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mmu_circAbcf3_535
Basic information of circular RNA
PanCircBase ID:
mmu_circAbcf3_535
mm39_Chr. Position ID:
chr16|20368493|20369437|+
Gene name:
Abcf3
Transcript:
ENSMUST00000003319.6
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
4,5,6,7
Exon/intron offsets:
0,260,458,677
Genomic length:
944
Exon/intron sizes in nt:
4,79,81,23,267
Flanking exon/introns:
chr16:20368064-20368493|chr16:20369437-20370223
Splice length:
535
Other database IDs:
circAtlas: mmu-Abcf3_0003
Human Ortholog IDs:
Mature spliced Sequence:
ACTGTGACACCAAACTTCCAGGACTGCTAAAGAGGGAACAGTCCTCGACAGTAAATGCGAAGAAACTAGAGAAGGCTGAAGCTCGACTGAAGGCAAAGCAGGAGAAGCGTTCAGAGAAGGAAACACTGAAGACCAGCAACCCTCTAGTCTTGGAGGAGGCGTCAGCTAGCCAGGCAGGCAGCAGAAAAGAGAGTCGATTGGAATCATCTGGCAAGAACAAGTCCTATGATGTGCGAATTGAGAACTTTGATGTCTCTTTTGGTGACAGGGTACTGCTGGCTGGAGCAGATGTAAACTTGGCATGGGGCCGACGCTACGGCCTGGTGGGACGCAATGGTCTGGGGAAGACGACATTGCTAAAGATGCTGGCTACCCGGAGCTTGCGTGTCCCAGCCCATATTTCCCTACTGCATGTAGAGCAGGAAGTTGCTGGAGATGACACTCCTGCCTTGCAGAGTGTGCTGGAAAGTGACACCGTACGAGAGGACCTGCTACGGCAGGAACGGGAGCTCAGCCTCAGGATTGCCGCTGGCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AGTGACACCGTACGAGAGGA
59.96
TGCCTTCAGTCGAGCTTCAG
60.04
163
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GTGACACCGTACGAGAGGAC
59.83
TGCCTTCAGTCGAGCTTCAG
60.04
162
PCR template sequence:
ATGACACTCCTGCCTTGCAGAGTGTGCTGGAAAGTGACACCGTACGAGAGGACCTGCTACGGCAGGAACGGGAGCTCAGCCTCAGGATTGCCGCTGGCAGACTGTGACACCAAACTTCCAGGACTGCTAAAGAGGGAACAGTCCTCGACAGTAAATGCGAAGAAACTAGAGAAGGCTGAAGCTCGACTGAAGGCAAAGCA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
6
Interacting miRNAs (#binding sites)
mmu-miR-339-5p(1), mmu-miR-10b-5p(1), mmu-miR-207(1), mmu-miR-3470b(1), mmu-miR-1904(1), mmu-miR-338-3p(1)
siRNAs for circular RNA silencing
Junction sequence
TTGCCGCTGGCAGACTGTGACACCAA
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCABCF3_535_ORF_1
0.8351
0.359499373
0.91073239
633
ORF sequence:
ATGACACTCCTGCCTTGCAGAGTGTGCTGGAAAGTGACACCGTACGAGAGGACCTGCTACGGCAGGAACGGGAGCTCAGCCTCAGGATTGCCGCTGGCAGACTGTGACACCAAACTTCCAGGACTGCTAAAGAGGGAACAGTCCTCGACAGTAAATGCGAAGAAACTAGAGAAGGCTGAAGCTCGACTGAAGGCAAAGCAGGAGAAGCGTTCAGAGAAGGAAACACTGAAGACCAGCAACCCTCTAGTCTTGGAGGAGGCGTCAGCTAGCCAGGCAGGCAGCAGAAAAGAGAGTCGATTGGAATCATCTGGCAAGAACAAGTCCTATGATGTGCGAATTGAGAACTTTGATGTCTCTTTTGGTGACAGGGTACTGCTGGCTGGAGCAGATGTAAACTTGGCATGGGGCCGACGCTACGGCCTGGTGGGACGCAATGGTCTGGGGAAGACGACATTGCTAAAGATGCTGGCTACCCGGAGCTTGCGTGTCCCAGCCCATATTTCCCTACTGCATGTAGAGCAGGAAGTTGCTGGAGATGACACTCCTGCCTTGCAGAGTGTGCTGGAAAGTGACACCGTACGAGAGGACCTGCTACGGCAGGAACGGGAGCTCAGCCTCAGGATTGCCGCTGGC
Peptide sequence:
MTLLPCRVCWKVTPYERTCYGRNGSSASGLPLADCDTKLPGLLKREQSSTVNAKKLEKAEARLKAKQEKRSEKETLKTSNPLVLEEASASQAGSRKESRLESSGKNKSYDVRIENFDVSFGDRVLLAGADVNLAWGRRYGLVGRNGLGKTTLLKMLATRSLRVPAHISLLHVEQEVAGDDTPALQSVLESDTVREDLLRQERELSLRIAAG
IRESfinder result
IRESfinder score
0.263600076
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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