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mmu_circAlcam_597
Basic information of circular RNA
PanCircBase ID:
mmu_circAlcam_597
mm39_Chr. Position ID:
chr16|52109280|52117347|-
Gene name:
Alcam
Transcript:
ENSMUST00000023312.14
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
8,7,6,5,4
Exon/intron offsets:
0,1959,6106,6745,8002
Genomic length:
8067
Exon/intron sizes in nt:
133,128,183,88,65
Flanking exon/introns:
chr16:52097263-52109280|chr16:52117347-52125921
Splice length:
597
Other database IDs:
circAtlas: mmu-Alcam_0011
Human Ortholog IDs:
Mature spliced Sequence:
AGCAACCATCTAAACCTGAAATTGTAAACAAAGCACCCTTTCTTGAAACAGATCAGCTGAAAAAGTTAGGTGACTGCATTTCAAGAGACAGTTACCCAGATGGCAACATCACATGGTACAGGAATGGCAAAGTGCTGCAACCTGTGGAAGGAGAGGTGGCCATACTTTTTAAAAAGGAAATTGATCCAGGAACTCAGTTGTATACCGTGACTTCCTCCTTGGAGTACAAGACAACCAGATCTGACATACAAATGCCATTCACCTGTTCTGTGACATATTATGGACCCTCCGGCCAGAAAACAATTTATTCCGAACAAGAAATCTTTGATATTTACTATCCTACAGAGCAGGTGACAATACAAGTGCTGCCACCAAAAAATGCCATCAAAGAAGGGGACAACATCACCCTTCAGTGTTTGGGGAATGGCAACCCACCTCCTGAGGAGTTCATGTTTTACTTACCAGGACAGCCTGAAGGCATAAGAAGCTCAAACACTTACACACTGACAGATGTGAGACGCAATGCCACAGGGGACTACAAATGCTCACTCATTGACAAAAGGAACATGGCGGCTTCAACGACCATCACAGTTCACT
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AGATGTGAGACGCAATGCCA
60.04
TGTCTCTTGAAATGCAGTCACC
58.86
179
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AGATGTGAGACGCAATGCCA
60.04
TGTCTCTTGAAATGCAGTCACCT
60.18
179
PCR template sequence:
TACACACTGACAGATGTGAGACGCAATGCCACAGGGGACTACAAATGCTCACTCATTGACAAAAGGAACATGGCGGCTTCAACGACCATCACAGTTCACTAGCAACCATCTAAACCTGAAATTGTAAACAAAGCACCCTTTCTTGAAACAGATCAGCTGAAAAAGTTAGGTGACTGCATTTCAAGAGACAGTTACCCAGA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
4
Interacting miRNAs (#binding sites)
mmu-miR-200a-3p(1), mmu-miR-141-3p(1), mmu-miR-200c-3p(1), mmu-miR-574-5p(1)
siRNAs for circular RNA silencing
Junction sequence
ATCACAGTTCACTAGCAACCATCTAA
siRNA sets
TAGATGGTTGCTAGTGAAC, TTAGATGGTTGCTAGTGAA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCALCAM_597_ORF_1
0.639
0.164588029
0.289352323
348
ORF sequence:
ATGCCATTCACCTGTTCTGTGACATATTATGGACCCTCCGGCCAGAAAACAATTTATTCCGAACAAGAAATCTTTGATATTTACTATCCTACAGAGCAGGTGACAATACAAGTGCTGCCACCAAAAAATGCCATCAAAGAAGGGGACAACATCACCCTTCAGTGTTTGGGGAATGGCAACCCACCTCCTGAGGAGTTCATGTTTTACTTACCAGGACAGCCTGAAGGCATAAGAAGCTCAAACACTTACACACTGACAGATGTGAGACGCAATGCCACAGGGGACTACAAATGCTCACTCATTGACAAAAGGAACATGGCGGCTTCAACGACCATCACAGTTCACTAG
Peptide sequence:
MPFTCSVTYYGPSGQKTIYSEQEIFDIYYPTEQVTIQVLPPKNAIKEGDNITLQCLGNGNPPPEEFMFYLPGQPEGIRSSNTYTLTDVRRNATGDYKCSLIDKRNMAASTTITVH
IRESfinder result
IRESfinder score
0.549226661
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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