top of page
mmu_circAbca3_275
Basic information of circular RNA
PanCircBase ID:
mmu_circAbca3_275
mm39_Chr. Position ID:
chr17|24576892|24580063|+
Gene name:
Abca3
Transcript:
ENSMUST00000039013.15
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
2
Exon/intron indexes:
2,3
Exon/intron offsets:
0,2969
Genomic length:
3171
Exon/intron sizes in nt:
73,202
Flanking exon/introns:
chr17:24571225-24576892|chr17:24580063-24583450
Splice length:
275
Other database IDs:
CIRCpedia: MMU_CIRCpedia_14094, circAtlas: mmu-Abca3_0005
Human Ortholog IDs:
Mature spliced Sequence:
AGAATACAAGAAAATTGCTCACTATCCCTCCACTGTGATGTACTGTCTTGTTCATTCTGCTTGGAAACAACTGGTGCCAGCACATCATGCCCGTGAGCCCCAGGTCCCTCCAGATGTCCCTGGAGATCTCAGCGTTCCTGCTCCCTAGGGCTGTTGCTTCTGTCCAGGGGACCACTGGCTCCACCCCAGGGTCATCTGTGTAGAACTGCTGACGCCAGGCGACTTCACCCGTAGCCTTGCAGTGACACCTTCAGCCAACCTTTCCTGGAACTAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TGTAGAACTGCTGACGCCAG
60.04
GTGCTGGCACCAGTTGTTTC
60.25
160
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TGTAGAACTGCTGACGCCAG
60.04
GGCACCAGTTGTTTCCAAGC
60.25
155
PCR template sequence:
TGGCTCCACCCCAGGGTCATCTGTGTAGAACTGCTGACGCCAGGCGACTTCACCCGTAGCCTTGCAGTGACACCTTCAGCCAACCTTTCCTGGAACTAAGAGAATACAAGAAAATTGCTCACTATCCCTCCACTGTGATGTACTGTCTTGTTCATTCTGCTTGGAAACAACTGGTGCCAGCACATCATGCCCGTGAGCCC
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-27b-3p(1), mmu-miR-27a-3p(1), mmu-miR-148b-3p(1), mmu-miR-296-3p(1)
siRNAs for circular RNA silencing
Junction sequence
TCCTGGAACTAAGAGAATACAAGAAA
siRNA sets
TTTCTTGTATTCTCTTAGT, CTTGTATTCTCTTAGTTCC, TTGTATTCTCTTAGTTCCA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
NA
NA
NA
NA
NA
ORF sequence:
NA
Peptide sequence:
NA
IRESfinder result
IRESfinder score
0.667103444
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
bottom of page