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mmu_circTut4_436
Basic information of circular RNA
PanCircBase ID:
mmu_circTut4_436
mm39_Chr. Position ID:
chr4|108348544|108356595|+
Gene name:
Tut4
Transcript:
ENSMUST00000043368.12
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
5,6,7,8
Exon/intron offsets:
0,3802,5619,7999
Genomic length:
8051
Exon/intron sizes in nt:
117,178,89,52
Flanking exon/introns:
chr4:108343814-108348544|chr4:108356595-108360162
Splice length:
436
Other database IDs:
circBase: mmu_circ_0011035, CIRCpedia: MMU_CIRCpedia_2365, circAtlas: mmu-Zcchc11_0002
circBase: hsa_circ_0003632, circAtlas: hsa-ZCCHC11_0001, CIRCpedia: HSA_CIRCpedia_32362
Human Ortholog IDs:
Mature spliced Sequence:
CGGTCACCAGAATATACCAATTGCCGCTATCTATGCAAACTTTGCTTAATTCACATTGAAAACATCCAAGGAGCACATAAACATATAAAAGAAAAACGACATAAGAAAAATATTTTGGAAAAACAAGAAGAGAGTGAACTTCGGTCTCTTCCATCTCCTTCCTCTGCTCACTTGGCTGCTTTAAGTGTTGCAGTTGTTGAGTTAGCAAAAGAACAAGGAATAACAGATGATGACCTCAGAATCCGCCAGGACATTGTGGAGGAAATGTCAAAGGTTATAATGACATTTTTACCAGAATGTTCACTGAGGTTGTATGGTTCATCTCTGACAAAGTTTGCTCTGAAAAGCAGTGATGTTAATATAGATATAAAATTTCCTCCCAAGATGAATCATCCAGATCTTCTGATACAAGTGCTTGGAATTCTGAAAAAAAGTG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GCTCTGAAAAGCAGTGATGT
56.35
AGTTTGCATAGATAGCGGCA
57.38
141
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GCTCTGAAAAGCAGTGATGTT
57.09
AGTTTGCATAGATAGCGGCA
57.38
141
PCR template sequence:
GCTCTGAAAAGCAGTGATGTTAATATAGATATAAAATTTCCTCCCAAGATGAATCATCCAGATCTTCTGATACAAGTGCTTGGAATTCTGAAAAAAAGTGCGGTCACCAGAATATACCAATTGCCGCTATCTATGCAAACTTTGCTTAATTCACATTGAAAACATCCAAGGAGCACATAAACATATAAAAGAAAAACGAC
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-298-5p(1), mmu-miR-143-3p(1), mmu-miR-1198-5p(1)
siRNAs for circular RNA silencing
Junction sequence
CTGAAAAAAAGTGCGGTCACCAGAAT
siRNA sets
TGACCGCACTTTTTTTCAG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCTUT4_436_ORF_1
0.9662
-0.268622268
0.052252582
231
ORF sequence:
ATGTCAAAGGTTATAATGACATTTTTACCAGAATGTTCACTGAGGTTGTATGGTTCATCTCTGACAAAGTTTGCTCTGAAAAGCAGTGATGTTAATATAGATATAAAATTTCCTCCCAAGATGAATCATCCAGATCTTCTGATACAAGTGCTTGGAATTCTGAAAAAAAGTGCGGTCACCAGAATATACCAATTGCCGCTATCTATGCAAACTTTGCTTAATTCACATTGA
Peptide sequence:
MSKVIMTFLPECSLRLYGSSLTKFALKSSDVNIDIKFPPKMNHPDLLIQVLGILKKSAVTRIYQLPLSMQTLLNSH
IRESfinder result
IRESfinder score
0.669729857
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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