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mmu_circSec24a_1297
Basic information of circular RNA
PanCircBase ID:
mmu_circSec24a_1297
mm39_Chr. Position ID:
chr11|51599761|51620405|-
Gene name:
Sec24a
Transcript:
ENSMUST00000109097.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
10
Exon/intron indexes:
17,16,15,14,13,12,11,10,9,8
Exon/intron offsets:
0,3254,4596,6190,7504,8789,12880,14649,17550,20517
Genomic length:
20644
Exon/intron sizes in nt:
11,11,74,15,91,21,20,70,00,00,00,00,00,000
Flanking exon/introns:
chr11:51598130-51599761|chr11:51620405-51622629
Splice length:
1297
Other database IDs:
circAtlas: mmu-Sec24a_0047
Human Ortholog IDs:
Mature spliced Sequence:
CAGTTGCCCGTGGTCACCTCCAGCACAATTGTGAGATGCCGTTCATGCAGGACTTACATTAACCCTTTCGTCAACTTCCTTGATCAAAGAAGGTGGAAATGTAACTTATGTTATCGAGTCAATGATGTTCCTGAAGAATTCATGTACAACCCTTTAACCAGAGTTTATGGAGAACCTCACAAAAGACCTGAAGTCCAGAATGCTACTATTGAGTTTATGGCTCCTTCAGAATACATGTTACGACCACCACAACCTCCAGTGTACCTCTTTGTATTTGATGTATCTCACAACGCAATAGAAACTGGATACTTGAATTCAGTTTGCCAGAGTTTGTTAGACAATCTGGATCTGCTTCCTGGCAACACTAGGACAAAAATCGGTTTCATAACATTTGATAGCACTATCCATTTCTACAGTCTTCAGGAAGGTCTCTCCCAGCCTCAGATGCTAATAGTTTCAGATATTGACGATGTTTTTATCCCTATGCCAGAGAACTTACTAGTAAACTTAAATGAAAGTAAAGAGCTTGTTCAAGATTTACTGAAAACGCTGCCACAAATGTTTACGAAGACGCTGGAGACCCAGAGTGCCTTGGGTCCTGCACTTCAGGCTGCATTCAAGCTGATATCACCAACTGGTGGTCGAATGTCTGTCTTCCAAACACAACTCCCAACGCTTGGTGTAGGAGCTCTGAAACCACGAGAGGAACCCAACCAAAGGTCATCTGCTAAGGAAATACATCTGACACCATCCACTGACTTCTATAAGAAATTAGCCTTGGACTGTTCTGGGCAGCAAGCAGCTGTTGACTTATTCCTTCTCAGTGGACAGTATTCTGATTTGGCTTCCCTAGGCTGCATCTCTCGGTACTCAGCGGGTAGTGTGTATTACTATCCCTCGTACCATCACCAGCACAACCCAGTGCAAGTACAGAAACTACAGAAGGAACTACACAGGTACCTCACTCGGAAGATTGGATTTGAGGCAGTCATGAGGATCCGGTGCACCAAAGGTCTTTCCATTCATACTTTCCATGGGAACTTCTTCGTCCGTTCTACAGACTTACTGTCTCTTCCCAATGTCAACCCAGATGCTGGGTATGCGGTCCAGATGTCAGTAGAAGAGAGTCTCACTGACACTCAGCTGGTTTCCTTCCAGTCAGCACTCTTATATACATCAAGCAAAGGTGAAAGAAGAATCCGTGTGCATACTTTGTGTTTGCCGGTAGTTTCTACCCTGAATGAAGTCTTTCTTGGAGCTGATGTGCAAGCAATTTCAGGGTTATTAGCCAATATGG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GCATACTTTGTGTTTGCCGGT
60
TGCATGAACGGCATCTCACA
60.32
141
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GCATACTTTGTGTTTGCCGGT
60
AAGTCCTGCATGAACGGCAT
60.32
147
PCR template sequence:
ATCCGTGTGCATACTTTGTGTTTGCCGGTAGTTTCTACCCTGAATGAAGTCTTTCTTGGAGCTGATGTGCAAGCAATTTCAGGGTTATTAGCCAATATGGCAGTTGCCCGTGGTCACCTCCAGCACAATTGTGAGATGCCGTTCATGCAGGACTTACATTAACCCTTTCGTCAACTTCCTTGATCAAAGAAGGTGGAAAT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
