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mmu_circAbraxas1_1108
Basic information of circular RNA
PanCircBase ID:
mmu_circAbraxas1_1108
mm39_Chr. Position ID:
chr5|100953763|100960068|-
Gene name:
Abraxas1
Transcript:
ENSMUST00000153302.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
8,7,6,5,4
Exon/intron offsets:
0,881,3656,3858,6111
Genomic length:
6305
Exon/intron sizes in nt:
592,112,90,120,194
Flanking exon/introns:
chr5:100953317-100953763|chr5:100960068-100963027
Splice length:
1108
Other database IDs:
circBase: mmu_circ_0001369, CIRCpedia: MMU_CIRCpedia_314, circAtlas: mmu-Fam175a_0002
Human Ortholog IDs:
Mature spliced Sequence:
ACTGTGGTGGGTTGGTATAAATTCCGTCGTCACTCGGATCAGATCATGACATTTAGAGAGCAGTTACTCCACAGAAACTTACAGACACATCTTTCAAGCCCTGAGCTGGTTTTCCTGTTGTTAACACCGAGTATAACAACAGAAAGCTGCTCCACTCACTGCCTGGAACACGCCTTATATAAACCTCAAAGGGGGCTTTTTCATAGGGTACCATTGGTGGTTACCAATCTGGGAATGTCTGATCAACTGGGTTATAAAACAGAACCTGCTTCCTGTACGTCCACTGTCTTTAGTAGAGCTGTGAGGACACACAGTTCTCAGTTCTTTAATGAAGATGGATCATTAAAGGAAGTCCATAAGATAAATGAAATGTATGCTGCTGTACAAGAAGAGTTAAAGGTGAGAGTATATGCCAAAAAGTTGAACAAAGTGAACGAGAAGTAGAGAAACTATTGATGGATGTAAACCAATTAAAAGAAGTTAGAAGAACCCAGCAAGCACGGGCTACAGGAGCAGGAGAGAAGAATGTCCAGAGAAACCCACAGGAGAACATCCTTCTTTGTCAAGCTTTGCGAACATTTTTTCCAGAGTCTGAAGTTCTTCATTCTTGCGTTATTTCTTTGAAAAATAGACACATTTCTCCCAGTGGGTGTAACGTTAACCACCATGTTGATGTAGTGGATCAGCTGACCTTAATGGTAGAGTATGTGTACAGCCCTGAAGCTAGTCCAGTGCCCACAGCCCAGCTACGTAAACGGAAGGCTCTAGACACACACGACCAGGGGTCTGTGAAGAGACCACGGCTGCTGGAGACAGAAAGCAGACCTTCTGTGGCAGCGTCCCGCAGCAGGCACCAAGACAAGGCTTCCTCAAGCAGCCTAGATATAGACATAGAGATGGGGAGCCCAGAAGATGATGCTGACTATCCTCGCTCTCCCACATTTTAATTTTTTTTAGACGACATTTCTTACTAGACTGAGGTTTCGGGCACTTGTTTTATTTTTACTCTTTGCCTTCTGGATTAATACACAGAAAAGTTTGTTTTTACTCTATTCACCTGTTTGTAATACATGGATATTTTTACTGTTCAACTGCTTATAATATATAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TGCCTTCTGGATTAATACACAGA
57.31
ATCTGATCCGAGTGACGACG
59.34
142
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TGCCTTCTGGATTAATACACAGAA
57.94
ATCTGATCCGAGTGACGACG
59.34
142
PCR template sequence:
TTTGCCTTCTGGATTAATACACAGAAAAGTTTGTTTTTACTCTATTCACCTGTTTGTAATACATGGATATTTTTACTGTTCAACTGCTTATAATATATAGACTGTGGTGGGTTGGTATAAATTCCGTCGTCACTCGGATCAGATCATGACATTTAGAGAGCAGTTACTCCACAGAAACTTACAGACACATCTTTCAAGCC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
13
Interacting miRNAs (#binding sites)
mmu-miR-15a-5p(1), mmu-miR-34c-5p(1), mmu-miR-34a-5p(1), mmu-miR-322-5p(1), mmu-miR-15b-5p(1), mmu-miR-146a-5p(1), mmu-miR-433-3p(1), mmu-miR-370-3p(1), mmu-miR-34b-5p(1), mmu-miR-705(1), mmu-miR-673-5p(1), mmu-miR-146b-5p(1), mmu-miR-7a-2-3p(1)
siRNAs for circular RNA silencing
Junction sequence
TTATAATATATAGACTGTGGTGGGTT
siRNA sets
NA
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
0.761009499
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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