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mmu_circTm9sf3_661
Basic information of circular RNA
PanCircBase ID:
mmu_circTm9sf3_661
mm39_Chr. Position ID:
chr19|41227116|41236467|-
Gene name:
Tm9sf3
Transcript:
ENSMUST00000025989.10
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
7,6,5,4,3
Exon/intron offsets:
0,1899,6766,7965,9228
Genomic length:
9351
Exon/intron sizes in nt:
1,67,13,27,81,61,123
Flanking exon/introns:
chr19:41223214-41227116|chr19:41236467-41244583
Splice length:
661
Other database IDs:
circAtlas: mmu-Tm9sf3_0018
CIRCpedia: HSA_CIRCpedia_368558
Human Ortholog IDs:
Mature spliced Sequence:
ATGATGTGATGCCAGGCACTTACTGTGAAATTGACTTAGATAAAGAGAAGAGAGATGCGTTTGTGTATGCTATCAAGAATCACTATTGGTATCAGATGTACATAGATGACTTACCAATATGGGGTATTGTTGGTGAAGCAGATGAAAATGGGGAAGATTACTATCTTTGGACCTACAAAAAACTTGAAATAGGCTTTAATGGAAATCGAATTGTTGATGTTAATCTAACTAGTGAAGGAAAGGTCAAGCTGGTTCCAAATACTAAAATACAGATGTCATATTCGGTAAAATGGAAAAAATCGGATGTAAAATTTGAAGATCGATTCGATAAATATCTTGATCCATCCTTTTTTCAGCATAGGATTCACTGGTTTTCAATTTTTAATTCCTTCATGATGGTGATCTTCTTAGTGGGATTAGTTTCAATGATTTTAATGAGAACTTTAAGGAAAGATTATGCCCGATACAGTAAAGAAGAAGAAATGGATGACATGGACAGAGACCTAGGAGACGAGTATGGCTGGAAGCAGGTGCATGGAGATGTGTTCAGACCGTCAAGTCACCCTCTGATCTTCTCCTCCCTCATTGGCTCTGGATGTCAGATATTTGCTGTGTCTCTCATTGTTATTATTGTTGCCATGATAGAGGACTTATATACAGA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TCTCCTCCCTCATTGGCTCT
59.66
GCATACACAAACGCATCTCTCT
59.07
158
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TCTCCTCCCTCATTGGCTCT
59.66
AGCATACACAAACGCATCTCTC
59.07
159
PCR template sequence:
ACCCTCTGATCTTCTCCTCCCTCATTGGCTCTGGATGTCAGATATTTGCTGTGTCTCTCATTGTTATTATTGTTGCCATGATAGAGGACTTATATACAGAATGATGTGATGCCAGGCACTTACTGTGAAATTGACTTAGATAAAGAGAAGAGAGATGCGTTTGTGTATGCTATCAAGAATCACTATTGGTATCAGATGTA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
3
Interacting miRNAs (#binding sites)
mmu-miR-467b-5p(1), mmu-miR-383-5p(1), mmu-miR-335-3p(1)
siRNAs for circular RNA silencing
Junction sequence
ACTTATATACAGAATGATGTGATGCC
siRNA sets
CATCATTCTGTATATAAGT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCTM9SF3_661_ORF_1
0.8008
0.053300026
0.763908139
657
ORF sequence:
ATGCCAGGCACTTACTGTGAAATTGACTTAGATAAAGAGAAGAGAGATGCGTTTGTGTATGCTATCAAGAATCACTATTGGTATCAGATGTACATAGATGACTTACCAATATGGGGTATTGTTGGTGAAGCAGATGAAAATGGGGAAGATTACTATCTTTGGACCTACAAAAAACTTGAAATAGGCTTTAATGGAAATCGAATTGTTGATGTTAATCTAACTAGTGAAGGAAAGGTCAAGCTGGTTCCAAATACTAAAATACAGATGTCATATTCGGTAAAATGGAAAAAATCGGATGTAAAATTTGAAGATCGATTCGATAAATATCTTGATCCATCCTTTTTTCAGCATAGGATTCACTGGTTTTCAATTTTTAATTCCTTCATGATGGTGATCTTCTTAGTGGGATTAGTTTCAATGATTTTAATGAGAACTTTAAGGAAAGATTATGCCCGATACAGTAAAGAAGAAGAAATGGATGACATGGACAGAGACCTAGGAGACGAGTATGGCTGGAAGCAGGTGCATGGAGATGTGTTCAGACCGTCAAGTCACCCTCTGATCTTCTCCTCCCTCATTGGCTCTGGATGTCAGATATTTGCTGTGTCTCTCATTGTTATTATTGTTGCCATGATAGAGGACTTATATACAGAATGA
Peptide sequence:
MPGTYCEIDLDKEKRDAFVYAIKNHYWYQMYIDDLPIWGIVGEADENGEDYYLWTYKKLEIGFNGNRIVDVNLTSEGKVKLVPNTKIQMSYSVKWKKSDVKFEDRFDKYLDPSFFQHRIHWFSIFNSFMMVIFLVGLVSMILMRTLRKDYARYSKEEEMDDMDRDLGDEYGWKQVHGDVFRPSSHPLIFSSLIGSGCQIFAVSLIVIIVAMIEDLYTE
IRESfinder result
IRESfinder score
0.589001576
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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