13
Interacting miRNAs (#binding sites)
mmu-miR-429-3p(1), mmu-miR-200b-3p(1), mmu-miR-30e-5p(1), mmu-miR-26a-5p(1), mmu-miR-7a-5p(1), mmu-miR-132-3p(1), mmu-miR-138-5p(1), mmu-miR-495-3p(1), mmu-miR-127-3p(1), mmu-miR-26b-5p(1), mmu-miR-680(1), mmu-miR-29b-2-5p(1), mmu-miR-338-3p(1)
siRNAs for circular RNA silencing
Junction sequence
TTAGCCAATATGGCAGTTGCCCGTGG
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSEC24A_1297_ORF_1
0.8208
0.066337951
0.994950323
1218
ORF sequence:
ATGTACAACCCTTTAACCAGAGTTTATGGAGAACCTCACAAAAGACCTGAAGTCCAGAATGCTACTATTGAGTTTATGGCTCCTTCAGAATACATGTTACGACCACCACAACCTCCAGTGTACCTCTTTGTATTTGATGTATCTCACAACGCAATAGAAACTGGATACTTGAATTCAGTTTGCCAGAGTTTGTTAGACAATCTGGATCTGCTTCCTGGCAACACTAGGACAAAAATCGGTTTCATAACATTTGATAGCACTATCCATTTCTACAGTCTTCAGGAAGGTCTCTCCCAGCCTCAGATGCTAATAGTTTCAGATATTGACGATGTTTTTATCCCTATGCCAGAGAACTTACTAGTAAACTTAAATGAAAGTAAAGAGCTTGTTCAAGATTTACTGAAAACGCTGCCACAAATGTTTACGAAGACGCTGGAGACCCAGAGTGCCTTGGGTCCTGCACTTCAGGCTGCATTCAAGCTGATATCACCAACTGGTGGTCGAATGTCTGTCTTCCAAACACAACTCCCAACGCTTGGTGTAGGAGCTCTGAAACCACGAGAGGAACCCAACCAAAGGTCATCTGCTAAGGAAATACATCTGACACCATCCACTGACTTCTATAAGAAATTAGCCTTGGACTGTTCTGGGCAGCAAGCAGCTGTTGACTTATTCCTTCTCAGTGGACAGTATTCTGATTTGGCTTCCCTAGGCTGCATCTCTCGGTACTCAGCGGGTAGTGTGTATTACTATCCCTCGTACCATCACCAGCACAACCCAGTGCAAGTACAGAAACTACAGAAGGAACTACACAGGTACCTCACTCGGAAGATTGGATTTGAGGCAGTCATGAGGATCCGGTGCACCAAAGGTCTTTCCATTCATACTTTCCATGGGAACTTCTTCGTCCGTTCTACAGACTTACTGTCTCTTCCCAATGTCAACCCAGATGCTGGGTATGCGGTCCAGATGTCAGTAGAAGAGAGTCTCACTGACACTCAGCTGGTTTCCTTCCAGTCAGCACTCTTATATACATCAAGCAAAGGTGAAAGAAGAATCCGTGTGCATACTTTGTGTTTGCCGGTAGTTTCTACCCTGAATGAAGTCTTTCTTGGAGCTGATGTGCAAGCAATTTCAGGGTTATTAGCCAATATGGCAGTTGCCCGTGGTCACCTCCAGCACAATTGTGAGATGCCGTTCATGCAGGACTTACATTAA
Peptide sequence:
MYNPLTRVYGEPHKRPEVQNATIEFMAPSEYMLRPPQPPVYLFVFDVSHNAIETGYLNSVCQSLLDNLDLLPGNTRTKIGFITFDSTIHFYSLQEGLSQPQMLIVSDIDDVFIPMPENLLVNLNESKELVQDLLKTLPQMFTKTLETQSALGPALQAAFKLISPTGGRMSVFQTQLPTLGVGALKPREEPNQRSSAKEIHLTPSTDFYKKLALDCSGQQAAVDLFLLSGQYSDLASLGCISRYSAGSVYYYPSYHHQHNPVQVQKLQKELHRYLTRKIGFEAVMRIRCTKGLSIHTFHGNFFVRSTDLLSLPNVNPDAGYAVQMSVEESLTDTQLVSFQSALLYTSSKGERRIRVHTLCLPVVSTLNEVFLGADVQAISGLLANMAVARGHLQHNCEMPFMQDLH
IRESfinder result
IRESfinder score
0.691401501
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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