top of page
mmu_circTom1l2_314
Basic information of circular RNA
PanCircBase ID:
mmu_circTom1l2_314
mm39_Chr. Position ID:
chr11|60161143|60171109|-
Gene name:
Tom1l2
Transcript:
ENSMUST00000095254.12
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
4,3,2
Exon/intron offsets:
0,4606,9881
Genomic length:
9966
Exon/intron sizes in nt:
150,79,85
Flanking exon/introns:
chr11:60153609-60161143|chr11:60171109-60243582
Splice length:
314
Other database IDs:
circBase: mmu_circ_0003169, CIRCpedia: MMU_CIRCpedia_24848, circAtlas: mmu-Tom1l2_0004
circBase: hsa_circ_0042266, circAtlas: hsa-TOM1L2_0008, CIRCpedia: HSA_CIRCpedia_19514
Human Ortholog IDs:
Mature spliced Sequence:
AGAAGGCAACAGATGGCTCCCTGCAGAGCGAGGACTGGACACTGAATATGGAGATCTGTGACATCATCAACGAGACAGAGGAAGGGCCAAAGGATGCCATCCGGGCTCTAAAGAAGCGGCTTAGTGGGAACCGAAACTACAGAGAAGTGATGTTGGCCCTGACGGTGCTGGAGACTTGTGTGAAGAACTGTGGCCACCGCTTTCATCTCCTCGTGGCCAACCGAGACTTCATCGACAGCGTTCTGGTCAAAATTATCTCTCCCAAGAATAACCCTCCCACTATCGTCCAGGACAAAGTGCTGGCTCTAATTCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GCCAACCGAGACTTCATCGA
60.11
ATTCAGTGTCCAGTCCTCGC
59.75
146
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
ACCGAGACTTCATCGACAGC
59.83
ATTCAGTGTCCAGTCCTCGC
59.75
142
PCR template sequence:
GGCCAACCGAGACTTCATCGACAGCGTTCTGGTCAAAATTATCTCTCCCAAGAATAACCCTCCCACTATCGTCCAGGACAAAGTGCTGGCTCTAATTCAGAGAAGGCAACAGATGGCTCCCTGCAGAGCGAGGACTGGACACTGAATATGGAGATCTGTGACATCATCAACGAGACAGAGGAAGGGCCAAAGGATGCCAT
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-328-3p(1), mmu-miR-143-3p(1)
siRNAs for circular RNA silencing
Junction sequence
GGCTCTAATTCAGAGAAGGCAACAGA
siRNA sets
TTGCCTTCTCTGAATTAGA, GTTGCCTTCTCTGAATTAG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCTOM1L2_314_ORF_1
1.1787
0.407511903
0.700944492
312
ORF sequence:
ATGGAGATCTGTGACATCATCAACGAGACAGAGGAAGGGCCAAAGGATGCCATCCGGGCTCTAAAGAAGCGGCTTAGTGGGAACCGAAACTACAGAGAAGTGATGTTGGCCCTGACGGTGCTGGAGACTTGTGTGAAGAACTGTGGCCACCGCTTTCATCTCCTCGTGGCCAACCGAGACTTCATCGACAGCGTTCTGGTCAAAATTATCTCTCCCAAGAATAACCCTCCCACTATCGTCCAGGACAAAGTGCTGGCTCTAATTCAGAGAAGGCAACAGATGGCTCCCTGCAGAGCGAGGACTGGACACTGA
Peptide sequence:
MEICDIINETEEGPKDAIRALKKRLSGNRNYREVMLALTVLETCVKNCGHRFHLLVANRDFIDSVLVKIISPKNNPPTIVQDKVLALIQRRQQMAPCRARTGH
IRESfinder result
IRESfinder score
0.355447123
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
bottom of page