACCATTTGTTAACTGGTGGGAAGTAAGGTGAAAGGCATCATTGCTGGATAAATGTGAGATCCAAAGGGCTGAAATGTTTTTCCTTAGCAGTTCTTGATATCACAGTGCAGTGTTAACAACAGTGCTTGATTTATGGTTGTCATGGGACCTTAGATGATGAAGCTTTTATATTGGGCTTATATTGTCAGCACTTTTTTCCCCTTCAGGCTACTACTATATTATAAATAAGCTATTTACTGTGTGTTCTTCTTGTTTGACTTAGAGCTAAAAGGATGAGAAATCTCCAGCTAAAATCGTTTTTCCTTCTCATCAGA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
ACTGTGTGTTCTTCTTGTTTGACT
59
ACATCAATCAAACAGACTCCACC
58.93
169
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GCTAAAAGGATGAGAAATCTCCAGC
59.99
ACATCAATCAAACAGACTCCACC
58.93
141
PCR template sequence:
TATATTATAAATAAGCTATTTACTGTGTGTTCTTCTTGTTTGACTTAGAGCTAAAAGGATGAGAAATCTCCAGCTAAAATCGTTTTTCCTTCTCATCAGAGTAAATTGTCTTTATCAGCAATGTCTTCTTCTGACCAATCAGTACAATATTATGATGATACACTAAAGGTGGAGTCTGTTTGATTGATGTAGTTGTGTGT
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-23b-3p(1), mmu-miR-20b-5p(1), mmu-miR-200a-3p(1), mmu-miR-141-3p(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-335-5p(1), mmu-miR-217-5p(1), mmu-miR-23a-3p(1), mmu-miR-483-5p(1), mmu-miR-129-5p(1), mmu-miR-540-3p(1)
siRNAs for circular RNA silencing
Junction sequence
CCTTCTCATCAGAGTAAATTGTCTTT
siRNA sets
AAAGACAATTTACTCTGAT, AAGACAATTTACTCTGATG, AGACAATTTACTCTGATGA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CICSDE1_698_ORF_1
1.0893
-0.315028235
0.022784013
108
ORF sequence:
ATGAGAAATCTCCAGCTAAAATCGTTTTTCCTTCTCATCAGAGTAAATTGTCTTTATCAGCAATGTCTTCTTCTGACCAATCAGTACAATATTATGATGATACACTAA
Peptide sequence:
MRNLQLKSFFLLIRVNCLYQQCLLLTNQYNIMMIH
IRESfinder result
IRESfinder score
0.853739104
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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