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mmu_circAbca6_894
Basic information of circular RNA
PanCircBase ID:
mmu_circAbca6_894
mm39_Chr. Position ID:
chr11|110104937|110111014|-
Gene name:
Abca6
Transcript:
ENSMUST00000044003.14
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
7
Exon/intron indexes:
18,17,16,15,14,13,12
Exon/intron offsets:
0,2404,4099,4751,5102,5428,5966
Genomic length:
6077
Exon/intron sizes in nt:
1,17,14,09,11,39,12,01,00,000
Flanking exon/introns:
chr11:110103200-110104937|chr11:110111014-110121314
Splice length:
894
Other database IDs:
circAtlas: mmu-Abca6_0002
circAtlas: hsa-SCAF8_0001
Human Ortholog IDs:
Mature spliced Sequence:
GCTTGTTCTTGGATATCTATGAGAGTCAAATCACAGCAATTCTGGGCCACAGTGGAGCGGGCAAATCTTCATTACTAAACATCCTCAGTGGATTGTATGTTCCAACTGCAGGGTCAGTCACAGTCTACAATAAAAATCTCTCTGATATGCAAGACTTGAAGGAAATCAGGAAGGCGATTGGTGTTTGTCCTCAACATAACGTTCAATTTGATGCACTCACTGTGAAGGAAAACCTCACTCTCTTTGCTAAAATAAAAGGGATTCTTCCACAGGACGTAGAGCAAGAGGTACAACAAATCTTATCAGAATTGGACATGCAGAATATTCGGGACGATCTAGCCGAACATTTAAGCGAAGGACAGAAGAGAAAGCTCACTTTTGGCATTGCCACTGTAGGAGATCCTCAAATTTTGCTCTTAGATGAACCTACTGTAGGACTCGATCCCTTTTCGAGGCAGCGAATATGGGGTTTCCTGAAGGAACGCAGGGCAGACCACGTGATCCTCTTCAGTACTCAGTTCATGGACGAGGCTGACATCCTTGCTGATAGGAAAGTGCTCATCGCCAACGGAGCTCTCAAGTGCACAGGGTCTTCCGTCTTTCTGAAGAGAAAATGGGGTCTTGGATATCACTTAAGTTTGTTTATGGATGAAACGTGTGATTCAGAGCGGCTAACATCCTTCATCAACCATCACATCCCATATGCTAAATTAAAGGCCAAAACCAAAGAAAAGCTTGTGTACATTTTGCCACTGGAAAGGACAAGCGAATTCCCAGAGTTCTTCAGTGATCTCGATAAATATTCTGGCCAGGGCTTGATGAGTTATGAAGTTTCCATGTCAACTCTCAATGATGTCTTCCTGAACCTGGAAGGAGAACCAAGTACCAAACAGG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GGCCAGGGCTTGATGAGTTA
59.74
ATGAAGATTTGCCCGCTCCA
60.03
160
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GGCCAGGGCTTGATGAGTTA
59.74
CTCCACTGTGGCCCAGAATT
59.96
145
PCR template sequence:
GATAAATATTCTGGCCAGGGCTTGATGAGTTATGAAGTTTCCATGTCAACTCTCAATGATGTCTTCCTGAACCTGGAAGGAGAACCAAGTACCAAACAGGGCTTGTTCTTGGATATCTATGAGAGTCAAATCACAGCAATTCTGGGCCACAGTGGAGCGGGCAAATCTTCATTACTAAACATCCTCAGTGGATTGTATGT
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-7b-5p(1), mmu-miR-148b-3p(1), mmu-miR-7a-5p(1), mmu-miR-139-5p(1), mmu-miR-495-3p(1)
siRNAs for circular RNA silencing
Junction sequence
AGTACCAAACAGGGCTTGTTCTTGGA
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCABCA6_894_ORF_1
1.0266
0.156466539
0.999889007
1641
ORF sequence:
