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mmu_ciAftph_1478
Basic information of circular RNA
PanCircBase ID:
mmu_ciAftph_1478
mm39_Chr. Position ID:
chr11|20646834|20648312|-
Gene name:
Aftph
Transcript:
ENSMUST00000146722.9
CircRNA type:
Circular intronic (ci)RNA
Exon/Intron count:
1
Exon/intron indexes:
6
Exon/intron offsets:
0
Genomic length:
1478
Exon/intron sizes in nt:
1478
Flanking exon/introns:
chr11:20646831-20648312
Splice length:
1478
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GTACGTCTCTCCGTAGAGCCTCTAGCACCAGGGCTAGAGCTAAGAAAGCTACACAGTTCAGACAGACTTCTCTCTGCTGATTTCCTTTTTTGTTTGAACATAACTTCTTATTCTTATCTTTGGAAATTCAGGCTTTCTTTCTAAATAGCAATTGCTCAAGATACCAGCCATTAATGTTACCAACAATATTAATGCTCAAGTAATGGTAGTAAGAATAAGGTAAAGTTTTAGTTTCTTTATCTTAAGTCAAAATTAGATAGTTTAAATGATATTTTAGCTAGGACCAATTTGTTTGAATGTTTTATAGCCTCCCTTTGTGAACTGTTCTTGGACACACAGTCTTGTGGCTAGCGGCTGCTCCAAAGCACAAAGCACAATTATTCACTTAACCAAGACCAGTGTGCAGATAGATCCAGATTATGACGTAATGTAGTCTTCAGACTCTGTAGCGTTTTATAGAGTACTTATATGCAAATGGAAGATGAATGATTTTCATGATTATTTTTAAACTTATCTCCAAATGCTAACAGAGCAGTTCCAGAAATCAGTGATTTTTTTTCTTAGGACTTTTAAACTCTAAACAGGGAGTAACTTATGCAAGTACCATAGGAACTTTCACACACAGTGCTAGTGTTCCAGTCCATGCTGTGGCTTTCCCATGGACCCTGATTTATAATTGCTATGTAATTAATTGAGCCATTGTCTAGAACACTATCACTGTCATCTCAGTGGTACTTAGCATGCCATTGCCTGAGACACTTACCAGCTTTTCCTAAGAGCTGGGATCCTAGGATACCTGGAAACCATCTATTGAATGTCCTGCTGAAGGAAAGCCTGGATGTACCTTTCGCTGTTGTCTGGTGTCTTTAGTCAAATCATCATGCTCTTTATTAACAATTTCTTTAAAAATGTATACTATTTGTGATTACTATTGCGGAGTTAAAGGGGAACAGTAGAGCGTGTGCATCAGGGCAGGGCAGTTACTACATCTATATTACGTTATGTTAAAGAAGTTCATGTATTGGTGCATGTCCTGAAACTCACAACTTTGTCATTCTTTTGAAAAGCATTCATTAGAAACCAGAAATTGCTCCTAGAAACTAACATGAAAGATGGGGCATGTAGTGACTTCATGCTGGGTTAAGACTAAGTGTTGTTTCCCTTTAACTAGTGTGCCTTCTCTGGTCTTTCTGATACTTTTCATTTTGGATTGAAAGAACTGACTTCTCACGAAAACCTAACAAAGTGTTACATTATTTACATTGTACACAAGGAAATCTACATTGAGTTAAATTGTTACTTTAGTTATAAAAACCTAATGCTGTACACATTGTTTTAATGTTGATTTTTAAAATGTGTAATGACTACTAATTATAACCTGCATGTTCAAGTGTGTGTCTTACCCCTTTTCACACGTAACCCCTCCTCCCTTGGCTTACCTTCTGTGTGGCTGCCCACCAACACGGTCACTGAATTCC
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CTGCATGTTCAAGTGTGTGTCT
59.38
CTTAGCTCTAGCCCTGGTGC
59.89
144
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TGCATGTTCAAGTGTGTGTCT
58.36
CTTAGCTCTAGCCCTGGTGC
59.89
143
PCR template sequence:
CTGCATGTTCAAGTGTGTGTCTTACCCCTTTTCACACGTAACCCCTCCTCCCTTGGCTTACCTTCTGTGTGGCTGCCCACCAACACGGTCACTGAATTCCGTACGTCTCTCCGTAGAGCCTCTAGCACCAGGGCTAGAGCTAAGAAAGCTACACAGTTCAGACAGACTTCTCTCTGCTGATTTCCTTTTTTGTTTGAACA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
18
Interacting miRNAs (#binding sites)
mmu-miR-29b-2-5p(2), mmu-miR-124-3p(1), mmu-miR-181a-5p(1), mmu-miR-223-3p(1), mmu-miR-18a-5p(1), mmu-miR-320-3p(1), mmu-miR-143-3p(1), mmu-miR-138-5p(1), mmu-miR-214-3p(1), mmu-miR-29b-1-5p(1), mmu-miR-411-3p(1), mmu-miR-501-3p(1), mmu-miR-194-5p(1), mmu-miR-340-5p(1), mmu-miR-224-5p(1), mmu-miR-669d-5p(1), mmu-miR-350-3p(1), mmu-miR-338-3p(1)
siRNAs for circular RNA silencing
Junction sequence
GTCACTGAATTCCGTACGTCTCTCCG
siRNA sets
AGAGACGTACGGAATTCAG, AGACGTACGGAATTCAGTG, ACGTACGGAATTCAGTGAC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIAFTPH_1478_ORF_1
0.4679
-0.278257301
0.020880421
240
ORF sequence:
ATGTTCAAGTGTGTGTCTTACCCCTTTTCACACGTAACCCCTCCTCCCTTGGCTTACCTTCTGTGTGGCTGCCCACCAACACGGTCACTGAATTCCGTACGTCTCTCCGTAGAGCCTCTAGCACCAGGGCTAGAGCTAAGAAAGCTACACAGTTCAGACAGACTTCTCTCTGCTGATTTCCTTTTTTGTTTGAACATAACTTCTTATTCTTATCTTTGGAAATTCAGGCTTTCTTTCTAA
Peptide sequence:
MFKCVSYPFSHVTPPPLAYLLCGCPPTRSLNSVRLSVEPLAPGLELRKLHSSDRLLSADFLFCLNITSYSYLWKFRLSF
IRESfinder result
IRESfinder score
0.901955064
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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