top of page
mmu_circAbraxas2_200
Basic information of circular RNA
PanCircBase ID:
mmu_circAbraxas2_200
mm39_Chr. Position ID:
chr7|132480257|132482610|+
Gene name:
Abraxas2
Transcript:
ENSMUST00000084497.12
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
2
Exon/intron indexes:
7,8
Exon/intron offsets:
0,2238
Genomic length:
2353
Exon/intron sizes in nt:
85,115
Flanking exon/introns:
chr7:132478446-132480257|chr7:132482610-132484763
Splice length:
200
Other database IDs:
CIRCpedia: MMU_CIRCpedia_7891, circAtlas: mmu-Fam175b_0004
Human Ortholog IDs:
Mature spliced Sequence:
TACTGACTTTTTTGACAAGGATGGAGTCATGAAGGACATCAGGGCAATTTATCAGGTTTATAATGCACTTCAGGAGAAAGTACAGGCAGTATGTGCAGATGTAGAAAAGAGTGAGCGAGTTGTTGAATCTTGTCAGGCAGAAGTGAACAAATTGAGAAGACAAATCACTCAGAAGAAAAATGAAAAGGAACAAGAAAGAA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AAGAGTGAGCGAGTTGTTGA
57.11
TGCCCTGATGTCCTTCATGAC
60.07
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AAGAGTGAGCGAGTTGTTGA
57.11
TGCCCTGATGTCCTTCATGA
58.71
140
PCR template sequence:
GTAGAAAAGAGTGAGCGAGTTGTTGAATCTTGTCAGGCAGAAGTGAACAAATTGAGAAGACAAATCACTCAGAAGAAAAATGAAAAGGAACAAGAAAGAATACTGACTTTTTTGACAAGGATGGAGTCATGAAGGACATCAGGGCAATTTATCAGGTTTATAATGCACTTCAGGAGAAAGTACAGGCAGTATGTGCAGAT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
3
Interacting miRNAs (#binding sites)
mmu-miR-205-5p(1), mmu-miR-335-3p(1), mmu-miR-544-5p(1)
siRNAs for circular RNA silencing
Junction sequence
GAACAAGAAAGAATACTGACTTTTTT
siRNA sets
AAAAAAGTCAGTATTCTTT,AGTCAGTATTCTTTCTTGT,AAAGTCAGTATTCTTTCTT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCABRAXAS2_200_ORF_1
0.9514
0.002514836
0.119120118
204
ORF sequence:
ATGAAGGACATCAGGGCAATTTATCAGGTTTATAATGCACTTCAGGAGAAAGTACAGGCAGTATGTGCAGATGTAGAAAAGAGTGAGCGAGTTGTTGAATCTTGTCAGGCAGAAGTGAACAAATTGAGAAGACAAATCACTCAGAAGAAAAATGAAAAGGAACAAGAAAGAATACTGACTTTTTTGACAAGGATGGAGTCATGA
Peptide sequence:
MKDIRAIYQVYNALQEKVQAVCADVEKSERVVESCQAEVNKLRRQITQKKNEKEQERILTFLTRMES
IRESfinder result
IRESfinder score
0.564410183
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
bottom of page