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mmu_circSec24a_1059
Basic information of circular RNA
PanCircBase ID:
mmu_circSec24a_1059
mm39_Chr. Position ID:
chr11|51603015|51617421|-
Gene name:
Sec24a
Transcript:
ENSMUST00000109097.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
8
Exon/intron indexes:
16,15,14,13,12,11,10,9
Exon/intron offsets:
0,1342,2936,4250,5535,9626,11395,14296
Genomic length:
14406
Exon/intron sizes in nt:
17,41,59,12,12,07,56,10,00,00,000
Flanking exon/introns:
chr11:51599872-51603015|chr11:51617421-51620278
Splice length:
1059
Other database IDs:
circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_153635
Human Ortholog IDs:
Mature spliced Sequence:
TTCCTGAAGAATTCATGTACAACCCTTTAACCAGAGTTTATGGAGAACCTCACAAAAGACCTGAAGTCCAGAATGCTACTATTGAGTTTATGGCTCCTTCAGAATACATGTTACGACCACCACAACCTCCAGTGTACCTCTTTGTATTTGATGTATCTCACAACGCAATAGAAACTGGATACTTGAATTCAGTTTGCCAGAGTTTGTTAGACAATCTGGATCTGCTTCCTGGCAACACTAGGACAAAAATCGGTTTCATAACATTTGATAGCACTATCCATTTCTACAGTCTTCAGGAAGGTCTCTCCCAGCCTCAGATGCTAATAGTTTCAGATATTGACGATGTTTTTATCCCTATGCCAGAGAACTTACTAGTAAACTTAAATGAAAGTAAAGAGCTTGTTCAAGATTTACTGAAAACGCTGCCACAAATGTTTACGAAGACGCTGGAGACCCAGAGTGCCTTGGGTCCTGCACTTCAGGCTGCATTCAAGCTGATATCACCAACTGGTGGTCGAATGTCTGTCTTCCAAACACAACTCCCAACGCTTGGTGTAGGAGCTCTGAAACCACGAGAGGAACCCAACCAAAGGTCATCTGCTAAGGAAATACATCTGACACCATCCACTGACTTCTATAAGAAATTAGCCTTGGACTGTTCTGGGCAGCAAGCAGCTGTTGACTTATTCCTTCTCAGTGGACAGTATTCTGATTTGGCTTCCCTAGGCTGCATCTCTCGGTACTCAGCGGGTAGTGTGTATTACTATCCCTCGTACCATCACCAGCACAACCCAGTGCAAGTACAGAAACTACAGAAGGAACTACACAGGTACCTCACTCGGAAGATTGGATTTGAGGCAGTCATGAGGATCCGGTGCACCAAAGGTCTTTCCATTCATACTTTCCATGGGAACTTCTTCGTCCGTTCTACAGACTTACTGTCTCTTCCCAATGTCAACCCAGATGCTGGGTATGCGGTCCAGATGTCAGTAGAAGAGAGTCTCACTGACACTCAGCTGGTTTCCTTCCAGTCAGCACTCTTATATACATCAAGCAAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GGGTATGCGGTCCAGATGTC
60.25
AGCATTCTGGACTTCAGGTCT
58.74
168
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GGTATGCGGTCCAGATGTCA
59.54
AGCATTCTGGACTTCAGGTCT
58.74
167
PCR template sequence:
CCAGATGCTGGGTATGCGGTCCAGATGTCAGTAGAAGAGAGTCTCACTGACACTCAGCTGGTTTCCTTCCAGTCAGCACTCTTATATACATCAAGCAAAGTTCCTGAAGAATTCATGTACAACCCTTTAACCAGAGTTTATGGAGAACCTCACAAAAGACCTGAAGTCCAGAATGCTACTATTGAGTTTATGGCTCCTTC
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
ACATCAAGCAAAGTTCCTGAAGAATT
siRNA sets
AATTCTTCAGGAACTTTGC, ATTCTTCAGGAACTTTGCT, TTCTTCAGGAACTTTGCTT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSEC24A_1059_ORF_1
0.8154
0.089134048
0.999992221
2103
ORF sequence:
