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mmu_circAbca3_669
Basic information of circular RNA
PanCircBase ID:
mmu_circAbca3_669
mm39_Chr. Position ID:
chr17|24583450|24585907|+
Gene name:
Abca3
Transcript:
ENSMUST00000133816.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
3,4,5,6
Exon/intron offsets:
0,216,1609,2291
Genomic length:
2457
Exon/intron sizes in nt:
1,10,26,51,28,166
Flanking exon/introns:
chr17:24580063-24583450|chr17:24585907-24593217
Splice length:
669
Other database IDs:
circAtlas: mmu-Abca3_0003
Human Ortholog IDs:
Mature spliced Sequence:
TTGTCCATCTTTAAGTCTTGATCTCTGGTTGGTGTTGGCACTGTGCCAGCAAGAAGATGGCAGTGCTGCGGCAGCTCACCCTCCTACTCTGGAAGAACTATACCCTGAAGAAACGGAAGGTTCTAGTGACAGTCCTGGAGCTCTTCCTGCCCCTGCTGTTTTCTGGGATCCTGATTTGGCTTCGCTTGAAGATCCAGTCGGAGAATGTGCCCAATGCCACTGTTTACCCGGACCAGTCCATCCAGGAGCTGCCCCTGTTTTTCTCATTCCCTCCACCTGGGGGGACCTGGGAGCTCGCCTATGTCCCTTCCCACAGCGATGCTGCCAGGACCATCACGGAGACGGTGAAAAGGGAATTCATGATCAAGATGAGAGTGCACGGCTTCTCCTCTGAGAAGGACTTCGAGGACTACATTCGCTATGACAACCACTCCTCCAGCGTGCTGGCAGCTGTGGTATTTGAGCACAGCTTCAACCACAGCCAGGACCCCCTGCCGCTGGCGGTGAAATACCACCTGCGCTTCAGTTACACACGAAGAAATTACATGTGGACCCAAACAGGAAATATTTTCCTAAAAGAGACTGAAGGCTGGCATACCACTTCACTTTTTCCACTTTTTCCAAGCCCCGGACCGCGGGAACCTTCATCACCTGATGGCGGTGAACCTG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GGCTGGCATACCACTTCACT
60.04
CCAGAGTAGGAGGGTGAGCT
60.03
174
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AGGCTGGCATACCACTTCAC
60.04
CCAGAGTAGGAGGGTGAGCT
60.03
175
PCR template sequence:
TTCCTAAAAGAGACTGAAGGCTGGCATACCACTTCACTTTTTCCACTTTTTCCAAGCCCCGGACCGCGGGAACCTTCATCACCTGATGGCGGTGAACCTGTTGTCCATCTTTAAGTCTTGATCTCTGGTTGGTGTTGGCACTGTGCCAGCAAGAAGATGGCAGTGCTGCGGCAGCTCACCCTCCTACTCTGGAAGAACTA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
7
Interacting miRNAs (#binding sites)
mmu-miR-103-3p(1), mmu-miR-211-5p(1), mmu-miR-204-5p(1), mmu-miR-214-3p(1), mmu-miR-22-3p(1), mmu-miR-107-3p(1), mmu-miR-452-3p(1)
siRNAs for circular RNA silencing
Junction sequence
GGCGGTGAACCTGTTGTCCATCTTTA
siRNA sets
TAAAGATGGACAACAGGTT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCABCA3_669_ORF_1
1.1247
0.29960628
0.928691161
627
ORF sequence:
ATGGCAGTGCTGCGGCAGCTCACCCTCCTACTCTGGAAGAACTATACCCTGAAGAAACGGAAGGTTCTAGTGACAGTCCTGGAGCTCTTCCTGCCCCTGCTGTTTTCTGGGATCCTGATTTGGCTTCGCTTGAAGATCCAGTCGGAGAATGTGCCCAATGCCACTGTTTACCCGGACCAGTCCATCCAGGAGCTGCCCCTGTTTTTCTCATTCCCTCCACCTGGGGGGACCTGGGAGCTCGCCTATGTCCCTTCCCACAGCGATGCTGCCAGGACCATCACGGAGACGGTGAAAAGGGAATTCATGATCAAGATGAGAGTGCACGGCTTCTCCTCTGAGAAGGACTTCGAGGACTACATTCGCTATGACAACCACTCCTCCAGCGTGCTGGCAGCTGTGGTATTTGAGCACAGCTTCAACCACAGCCAGGACCCCCTGCCGCTGGCGGTGAAATACCACCTGCGCTTCAGTTACACACGAAGAAATTACATGTGGACCCAAACAGGAAATATTTTCCTAAAAGAGACTGAAGGCTGGCATACCACTTCACTTTTTCCACTTTTTCCAAGCCCCGGACCGCGGGAACCTTCATCACCTGATGGCGGTGAACCTGTTGTCCATCTTTAA
Peptide sequence:
MAVLRQLTLLLWKNYTLKKRKVLVTVLELFLPLLFSGILIWLRLKIQSENVPNATVYPDQSIQELPLFFSFPPPGGTWELAYVPSHSDAARTITETVKREFMIKMRVHGFSSEKDFEDYIRYDNHSSSVLAAVVFEHSFNHSQDPLPLAVKYHLRFSYTRRNYMWTQTGNIFLKETEGWHTTSLFPLFPSPGPREPSSPDGGEPVVHL
IRESfinder result
IRESfinder score
0.499149623
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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