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mmu_circTtc4_300
Basic information of circular RNA
PanCircBase ID:
mmu_circTtc4_300
mm39_Chr. Position ID:
chr4|106524692|106525451|-
Gene name:
Ttc4
Transcript:
ENSMUST00000026480.13
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
2
Exon/intron indexes:
8,7
Exon/intron offsets:
0,541
Genomic length:
759
Exon/intron sizes in nt:
82,218
Flanking exon/introns:
chr4:106522935-106524692|chr4:106525451-106527645
Splice length:
300
Other database IDs:
circBase: hsa_circ_0012665, circAtlas: hsa-MROH7-TTC4_0016, CIRCpedia: HSA_CIRCpedia_32490
Human Ortholog IDs:
Mature spliced Sequence:
GCTAGGAACATCAGGCTTGTCTCTGAATCAGCCGGTGAGGATGAAGATTCAGCCTCCAATGGTCCAGCTGAGATACTCCTGGATGGGCTCAGCTCTGAGAACCCCTATGGAGCCAGGCTAAGTATAGATGACCAGGGCAGGCTGAGCTGGCCTGTGCTGTTCCTGTACCCGGAGTACGCGCAATCAGACTTCATCTCTGCTTTTCATGAGGACACCAGGTTTATTGACCATCTAATGGCGATGTTTAGTGAAGCACCCTCCTGGGACTCAGAGCACAAGTACCACCCAGAGAATCTGGAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TCCTGGGACTCAGAGCACAA
60.47
TCAGAGCTGAGCCCATCCA
60.31
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TCCTGGGACTCAGAGCACAA
60.47
TCAGAGCTGAGCCCATCCAG
61.34
140
PCR template sequence:
TTTTCATGAGGACACCAGGTTTATTGACCATCTAATGGCGATGTTTAGTGAAGCACCCTCCTGGGACTCAGAGCACAAGTACCACCCAGAGAATCTGGAGGCTAGGAACATCAGGCTTGTCTCTGAATCAGCCGGTGAGGATGAAGATTCAGCCTCCAATGGTCCAGCTGAGATACTCCTGGATGGGCTCAGCTCTGAGA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
5
Interacting miRNAs (#binding sites)
mmu-miR-216a-5p(1), mmu-miR-143-3p(1), mmu-miR-149-5p(1), mmu-miR-1199-5p(1), mmu-miR-490-3p(1)
siRNAs for circular RNA silencing
Junction sequence
AGAGAATCTGGAGGCTAGGAACATCA
siRNA sets
TGATGTTCCTAGCCTCCAG, TTCCTAGCCTCCAGATTCT, GATGTTCCTAGCCTCCAGA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCTTC4_300_ORF_1
0.9259
0.294329955
0.576702059
366
ORF sequence:
ATGGCGATGTTTAGTGAAGCACCCTCCTGGGACTCAGAGCACAAGTACCACCCAGAGAATCTGGAGGCTAGGAACATCAGGCTTGTCTCTGAATCAGCCGGTGAGGATGAAGATTCAGCCTCCAATGGTCCAGCTGAGATACTCCTGGATGGGCTCAGCTCTGAGAACCCCTATGGAGCCAGGCTAAGTATAGATGACCAGGGCAGGCTGAGCTGGCCTGTGCTGTTCCTGTACCCGGAGTACGCGCAATCAGACTTCATCTCTGCTTTTCATGAGGACACCAGGTTTATTGACCATCTAATGGCGATGTTTAGTGAAGCACCCTCCTGGGACTCAGAGCACAAGTACCACCCAGAGAATCTGGAG
Peptide sequence:
MAMFSEAPSWDSEHKYHPENLEARNIRLVSESAGEDEDSASNGPAEILLDGLSSENPYGARLSIDDQGRLSWPVLFLYPEYAQSDFISAFHEDTRFIDHLMAMFSEAPSWDSEHKYHPENLE
IRESfinder result
IRESfinder score
0.424278745
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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