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mmu_circTmtc2_383
Basic information of circular RNA
PanCircBase ID:
mmu_circTmtc2_383
mm39_Chr. Position ID:
chr10|105079449|105139576|-
Gene name:
Tmtc2
Transcript:
ENSMUST00000061506.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
11,10,9,8
Exon/intron offsets:
0,11206,27910,60005
Genomic length:
60127
Exon/intron sizes in nt:
6,41,15,82,122
Flanking exon/introns:
chr10:105026135-105079449|chr10:105139576-105157256
Splice length:
383
Other database IDs:
circBase: mmu_circ_0001911, CIRCpedia: MMU_CIRCpedia_36618, circAtlas: mmu-Tmtc2_0015
circBase: hsa_circ_0099374, circAtlas: hsa-TMTC2_0014, CIRCpedia: HSA_CIRCpedia_9699
Human Ortholog IDs:
Mature spliced Sequence:
GTGAAGCCTACATGAGACTGAGTAAGCTTCCTGAAGCTGAGCATTGGTACATGGAATCACTGAGATCCAAGACCGATCACATCCCTGCTCATCTCACCTACGGGAAGCTGCTCGCCTTAACAGGTCGTAAGAGTGAGGCTGAAAAGTTCTTCTTGAAGGCTATTGAGCTGGATCCTACCAAAGGAAACTGTTACATGCACTATGGTCAGTTTCTCCTAGAAGAGTCTCGCCTCACAGAAGCAGCAGAGATGGCAAAGAAAGCAGCTGAGCTGGACAACACAGAGTTCGATGTCGTCTTCAATGCTGCCCATATGCTCAGACAAGCAAGCCTCAATGAAGCCGCTGAGAAGTATTACGATCTGGCAGCAAGACTGAGACCTAAT
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TCGTCTTCAATGCTGCCCAT
60.04
GCAGGGATGTGATCGGTCTT
59.82
180
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CCTCAATGAAGCCGCTGAGA
60.11
GCAGGGATGTGATCGGTCTT
59.82
143
PCR template sequence:
GTTCGATGTCGTCTTCAATGCTGCCCATATGCTCAGACAAGCAAGCCTCAATGAAGCCGCTGAGAAGTATTACGATCTGGCAGCAAGACTGAGACCTAATGTGAAGCCTACATGAGACTGAGTAAGCTTCCTGAAGCTGAGCATTGGTACATGGAATCACTGAGATCCAAGACCGATCACATCCCTGCTCATCTCACCTA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
8
Interacting miRNAs (#binding sites)
mmu-miR-9-5p(1), mmu-miR-103-3p(1), mmu-miR-431-5p(1), mmu-miR-411-3p(1), mmu-miR-107-3p(1), mmu-miR-539-5p(1), mmu-miR-452-3p(1), mmu-miR-344-3p(1)
siRNAs for circular RNA silencing
Junction sequence
ACTGAGACCTAATGTGAAGCCTACAT
siRNA sets
ATGTAGGCTTCACATTAGG, TGTAGGCTTCACATTAGGT, CTTCACATTAGGTCTCAGT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCTMTC2_383_ORF_1
1.0786
0.289943713
0.673258931
387
ORF sequence:
ATGAGACTGAGTAAGCTTCCTGAAGCTGAGCATTGGTACATGGAATCACTGAGATCCAAGACCGATCACATCCCTGCTCATCTCACCTACGGGAAGCTGCTCGCCTTAACAGGTCGTAAGAGTGAGGCTGAAAAGTTCTTCTTGAAGGCTATTGAGCTGGATCCTACCAAAGGAAACTGTTACATGCACTATGGTCAGTTTCTCCTAGAAGAGTCTCGCCTCACAGAAGCAGCAGAGATGGCAAAGAAAGCAGCTGAGCTGGACAACACAGAGTTCGATGTCGTCTTCAATGCTGCCCATATGCTCAGACAAGCAAGCCTCAATGAAGCCGCTGAGAAGTATTACGATCTGGCAGCAAGACTGAGACCTAATGTGAAGCCTACATGA
Peptide sequence:
MRLSKLPEAEHWYMESLRSKTDHIPAHLTYGKLLALTGRKSEAEKFFLKAIELDPTKGNCYMHYGQFLLEESRLTEAAEMAKKAAELDNTEFDVVFNAAHMLRQASLNEAAEKYYDLAARLRPNVKPT
IRESfinder result
IRESfinder score
0.418297896
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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