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mmu_circTyw1_407
Basic information of circular RNA
PanCircBase ID:
mmu_circTyw1_407
mm39_Chr. Position ID:
chr5|130316083|130325642|+
Gene name:
Tyw1
Transcript:
ENSMUST00000040213.13
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
10,11,12
Exon/intron offsets:
0,1610,9381
Genomic length:
9559
Exon/intron sizes in nt:
11,91,10,178
Flanking exon/introns:
chr5:130310674-130316083|chr5:130325642-130328744
Splice length:
407
Other database IDs:
circAtlas: mmu-Tyw1_0029
circBase: hsa_circ_0134597, circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_58669
Human Ortholog IDs:
Mature spliced Sequence:
TCGATGCTGCGGGGGAGAGGAGGTTGCTACAAACACACATTCTACGGCATTGAGAGCCACCGCTGCATGGAAGCCACCCCAAGCTTGGCGTGTGCGAATAAATGTGTCTTCTGCTGGCGGCACCATACCAATCCTGTGGGCACTGAGTGGCGGTGGAAGATGGACCAGCCAGAATTGATCTTGAAGGAAGCCATTGAGAACCATCAGAACATGATTAAACAGTTCAAAGGCGTGCCAGGCCTCAAGGCGGAGCGCTTTGAAGAGGGGATGGAGGTCAAGCACTGTGCGCTGTCACTCGTGGGTGAGCCGATCATGTACCCAGAAATCAACAGGCTTTTGAAGCTGCTCCACCAGCACGGCATCTCCAGCTTCCTTGTCACCAATGCGCAGTTCCCTGAGGAGATCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GGCATCTCCAGCTTCCTTGT
60.03
TATTCGCACACGCCAAGCTT
60.95
150
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GCTTCCTTGTCACCAATGCG
60.11
TATTCGCACACGCCAAGCTT
60.95
140
PCR template sequence:
CGATCATGTACCCAGAAATCAACAGGCTTTTGAAGCTGCTCCACCAGCACGGCATCTCCAGCTTCCTTGTCACCAATGCGCAGTTCCCTGAGGAGATCAGTCGATGCTGCGGGGGAGAGGAGGTTGCTACAAACACACATTCTACGGCATTGAGAGCCACCGCTGCATGGAAGCCACCCCAAGCTTGGCGTGTGCGAATA
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-1187(1), mmu-miR-574-5p(1)
siRNAs for circular RNA silencing
Junction sequence
CTGAGGAGATCAGTCGATGCTGCGGG
siRNA sets
CAGCATCGACTGATCTCCT, GCAGCATCGACTGATCTCC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCTYW1_407_ORF_1
0.8621
0.227566844
0.813264659
582
ORF sequence:
ATGCTGCGGGGGAGAGGAGGTTGCTACAAACACACATTCTACGGCATTGAGAGCCACCGCTGCATGGAAGCCACCCCAAGCTTGGCGTGTGCGAATAAATGTGTCTTCTGCTGGCGGCACCATACCAATCCTGTGGGCACTGAGTGGCGGTGGAAGATGGACCAGCCAGAATTGATCTTGAAGGAAGCCATTGAGAACCATCAGAACATGATTAAACAGTTCAAAGGCGTGCCAGGCCTCAAGGCGGAGCGCTTTGAAGAGGGGATGGAGGTCAAGCACTGTGCGCTGTCACTCGTGGGTGAGCCGATCATGTACCCAGAAATCAACAGGCTTTTGAAGCTGCTCCACCAGCACGGCATCTCCAGCTTCCTTGTCACCAATGCGCAGTTCCCTGAGGAGATCAGTCGATGCTGCGGGGGAGAGGAGGTTGCTACAAACACACATTCTACGGCATTGAGAGCCACCGCTGCATGGAAGCCACCCCAAGCTTGGCGTGTGCGAATAAATGTGTCTTCTGCTGGCGGCACCATACCAATCCTGTGGGCACTGAGTGGCGGTGGAAGATGGACCAGCCAGAATTGA
Peptide sequence:
MLRGRGGCYKHTFYGIESHRCMEATPSLACANKCVFCWRHHTNPVGTEWRWKMDQPELILKEAIENHQNMIKQFKGVPGLKAERFEEGMEVKHCALSLVGEPIMYPEINRLLKLLHQHGISSFLVTNAQFPEEISRCCGGEEVATNTHSTALRATAAWKPPQAWRVRINVSSAGGTIPILWALSGGGRWTSQN
IRESfinder result
IRESfinder score
0.34894424
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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