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mmu_circItch_700_1
Basic information of circular RNA
PanCircBase ID:
mmu_circItch_700_1
mm39_Chr. Position ID:
chr2|155005312|155022631|+
Gene name:
Itch
Transcript:
ENSMUST00000029126.15
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
6
Exon/intron indexes:
3,4,5,6,7,8
Exon/intron offsets:
0,5291,9064,10541,15649,17161
Genomic length:
17319
Exon/intron sizes in nt:
9,11,42,12,51,38,46,150
Flanking exon/introns:
chr2:154980192-155005312|chr2:155022631-155024077
Splice length:
700
Other database IDs:
CIRCpedia: MMU_CIRCpedia_10556, circAtlas: mmu-Itch_0056
CIRCpedia: HSA_CIRCpedia_152973
Human Ortholog IDs:
Mature spliced Sequence:
GTTTGCTGTCTTATTGATGGTATGTCTGACAGTGGACCACAGCTTGATTCCATGGGTAGTCTGACCATGAAATCTCAACTTCAGATCACTGTCATCTCAGCCAAACTTAAAGAAAATAAAAAGAATTGGTTTGGACCAAGTCCTTATGTAGAAGTCACAGTAGATGGACAGTCAAAGAAGACAGAAAAATGCAATAATACAAACAGTCCCAAGTGGAAGCAGCCCCTCACAGTTATTGTTACCCCTACGAGTAAATTATGTTTTCGTGTGTGGAGTCACCAGACCCTGAAGTCTGATGTTTTATTGGGAACTGCTGGATTAGATATTTATGAAACATTAAAGTCAAACAATATGAAACTTGAAGAAGTAGTTATGACTTTGCAGCTTGTAGGTGACAAAGAGCCAACAGAGACGATGGGAGATTTGTCAGTTTGTCTTGATGGGCTGCAAGTAGAAGCTGAGGTTGTTACTAACGGTGAAACGTCATGCTCCGAGAGTACTACACAGAATGATGATGGCTGCAGAACCAGAGATGATACAAGAGTGAGCACAAATGGATCAGAGGACCCTGAGGTTGCAGCGTCAGGGGAAAACAAGAGGGCCAATGGGAACAATTCTCCGTCCCTTTCAAATGGTGGTTTTAAGCCTTCTAGACCTCCTAGACCTTCGAGACCACCTCCACCCACCCCACGAAGACCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TGGGAACAATTCTCCGTCCC
59.67
TCAAGCTGTGGTCCACTGTC
59.89
142
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TGGGAACAATTCTCCGTCCC
59.67
AAGCTGTGGTCCACTGTCAG
59.89
140
PCR template sequence:
GCCAATGGGAACAATTCTCCGTCCCTTTCAAATGGTGGTTTTAAGCCTTCTAGACCTCCTAGACCTTCGAGACCACCTCCACCCACCCCACGAAGACCAGGTTTGCTGTCTTATTGATGGTATGTCTGACAGTGGACCACAGCTTGATTCCATGGGTAGTCTGACCATGAAATCTCAACTTCAGATCACTGTCATCTCAG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
4
Interacting miRNAs (#binding sites)
mmu-miR-9-5p(1), mmu-miR-328-3p(1), mmu-miR-184-3p(1), mmu-miR-5101(1)
siRNAs for circular RNA silencing
Junction sequence
CCACGAAGACCAGGTTTGCTGTCTTA
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCITCH_700_1_ORF_1
0.9218
0.04194366
0.937899442
846
ORF sequence:
ATGGATCAGAGGACCCTGAGGTTGCAGCGTCAGGGGAAAACAAGAGGGCCAATGGGAACAATTCTCCGTCCCTTTCAAATGGTGGTTTTAAGCCTTCTAGACCTCCTAGACCTTCGAGACCACCTCCACCCACCCCACGAAGACCAGGTTTGCTGTCTTATTGATGGTATGTCTGACAGTGGACCACAGCTTGATTCCATGGGTAGTCTGACCATGAAATCTCAACTTCAGATCACTGTCATCTCAGCCAAACTTAAAGAAAATAAAAAGAATTGGTTTGGACCAAGTCCTTATGTAGAAGTCACAGTAGATGGACAGTCAAAGAAGACAGAAAAATGCAATAATACAAACAGTCCCAAGTGGAAGCAGCCCCTCACAGTTATTGTTACCCCTACGAGTAAATTATGTTTTCGTGTGTGGAGTCACCAGACCCTGAAGTCTGATGTTTTATTGGGAACTGCTGGATTAGATATTTATGAAACATTAAAGTCAAACAATATGAAACTTGAAGAAGTAGTTATGACTTTGCAGCTTGTAGGTGACAAAGAGCCAACAGAGACGATGGGAGATTTGTCAGTTTGTCTTGATGGGCTGCAAGTAGAAGCTGAGGTTGTTACTAACGGTGAAACGTCATGCTCCGAGAGTACTACACAGAATGATGATGGCTGCAGAACCAGAGATGATACAAGAGTGAGCACAAATGGATCAGAGGACCCTGAGGTTGCAGCGTCAGGGGAAAACAAGAGGGCCAATGGGAACAATTCTCCGTCCCTTTCAAATGGTGGTTTTAAGCCTTCTAGACCTCCTAGACCTTCGAGACCACCTCCACCCACCCCACGAAGACCA
Peptide sequence:
MDQRTLRLQRQGKTRGPMGTILRPFQMVVLSLLDLLDLRDHLHPPHEDQVCCLIDGMSDSGPQLDSMGSLTMKSQLQITVISAKLKENKKNWFGPSPYVEVTVDGQSKKTEKCNNTNSPKWKQPLTVIVTPTSKLCFRVWSHQTLKSDVLLGTAGLDIYETLKSNNMKLEEVVMTLQLVGDKEPTETMGDLSVCLDGLQVEAEVVTNGETSCSESTTQNDDGCRTRDDTRVSTNGSEDPEVAASGENKRANGNNSPSLSNGGFKPSRPPRPSRPPPPTPRRP
IRESfinder result
IRESfinder score
0.587548751
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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