ATGCAAGACTTGAAGGAAATCAGGAAGGCGATTGGTGTTTGTCCTCAACATAACGTTCAATTTGATGCACTCACTGTGAAGGAAAACCTCACTCTCTTTGCTAAAATAAAAGGGATTCTTCCACAGGACGTAGAGCAAGAGGTACAACAAATCTTATCAGAATTGGACATGCAGAATATTCGGGACGATCTAGCCGAACATTTAAGCGAAGGACAGAAGAGAAAGCTCACTTTTGGCATTGCCACTGTAGGAGATCCTCAAATTTTGCTCTTAGATGAACCTACTGTAGGACTCGATCCCTTTTCGAGGCAGCGAATATGGGGTTTCCTGAAGGAACGCAGGGCAGACCACGTGATCCTCTTCAGTACTCAGTTCATGGACGAGGCTGACATCCTTGCTGATAGGAAAGTGCTCATCGCCAACGGAGCTCTCAAGTGCACAGGGTCTTCCGTCTTTCTGAAGAGAAAATGGGGTCTTGGATATCACTTAAGTTTGTTTATGGATGAAACGTGTGATTCAGAGCGGCTAACATCCTTCATCAACCATCACATCCCATATGCTAAATTAAAGGCCAAAACCAAAGAAAAGCTTGTGTACATTTTGCCACTGGAAAGGACAAGCGAATTCCCAGAGTTCTTCAGTGATCTCGATAAATATTCTGGCCAGGGCTTGATGAGTTATGAAGTTTCCATGTCAACTCTCAATGATGTCTTCCTGAACCTGGAAGGAGAACCAAGTACCAAACAGGGCTTGTTCTTGGATATCTATGAGAGTCAAATCACAGCAATTCTGGGCCACAGTGGAGCGGGCAAATCTTCATTACTAAACATCCTCAGTGGATTGTATGTTCCAACTGCAGGGTCAGTCACAGTCTACAATAAAAATCTCTCTGATATGCAAGACTTGAAGGAAATCAGGAAGGCGATTGGTGTTTGTCCTCAACATAACGTTCAATTTGATGCACTCACTGTGAAGGAAAACCTCACTCTCTTTGCTAAAATAAAAGGGATTCTTCCACAGGACGTAGAGCAAGAGGTACAACAAATCTTATCAGAATTGGACATGCAGAATATTCGGGACGATCTAGCCGAACATTTAAGCGAAGGACAGAAGAGAAAGCTCACTTTTGGCATTGCCACTGTAGGAGATCCTCAAATTTTGCTCTTAGATGAACCTACTGTAGGACTCGATCCCTTTTCGAGGCAGCGAATATGGGGTTTCCTGAAGGAACGCAGGGCAGACCACGTGATCCTCTTCAGTACTCAGTTCATGGACGAGGCTGACATCCTTGCTGATAGGAAAGTGCTCATCGCCAACGGAGCTCTCAAGTGCACAGGGTCTTCCGTCTTTCTGAAGAGAAAATGGGGTCTTGGATATCACTTAAGTTTGTTTATGGATGAAACGTGTGATTCAGAGCGGCTAACATCCTTCATCAACCATCACATCCCATATGCTAAATTAAAGGCCAAAACCAAAGAAAAGCTTGTGTACATTTTGCCACTGGAAAGGACAAGCGAATTCCCAGAGTTCTTCAGTGATCTCGATAAATATTCTGGCCAGGGCTTGATGAGTTATGAAGTTTCCATGTCAACTCTCAATGATGTCTTCCTGAACCTGGAAGGAGAACCAAGTACCAAACAG
Peptide sequence:
MQDLKEIRKAIGVCPQHNVQFDALTVKENLTLFAKIKGILPQDVEQEVQQILSELDMQNIRDDLAEHLSEGQKRKLTFGIATVGDPQILLLDEPTVGLDPFSRQRIWGFLKERRADHVILFSTQFMDEADILADRKVLIANGALKCTGSSVFLKRKWGLGYHLSLFMDETCDSERLTSFINHHIPYAKLKAKTKEKLVYILPLERTSEFPEFFSDLDKYSGQGLMSYEVSMSTLNDVFLNLEGEPSTKQGLFLDIYESQITAILGHSGAGKSSLLNILSGLYVPTAGSVTVYNKNLSDMQDLKEIRKAIGVCPQHNVQFDALTVKENLTLFAKIKGILPQDVEQEVQQILSELDMQNIRDDLAEHLSEGQKRKLTFGIATVGDPQILLLDEPTVGLDPFSRQRIWGFLKERRADHVILFSTQFMDEADILADRKVLIANGALKCTGSSVFLKRKWGLGYHLSLFMDETCDSERLTSFINHHIPYAKLKAKTKEKLVYILPLERTSEFPEFFSDLDKYSGQGLMSYEVSMSTLNDVFLNLEGEPSTKQ
IRESfinder result
IRESfinder score
0.618876149
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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