ATGTACAACCCTTTAACCAGAGTTTATGGAGAACCTCACAAAAGACCTGAAGTCCAGAATGCTACTATTGAGTTTATGGCTCCTTCAGAATACATGTTACGACCACCACAACCTCCAGTGTACCTCTTTGTATTTGATGTATCTCACAACGCAATAGAAACTGGATACTTGAATTCAGTTTGCCAGAGTTTGTTAGACAATCTGGATCTGCTTCCTGGCAACACTAGGACAAAAATCGGTTTCATAACATTTGATAGCACTATCCATTTCTACAGTCTTCAGGAAGGTCTCTCCCAGCCTCAGATGCTAATAGTTTCAGATATTGACGATGTTTTTATCCCTATGCCAGAGAACTTACTAGTAAACTTAAATGAAAGTAAAGAGCTTGTTCAAGATTTACTGAAAACGCTGCCACAAATGTTTACGAAGACGCTGGAGACCCAGAGTGCCTTGGGTCCTGCACTTCAGGCTGCATTCAAGCTGATATCACCAACTGGTGGTCGAATGTCTGTCTTCCAAACACAACTCCCAACGCTTGGTGTAGGAGCTCTGAAACCACGAGAGGAACCCAACCAAAGGTCATCTGCTAAGGAAATACATCTGACACCATCCACTGACTTCTATAAGAAATTAGCCTTGGACTGTTCTGGGCAGCAAGCAGCTGTTGACTTATTCCTTCTCAGTGGACAGTATTCTGATTTGGCTTCCCTAGGCTGCATCTCTCGGTACTCAGCGGGTAGTGTGTATTACTATCCCTCGTACCATCACCAGCACAACCCAGTGCAAGTACAGAAACTACAGAAGGAACTACACAGGTACCTCACTCGGAAGATTGGATTTGAGGCAGTCATGAGGATCCGGTGCACCAAAGGTCTTTCCATTCATACTTTCCATGGGAACTTCTTCGTCCGTTCTACAGACTTACTGTCTCTTCCCAATGTCAACCCAGATGCTGGGTATGCGGTCCAGATGTCAGTAGAAGAGAGTCTCACTGACACTCAGCTGGTTTCCTTCCAGTCAGCACTCTTATATACATCAAGCAAAGTTCCTGAAGAATTCATGTACAACCCTTTAACCAGAGTTTATGGAGAACCTCACAAAAGACCTGAAGTCCAGAATGCTACTATTGAGTTTATGGCTCCTTCAGAATACATGTTACGACCACCACAACCTCCAGTGTACCTCTTTGTATTTGATGTATCTCACAACGCAATAGAAACTGGATACTTGAATTCAGTTTGCCAGAGTTTGTTAGACAATCTGGATCTGCTTCCTGGCAACACTAGGACAAAAATCGGTTTCATAACATTTGATAGCACTATCCATTTCTACAGTCTTCAGGAAGGTCTCTCCCAGCCTCAGATGCTAATAGTTTCAGATATTGACGATGTTTTTATCCCTATGCCAGAGAACTTACTAGTAAACTTAAATGAAAGTAAAGAGCTTGTTCAAGATTTACTGAAAACGCTGCCACAAATGTTTACGAAGACGCTGGAGACCCAGAGTGCCTTGGGTCCTGCACTTCAGGCTGCATTCAAGCTGATATCACCAACTGGTGGTCGAATGTCTGTCTTCCAAACACAACTCCCAACGCTTGGTGTAGGAGCTCTGAAACCACGAGAGGAACCCAACCAAAGGTCATCTGCTAAGGAAATACATCTGACACCATCCACTGACTTCTATAAGAAATTAGCCTTGGACTGTTCTGGGCAGCAAGCAGCTGTTGACTTATTCCTTCTCAGTGGACAGTATTCTGATTTGGCTTCCCTAGGCTGCATCTCTCGGTACTCAGCGGGTAGTGTGTATTACTATCCCTCGTACCATCACCAGCACAACCCAGTGCAAGTACAGAAACTACAGAAGGAACTACACAGGTACCTCACTCGGAAGATTGGATTTGAGGCAGTCATGAGGATCCGGTGCACCAAAGGTCTTTCCATTCATACTTTCCATGGGAACTTCTTCGTCCGTTCTACAGACTTACTGTCTCTTCCCAATGTCAACCCAGATGCTGGGTATGCGGTCCAGATGTCAGTAGAAGAGAGTCTCACTGACACTCAGCTGGTTTCCTTCCAGTCAGCACTCTTATATACATCAAGCAAA
Peptide sequence:
MYNPLTRVYGEPHKRPEVQNATIEFMAPSEYMLRPPQPPVYLFVFDVSHNAIETGYLNSVCQSLLDNLDLLPGNTRTKIGFITFDSTIHFYSLQEGLSQPQMLIVSDIDDVFIPMPENLLVNLNESKELVQDLLKTLPQMFTKTLETQSALGPALQAAFKLISPTGGRMSVFQTQLPTLGVGALKPREEPNQRSSAKEIHLTPSTDFYKKLALDCSGQQAAVDLFLLSGQYSDLASLGCISRYSAGSVYYYPSYHHQHNPVQVQKLQKELHRYLTRKIGFEAVMRIRCTKGLSIHTFHGNFFVRSTDLLSLPNVNPDAGYAVQMSVEESLTDTQLVSFQSALLYTSSKVPEEFMYNPLTRVYGEPHKRPEVQNATIEFMAPSEYMLRPPQPPVYLFVFDVSHNAIETGYLNSVCQSLLDNLDLLPGNTRTKIGFITFDSTIHFYSLQEGLSQPQMLIVSDIDDVFIPMPENLLVNLNESKELVQDLLKTLPQMFTKTLETQSALGPALQAAFKLISPTGGRMSVFQTQLPTLGVGALKPREEPNQRSSAKEIHLTPSTDFYKKLALDCSGQQAAVDLFLLSGQYSDLASLGCISRYSAGSVYYYPSYHHQHNPVQVQKLQKELHRYLTRKIGFEAVMRIRCTKGLSIHTFHGNFFVRSTDLLSLPNVNPDAGYAVQMSVEESLTDTQLVSFQSALLYTSSK
IRESfinder result
IRESfinder score
0.704444253
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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