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mmu_circGgta1_510
Basic information of circular RNA
PanCircBase ID:
mmu_circGgta1_510
mm39_Chr. Position ID:
chr2|35297956|35313424|-
Gene name:
Ggta1
Transcript:
ENSMUST00000079424.11
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
5,4,3,2
Exon/intron offsets:
0,5381,14235,15287
Genomic length:
15468
Exon/intron sizes in nt:
13,81,02,89,181
Flanking exon/introns:
chr2:35292814-35297956|chr2:35313424-35322525
Splice length:
510
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GCTGACTTTGAACTCAAGAGATCTGCTTACCCCAGTCTCCTGGAATTAAAGGCCTGTACTACATTTGCCTGGACCTAAGATTTTCATGATCACTATGCTTCAAGATCTCCATGTCAACAAGATCTCCATGTCAAGATCCAAGTCAGAAACAAGTCTTCCATCCTCAAGATCTGGATCACAGGAGAAAATAATGAATGTCAAGGGAAAAGTAATCCTGTTGATGCTGATTGTCTCAACCGTGGTTGTCGTGTTTTGGGAATATGTCAACAGGACCCACAGTTATCAAGAAGACAACGTAGAAGGACGGAGAGAAAAGGGTAGAAATGGAGATCGCATTGAAGAGCCTCAGCTATGGGACTGGTTCAATCCAAAGAACCGCCCGGATGTTTTGACAGTGACCCCGTGGAAGGCGCCGATTGTGTGGGAAGGCACTTATGACACAGCTCTGCTGGAAAAGTACTACGCCACACAGAAACTCACTGTGGGGCTGACAGTGTTTGCTGTGGGAAA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CGCCGATTGTGTGGGAAGG
61.4
AGGAGACTGGGGTAAGCAGA
59.59
141
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GCCGATTGTGTGGGAAGGC
61.7
AGGAGACTGGGGTAAGCAGA
59.59
140
PCR template sequence:
CGCCGATTGTGTGGGAAGGCACTTATGACACAGCTCTGCTGGAAAAGTACTACGCCACACAGAAACTCACTGTGGGGCTGACAGTGTTTGCTGTGGGAAAGCTGACTTTGAACTCAAGAGATCTGCTTACCCCAGTCTCCTGGAATTAAAGGCCTGTACTACATTTGCCTGGACCTAAGATTTTCATGATCACTATGCTT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
9
Interacting miRNAs (#binding sites)
mmu-miR-200a-3p(1), mmu-miR-141-3p(1), mmu-miR-7b-5p(1), mmu-miR-7a-5p(1), mmu-miR-181b-5p(1), mmu-miR-434-3p(1), mmu-miR-467b-5p(1), mmu-miR-188-3p(1), mmu-miR-181d-5p(1)
siRNAs for circular RNA silencing
Junction sequence
TTGCTGTGGGAAAGCTGACTTTGAAC
siRNA sets
GTTCAAAGTCAGCTTTCCC, TTCAAAGTCAGCTTTCCCA, AAAGTCAGCTTTCCCACAG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCGGTA1_510_ORF_1
0.9406
0.154417845
0.630440283
474
ORF sequence:
ATGATCACTATGCTTCAAGATCTCCATGTCAACAAGATCTCCATGTCAAGATCCAAGTCAGAAACAAGTCTTCCATCCTCAAGATCTGGATCACAGGAGAAAATAATGAATGTCAAGGGAAAAGTAATCCTGTTGATGCTGATTGTCTCAACCGTGGTTGTCGTGTTTTGGGAATATGTCAACAGGACCCACAGTTATCAAGAAGACAACGTAGAAGGACGGAGAGAAAAGGGTAGAAATGGAGATCGCATTGAAGAGCCTCAGCTATGGGACTGGTTCAATCCAAAGAACCGCCCGGATGTTTTGACAGTGACCCCGTGGAAGGCGCCGATTGTGTGGGAAGGCACTTATGACACAGCTCTGCTGGAAAAGTACTACGCCACACAGAAACTCACTGTGGGGCTGACAGTGTTTGCTGTGGGAAAGCTGACTTTGAACTCAAGAGATCTGCTTACCCCAGTCTCCTGGAATTAA
Peptide sequence:
MITMLQDLHVNKISMSRSKSETSLPSSRSGSQEKIMNVKGKVILLMLIVSTVVVVFWEYVNRTHSYQEDNVEGRREKGRNGDRIEEPQLWDWFNPKNRPDVLTVTPWKAPIVWEGTYDTALLEKYYATQKLTVGLTVFAVGKLTLNSRDLLTPVSWN
IRESfinder result
IRESfinder score
0.430117682
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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