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mmu_circItch_698
Basic information of circular RNA
PanCircBase ID:
mmu_circItch_698
mm39_Chr. Position ID:
chr2|154999693|155015991|+
Gene name:
Itch
Transcript:
ENSMUST00000109685.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
3,4,5,6,7
Exon/intron offsets:
0,5619,10910,14683,16160
Genomic length:
16298
Exon/intron sizes in nt:
2,02,91,14,21,25,138
Flanking exon/introns:
chr2:154980192-154999693|chr2:155015991-155020961
Splice length:
698
Other database IDs:
circBase: mmu_circ_0009462, CIRCpedia: MMU_CIRCpedia_10554, circAtlas: mmu-Itch_0060
Human Ortholog IDs:
Mature spliced Sequence:
GTCTGCTGTAACAGTACAAGCTGGGCATGGTGGTTCATTCCTGCAGTGCCAGACTTTGGAGGCTGAGGAAGGAAGACTGCTGCAAACTTGAGGCCAGCCTGGACTATAGAGTGAGACTTTATCTTGTAAAGCCAGGAACAAACATTCCCTCCGAAATTACCCTAAAGTTGTGGGGATGGAAACGTAATGTTTTGCAGTTCAGGTTTGCTGTCTTATTGATGGTATGTCTGACAGTGGACCACAGCTTGATTCCATGGGTAGTCTGACCATGAAATCTCAACTTCAGATCACTGTCATCTCAGCCAAACTTAAAGAAAATAAAAAGAATTGGTTTGGACCAAGTCCTTATGTAGAAGTCACAGTAGATGGACAGTCAAAGAAGACAGAAAAATGCAATAATACAAACAGTCCCAAGTGGAAGCAGCCCCTCACAGTTATTGTTACCCCTACGAGTAAATTATGTTTTCGTGTGTGGAGTCACCAGACCCTGAAGTCTGATGTTTTATTGGGAACTGCTGGATTAGATATTTATGAAACATTAAAGTCAAACAATATGAAACTTGAAGAAGTAGTTATGACTTTGCAGCTTGTAGGTGACAAAGAGCCAACAGAGACGATGGGAGATTTGTCAGTTTGTCTTGATGGGCTGCAAGTAGAAGCTGAGGTTGTTACTAACGGTGAAACGTCATGCTCCGAGA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TGTCTTGATGGGCTGCAAGT
59.89
GCCTCAAGTTTGCAGCAGTC
60.04
158
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TGTCTTGATGGGCTGCAAGT
59.89
TCTTCCTTCCTCAGCCTCCA
59.88
140
PCR template sequence:
AAAGAGCCAACAGAGACGATGGGAGATTTGTCAGTTTGTCTTGATGGGCTGCAAGTAGAAGCTGAGGTTGTTACTAACGGTGAAACGTCATGCTCCGAGAGTCTGCTGTAACAGTACAAGCTGGGCATGGTGGTTCATTCCTGCAGTGCCAGACTTTGGAGGCTGAGGAAGGAAGACTGCTGCAAACTTGAGGCCAGCCT
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-5101(1), mmu-miR-3470b(1)
siRNAs for circular RNA silencing
Junction sequence
TCATGCTCCGAGAGTCTGCTGTAACA
siRNA sets
TTACAGCAGACTCTCGGAG,TGTTACAGCAGACTCTCGG,TACAGCAGACTCTCGGAGC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCITCH_698_ORF_1
1.0839
0.01148022
0.572978751
486
ORF sequence:
ATGTCTGACAGTGGACCACAGCTTGATTCCATGGGTAGTCTGACCATGAAATCTCAACTTCAGATCACTGTCATCTCAGCCAAACTTAAAGAAAATAAAAAGAATTGGTTTGGACCAAGTCCTTATGTAGAAGTCACAGTAGATGGACAGTCAAAGAAGACAGAAAAATGCAATAATACAAACAGTCCCAAGTGGAAGCAGCCCCTCACAGTTATTGTTACCCCTACGAGTAAATTATGTTTTCGTGTGTGGAGTCACCAGACCCTGAAGTCTGATGTTTTATTGGGAACTGCTGGATTAGATATTTATGAAACATTAAAGTCAAACAATATGAAACTTGAAGAAGTAGTTATGACTTTGCAGCTTGTAGGTGACAAAGAGCCAACAGAGACGATGGGAGATTTGTCAGTTTGTCTTGATGGGCTGCAAGTAGAAGCTGAGGTTGTTACTAACGGTGAAACGTCATGCTCCGAGAGTCTGCTGTAA
Peptide sequence:
MSDSGPQLDSMGSLTMKSQLQITVISAKLKENKKNWFGPSPYVEVTVDGQSKKTEKCNNTNSPKWKQPLTVIVTPTSKLCFRVWSHQTLKSDVLLGTAGLDIYETLKSNNMKLEEVVMTLQLVGDKEPTETMGDLSVCLDGLQVEAEVVTNGETSCSESLL
IRESfinder result
IRESfinder score
0.631214988
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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