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mmu_circTimp2_335
Basic information of circular RNA
PanCircBase ID:
mmu_circTimp2_335
mm39_Chr. Position ID:
chr11|118201401|118211035|-
Gene name:
Timp2
Transcript:
ENSMUST00000017610.10
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
4,3,2
Exon/intron offsets:
0,6843,9533
Genomic length:
9634
Exon/intron sizes in nt:
12,51,09,101
Flanking exon/introns:
chr11:118194722-118201401|chr11:118211035-118245786
Splice length:
335
Other database IDs:
CIRCpedia: MMU_CIRCpedia_229893, circAtlas: mmu-Timp2_0002
circBase: hsa_circ_0045947, circAtlas: hsa-SCAF8_0001
Human Ortholog IDs:
Mature spliced Sequence:
TGATCAGAGCCAAAGCAGTGAGCGAGAAGGAGGTGGATTCCGGGAATGACATCTATGGCAACCCCATCAAGAGGATTCAGTATGAGATCAAGCAGATAAAGATGTTCAAAGGACCTGACAAAGACATCGAGTTTATCTACACGGCCCCCTCTTCAGCAGTGTGCGGGGTCTCGCTGGACGTTGGAGGAAAGAAGGAGTATCTAATTGCAGGAAAGGCAGAAGGAGATGGCAAGATGCACATTACCCTCTGTGACTTCATTGTGCCCTGGGACACGCTTAGCATCACCCAGAAGAAGAGCCTGAACCACAGGTACCAGATGGGCTGTGAGTGCAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GACTTCATTGTGCCCTGGGA
59.96
CCTCTTGATGGGGTTGCCAT
60.03
158
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CTGGGACACGCTTAGCATCA
60.11
CCTCTTGATGGGGTTGCCAT
60.03
144
PCR template sequence:
GCACATTACCCTCTGTGACTTCATTGTGCCCTGGGACACGCTTAGCATCACCCAGAAGAAGAGCCTGAACCACAGGTACCAGATGGGCTGTGAGTGCAAGTGATCAGAGCCAAAGCAGTGAGCGAGAAGGAGGTGGATTCCGGGAATGACATCTATGGCAACCCCATCAAGAGGATTCAGTATGAGATCAAGCAGATAAA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
2
Interacting miRNAs (#binding sites)
mmu-miR-224-5p(1), mmu-miR-673-5p(1)
siRNAs for circular RNA silencing
Junction sequence
CTGTGAGTGCAAGTGATCAGAGCCAA
siRNA sets
TCTGATCACTTGCACTCAC, TTGGCTCTGATCACTTGCA, TGATCACTTGCACTCACAG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCTIMP2_335_ORF_1
0.9987
0.366132466
0.451567621
237
ORF sequence:
ATGTTCAAAGGACCTGACAAAGACATCGAGTTTATCTACACGGCCCCCTCTTCAGCAGTGTGCGGGGTCTCGCTGGACGTTGGAGGAAAGAAGGAGTATCTAATTGCAGGAAAGGCAGAAGGAGATGGCAAGATGCACATTACCCTCTGTGACTTCATTGTGCCCTGGGACACGCTTAGCATCACCCAGAAGAAGAGCCTGAACCACAGGTACCAGATGGGCTGTGAGTGCAAGTGA
Peptide sequence:
MFKGPDKDIEFIYTAPSSAVCGVSLDVGGKKEYLIAGKAEGDGKMHITLCDFIVPWDTLSITQKKSLNHRYQMGCECK
IRESfinder result
IRESfinder score
0.345801007
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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