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mmu_circChka_495
Basic information of circular RNA
PanCircBase ID:
mmu_circChka_495
mm39_Chr. Position ID:
chr19|3935859|3939988|+
Gene name:
Chka
Transcript:
ENSMUST00000128694.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
6,7,8,9,10
Exon/intron offsets:
0,502,1529,3163,4020
Genomic length:
4129
Exon/intron sizes in nt:
13,41,05,59,88,109
Flanking exon/introns:
chr19:3934585-3935859|chr19:3939988-3942106
Splice length:
495
Other database IDs:
circAtlas: mmu-Chka_0005
circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_128364
Human Ortholog IDs:
Mature spliced Sequence:
AGCCGGCGATTGGACACTGAAGAGTTACGTTTACCAGATATTTCTGCAGAAATAGCTGAGAAAATGGCCACATTTCATGGTATGAAAATGCCATTCAATAAGGAACCAAAATGGCTTTTTGGAACAATGGAAAAATACCTGAATCAAGTACTAAGACTCAAATTCAGCAGGGAGGCCAGAGTTCAGCAACTGCACAAGATCCTCTCTTACAACCTGCCTCTTGAGCTCGAGAACCTGAGGTCATTGCTGCAGTATACTAGATCTCCAGTTGTATTTTGTCATAATGACTGTCAAGAAGGTAATATCTTATTGTTGGAAGGCCAGGAGAACTCTGAAAGGCGGAAGCTGATGCTTATTGACTTTGAGTACAGCAGTTACAATTACAGGGGATTTGACATTGGAAATCATTTCTGTGAATGGATGTATGATTATACCTATGAGAAGTATCCTTTCTTCAGAGCGAACATTCAGAAGTATCCTTCCCGAAAACAACAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AGAAGTATCCTTTCTTCAGAGCGA
59.29
TCATACCATGAAATGTGGCCA
57.62
141
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GAAGTATCCTTTCTTCAGAGCGA
58
TCATACCATGAAATGTGGCCA
57.62
140
PCR template sequence:
CATTGGAAATCATTTCTGTGAATGGATGTATGATTATACCTATGAGAAGTATCCTTTCTTCAGAGCGAACATTCAGAAGTATCCTTCCCGAAAACAACAGAGCCGGCGATTGGACACTGAAGAGTTACGTTTACCAGATATTTCTGCAGAAATAGCTGAGAAAATGGCCACATTTCATGGTATGAAAATGCCATTCAATA
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-199a-5p(1), mmu-miR-382-3p(1), mmu-miR-370-3p(1), mmu-miR-207(1)
siRNAs for circular RNA silencing
Junction sequence
CCGAAAACAACAGAGCCGGCGATTGG
siRNA sets
AATCGCCGGCTCTGTTGTT, CAATCGCCGGCTCTGTTGT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCCHKA_495_ORF_1
0.8223
0.096791679
0.966045622
927
ORF sequence:
ATGGCCACATTTCATGGTATGAAAATGCCATTCAATAAGGAACCAAAATGGCTTTTTGGAACAATGGAAAAATACCTGAATCAAGTACTAAGACTCAAATTCAGCAGGGAGGCCAGAGTTCAGCAACTGCACAAGATCCTCTCTTACAACCTGCCTCTTGAGCTCGAGAACCTGAGGTCATTGCTGCAGTATACTAGATCTCCAGTTGTATTTTGTCATAATGACTGTCAAGAAGGTAATATCTTATTGTTGGAAGGCCAGGAGAACTCTGAAAGGCGGAAGCTGATGCTTATTGACTTTGAGTACAGCAGTTACAATTACAGGGGATTTGACATTGGAAATCATTTCTGTGAATGGATGTATGATTATACCTATGAGAAGTATCCTTTCTTCAGAGCGAACATTCAGAAGTATCCTTCCCGAAAACAACAGAGCCGGCGATTGGACACTGAAGAGTTACGTTTACCAGATATTTCTGCAGAAATAGCTGAGAAAATGGCCACATTTCATGGTATGAAAATGCCATTCAATAAGGAACCAAAATGGCTTTTTGGAACAATGGAAAAATACCTGAATCAAGTACTAAGACTCAAATTCAGCAGGGAGGCCAGAGTTCAGCAACTGCACAAGATCCTCTCTTACAACCTGCCTCTTGAGCTCGAGAACCTGAGGTCATTGCTGCAGTATACTAGATCTCCAGTTGTATTTTGTCATAATGACTGTCAAGAAGGTAATATCTTATTGTTGGAAGGCCAGGAGAACTCTGAAAGGCGGAAGCTGATGCTTATTGACTTTGAGTACAGCAGTTACAATTACAGGGGATTTGACATTGGAAATCATTTCTGTGAATGGATGTATGATTATACCTATGAGAAGTATCCTTTCTTCAGAGCGAACATTCAGAAGTATCCTTCCCGAAAACAACAG
Peptide sequence:
MATFHGMKMPFNKEPKWLFGTMEKYLNQVLRLKFSREARVQQLHKILSYNLPLELENLRSLLQYTRSPVVFCHNDCQEGNILLLEGQENSERRKLMLIDFEYSSYNYRGFDIGNHFCEWMYDYTYEKYPFFRANIQKYPSRKQQSRRLDTEELRLPDISAEIAEKMATFHGMKMPFNKEPKWLFGTMEKYLNQVLRLKFSREARVQQLHKILSYNLPLELENLRSLLQYTRSPVVFCHNDCQEGNILLLEGQENSERRKLMLIDFEYSSYNYRGFDIGNHFCEWMYDYTYEKYPFFRANIQKYPSRKQQ
IRESfinder result
IRESfinder score
0.645541575
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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