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mmu_ciRtca_1892
Basic information of circular RNA
PanCircBase ID:
mmu_ciRtca_1892
mm39_Chr. Position ID:
chr3|116296101|116297993|-
Gene name:
Rtca
Transcript:
ENSMUST00000000348.15
CircRNA type:
Circular intronic (ci)RNA
Exon/Intron count:
1
Exon/intron indexes:
4
Exon/intron offsets:
0
Genomic length:
1892
Exon/intron sizes in nt:
1892
Flanking exon/introns:
chr3:116294819-116297993
Splice length:
1892
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GTAAGGGCGCCATGGTCTCTGTTTAAATGTCGGCAGCATCCTCACAGACATCCTGTTCACACATTTCCTAGTTCTTTTGTAGGAGAGGGCACAGGTTAGGTTTACTTTAGGGTTTGCATTATAAATTAAGATAGTGTTCAGACTGATTCTTTTTAAGGACCTAAAATATAATTATGTAAATTATCAGTTATCATATAAATTGCCTGTTTTTATTTTAGTGTTGGCATGTCTATAAGGAAGAAAATGGGTCCAGGTTGAGTATCTCTAGTCTGAAATACTGAGTGAGCCAGAATTTGAGCCAGTGAGATGGCTCATTGGGTGAGAGCACTTGCTACGCTAGCCAGATGACCTAAGTTTAGCTCCCAGAACTGAAGAAAGGCCAGAGCTAAGTCCTGAAAAGTGACCTCTTGACTATCACACTCCCCTCCCCACACACACACACTCAGATAACACAATTCTTAAAGATAACTATAAAATTCAAAACTATTTGAGTACCAACATGATGATCCAAGTAGGTGGACATGTCCCACCTGACTCTATGTGGTGTGCTGTGGTCACAACCTTGGGGCACAGGTCACTGTAAGGCGGTGTGCAAGGTCTGTGTATAACGAGTGAAACACAAGTCAATTTCATGTTTGCATCCTGTGTGTTTGTGCAAATACTACGGACTCTGAACAAGTCAGATGCACCTCTGGCTCTGAGCATCTTCAGGCAAGGATATTCAATCTGTATTAGTGGTTTTTTTCTTCTCCAGGTTTATTGTGGCATAGTTCTTCACAACTAAATTTACTCCTTTAAATGTACTTTTAAGAATTTTGTACAAATATATATCTGTGAACCATTTCCAGAACCAAAGTGAGGGTAAAAAAAAAGTTTTATTAAAAAAGAAAGAAGGAAAATTACAAACCTTTGTAGCTAGTTTTGTCCCCAGCTACTGCCAACCACTGTTCTGAGTTCTGCCCTTTCACAATGTCATACAAAATACAAATGCTGTACGTGGCTTTAGAATTTGGTGGGTTTTCCTCTTTTGAGACAGGGTCTTATGTATCCCGGGCTGGCCTTACATTTGATATGTACAGAGGATGACCTTGGACTTGTGACCCCTGCTTCTACCTCCAGAGCCCTAGAGTTAAAAGTGTGCCCAGTGCCATGGCCAGTGGATACAGTGTGAGCACAGGCAAGGCAAGGCAAGGCAAGTACACTGCCCACCAATCTCCAGGGCCAGCTCAGGGACAGGTTTTTTTTTCCTCCCCAGTTATATTTTGAGACTCCGTGTCTCTCCAGTAAAGGCCAAGTGGCTTAACTCTGAGCTGAGCATGAGTCGAAGGCCCTTGCATTGCCTCCATCATTTGTCAGTTTTGAACAAATTCACTAGAGACTACTGAAATGTTTTTAGCCCTGTCCTTTTCTTACCCCATGAGAGCTCCTTTTCTTCTGCATCTTACCCAGCACTAGATACAGAGCCTCTGTGCTTTAACACCCCCACCCTAAATTGAGTTTTGAAATGTTTGGGGAGAAAATACCAAGGCTTTACACGTTAGGCAACTGCTCTGCTGTGGGCTACATCACCACTCCTGTGTTTGATGAAAAAGCAAAACCATAGACATTTAGTCTATCCCTTTGACACATATGGTGATAGTCTGGGGAACTGAGTAAAAGTCTCCATAGGTCTCATATATTTTCAAGGCTTTAGGTTTAAACACCATCTTTTTCTGAAACCCTGCCATTCTGATGGGTGCTATCATCTTTGGTCAGTGTGTGGAGACATGTAATAAAAGCTACTTTCAACCTGGTGAACATGGCACACTTTTTCAATCCCAGCACTCGGGAGGCAGAGACAGGTGGATCTCTGAGTTTGAGACCACCCTGATCTACAGAGCAAGTTCCAGGAC
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AGGCAGAGACAGGTGGATCT
59.96
ACCTGTGCCCTCTCCTACAA
60.18
159
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AGGCAGAGACAGGTGGATCT
59.96
AACCTGTGCCCTCTCCTACA
60.18
160
PCR template sequence:
GTGAACATGGCACACTTTTTCAATCCCAGCACTCGGGAGGCAGAGACAGGTGGATCTCTGAGTTTGAGACCACCCTGATCTACAGAGCAAGTTCCAGGACGTAAGGGCGCCATGGTCTCTGTTTAAATGTCGGCAGCATCCTCACAGACATCCTGTTCACACATTTCCTAGTTCTTTTGTAGGAGAGGGCACAGGTTAGG
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-9-5p(1), mmu-let-7e-5p(1), mmu-let-7b-5p(1), mmu-miR-34c-5p(1), mmu-miR-34a-5p(1), mmu-miR-122-5p(1), mmu-miR-185-5p(1), mmu-miR-339-5p(1), mmu-miR-149-5p(1), mmu-miR-351-5p(1), mmu-miR-96-5p(1), mmu-miR-199b-3p(1), mmu-miR-199a-3p(1), mmu-miR-183-5p(1), mmu-miR-758-3p(1), mmu-miR-34b-5p(1), mmu-miR-342-3p(1), mmu-miR-466a-5p(1), mmu-miR-1187(1), mmu-miR-466p-5p(1), mmu-miR-300-3p(1), mmu-miR-669d-5p(1), mmu-miR-670-5p(1), mmu-miR-490-3p(1), mmu-miR-574-5p(1), mmu-miR-338-3p(1)
siRNAs for circular RNA silencing
Junction sequence
CAAGTTCCAGGACGTAAGGGCGCCAT
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRTCA_1892_ORF_1
0.6455
-0.043260608
0.042397729
165
ORF sequence:
ATGGGTGCTATCATCTTTGGTCAGTGTGTGGAGACATGTAATAAAAGCTACTTTCAACCTGGTGAACATGGCACACTTTTTCAATCCCAGCACTCGGGAGGCAGAGACAGGTGGATCTCTGAGTTTGAGACCACCCTGATCTACAGAGCAAGTTCCAGGACGTAA
Peptide sequence:
MGAIIFGQCVETCNKSYFQPGEHGTLFQSQHSGGRDRWISEFETTLIYRASSRT
IRESfinder result
IRESfinder score
0.807994846
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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