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mmu_circItch_370
Basic information of circular RNA
PanCircBase ID:
mmu_circItch_370
mm39_Chr. Position ID:
chr2|154980115|155005403|+
Gene name:
Itch
Transcript:
ENSMUST00000155360.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
2,3,4
Exon/intron offsets:
0,19578,25197
Genomic length:
25288
Exon/intron sizes in nt:
77,202,91
Flanking exon/introns:
chr2:154975505-154980115|chr2:155005403-155010603
Splice length:
370
Other database IDs:
circAtlas: mmu-Itch_0039
Human Ortholog IDs:
Mature spliced Sequence:
GTAACATGCATTTCACAGTGGCCTTCTGGAAACAACGCCTTAACCCTAAGAAGTGACTCAGCCATTGAGAACTTCAGGTCTGCTGTAACAGTACAAGCTGGGCATGGTGGTTCATTCCTGCAGTGCCAGACTTTGGAGGCTGAGGAAGGAAGACTGCTGCAAACTTGAGGCCAGCCTGGACTATAGAGTGAGACTTTATCTTGTAAAGCCAGGAACAAACATTCCCTCCGAAATTACCCTAAAGTTGTGGGGATGGAAACGTAATGTTTTGCAGTTCAGGTTTGCTGTCTTATTGATGGTATGTCTGACAGTGGACCACAGCTTGATTCCATGGGTAGTCTGACCATGAAATCTCAACTTCAGATCACTG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GACAGTGGACCACAGCTTGA
59.89
ACAGCAGACCTGAAGTTCTCA
58.96
150
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CTGACAGTGGACCACAGCTT
59.89
ACAGCAGACCTGAAGTTCTCA
58.96
152
PCR template sequence:
GCAGTTCAGGTTTGCTGTCTTATTGATGGTATGTCTGACAGTGGACCACAGCTTGATTCCATGGGTAGTCTGACCATGAAATCTCAACTTCAGATCACTGGTAACATGCATTTCACAGTGGCCTTCTGGAAACAACGCCTTAACCCTAAGAAGTGACTCAGCCATTGAGAACTTCAGGTCTGCTGTAACAGTACAAGCTG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
1
Interacting miRNAs (#binding sites)
mmu-miR-3470b(1)
siRNAs for circular RNA silencing
Junction sequence
CTTCAGATCACTGGTAACATGCATTT
siRNA sets
AAATGCATGTTACCAGTGA, ATGCATGTTACCAGTGATC, AATGCATGTTACCAGTGAT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCITCH_370_ORF_3
0.8436
0.122437343
0.092643081
126
ORF sequence:
ATGTCTGACAGTGGACCACAGCTTGATTCCATGGGTAGTCTGACCATGAAATCTCAACTTCAGATCACTGGTAACATGCATTTCACAGTGGCCTTCTGGAAACAACGCCTTAACCCTAAGAAGTGA
Peptide sequence:
MSDSGPQLDSMGSLTMKSQLQITGNMHFTVAFWKQRLNPKK
IRESfinder result
IRESfinder score
0.700932648
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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