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mmu_ciAbca1_1503

Basic information of circular RNA
PanCircBase ID:

mmu_ciAbca1_1503

mm39_Chr. Position ID:

chr4|53067183|53068686|-

Gene name:

Abca1

Transcript:

ENSMUST00000030010.4

CircRNA type:

Circular intronic (ci)RNA

Exon/Intron count:

1

Exon/intron indexes:

28

Exon/intron offsets:

0

Genomic length:

1503

Exon/intron sizes in nt:

1503

Flanking exon/introns:

chr4:53067155-53068686

Splice length:

1503

Other database IDs:

​

​

Human Ortholog IDs:
Mature spliced Sequence:

GTGAGGTGTGCTGGGCTCTGCCTTCTTGGACTGGTGAAGACAGGCTAGGACTGTGGTCAAGATAGAGATGCTGGGCCAGTATGCCAGTGATTTCCCTGGGCTTCAAATTCTTCATCTGAAAATGAGCGGGGATGTGTGGCTGTTAGGGGGATGAAACGAATTTATTTAGAATGGACTTTGACATTACTTGGGGAGGTGGCTATAATTTAGAGGAGATCATGGCAGGGACACAGTTTAGACAAACCAGTTGGGAAAATTCAACTCTCATAACATGAGAGTCGCCATGCTGAGTTGTGCTTGGCAGTGTACTTATTATTAGAAACATGGTGGGTATGTTTTTCTCTTAATTGACGAGAGCGAGAGAGCTAGGAATGGAACAGGCCCATTGATTCCCCCATATCACAGTTTGCATGCTGACTTATCAGTTAAAGACAGCTATAAAGTTACTTCATTCTACAAAATGAAGAATTATAGAGAACACGTCCATGAAGCCCTCCCTGCAGCCCACCTGGGCAACACTAACTCAGAGCATGAGCATGAAGCCTGCAGATCTGGATTTGGAATCTGGTTCAGTGAATCACTGGCTGACTTCCCTCAGATCCATGATGCTCTAGTTTGTGAATGGTGATAATGATACTAACACCACCAATAACTACGAAATAGGATATTAAGGGGGCTGATTCTCACTACAGTACTTTCCAGTGGAATTATTCATCCAGTGATAATTTTCTATATTGAAATATAGGAATATTAAAATCAGAGTGATTGTTTGGATTCTTATGGCTCTGGGGATGGAATCCCAGGGTGTGTGAGCTCTCTACTACCAAGTTACACCTGCAGCCAGGGTTACCATTGAATCACTGAAGTTTTTAAAGGGTAAATTTCTCAGAAAGGAAGGAAGAGATCCCTTAGCTGACCCATACATTATGTTGTTTTCAGAGAAGGGATATAGGAAATTTGGGGAATTTCAAGGAAAGATTTAGATAATTATGCTTTTCGCAGTGCTCATAGGAGAGATGCTGGCTGCTGCTGCTTCTGGCGGGGGAGTTGGTGTCATGTTCTCAGTCCTCAGATTTACTGATGTCACATAGGACCCCTGCAAGTGGAGATGGAACCAGGATTCAGTCTCCTGGCTCCCAGTCCAGGGCTGTTCAGCCTTCTACCTGAGTCTATGATCCAGGCTGGTTTTTCCTCAGTCTTTGGAGGGGAGAAAGGATTGAGCCTAAAGAGTCAGTCACTCTGACTCTTTACTCTGTGACATTCCCAGCTTTTGCCTCTGTTAGGTGACCATAGCCTCTGTCTTTGTGCTGTTAGCATCCGGAAATGCCTTGGGAGAAAGGGGCTTAATTTTCAGTCTCCTTTCTCTTCAAGCTGCCAGAAATACCTTGGTAGAACTCAGCCCCAGGCCTTGCCTGTATTCCTCATTCCTGTGTTGCTAGGCTATGGGGCTGGCTAGACTTTCAGGGGCTTGCTCTTCAGGCTTCTAAAAACGTGTCCTATTGT

Divergent primers for circular RNA PCR

Primer Set-1

Forward primer
Tm
Reverse primer
Tm
Product size

GGCCTTGCCTGTATTCCTCA

59.74

GCCTGTCTTCACCAGTCCAA

59.89

144

Primer Set-2

Forward primer
Tm
Reverse primer
Tm
Product size

GGCCTTGCCTGTATTCCTCA

59.74

ACCACAGTCCTAGCCTGTCT

59.88

156

PCR template sequence:

AGGCCTTGCCTGTATTCCTCATTCCTGTGTTGCTAGGCTATGGGGCTGGCTAGACTTTCAGGGGCTTGCTCTTCAGGCTTCTAAAAACGTGTCCTATTGTGTGAGGTGTGCTGGGCTCTGCCTTCTTGGACTGGTGAAGACAGGCTAGGACTGTGGTCAAGATAGAGATGCTGGGCCAGTATGCCAGTGATTTCCCTGGG

Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs

16

Interacting miRNAs (#binding sites)

mmu-let-7a-5p(1), mmu-miR-1a-3p(1), mmu-miR-206-3p(1), mmu-let-7e-5p(1), mmu-let-7c-5p(1), mmu-miR-322-5p(1), mmu-miR-15b-5p(1), mmu-miR-320-3p(1), mmu-let-7d-5p(1), mmu-miR-382-3p(1), mmu-miR-127-5p(1), mmu-miR-425-5p(1), mmu-miR-539-5p(1), mmu-miR-484(1), mmu-miR-193b-3p(1), mmu-miR-338-3p(1)

siRNAs for circular RNA silencing
Junction sequence

CGTGTCCTATTGTGTGAGGTGTGCTG

siRNA sets

ACACCTCACACAATAGGAC, GCACACCTCACACAATAGG, CACACCTCACACAATAGGA

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

0.759597454

IRES/non IRES

IRES

riboCIRC information

riboCIRC ID

NA

NA

Evidence
Peptide sequence:

NA

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