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mmu_circSec24a_885
Basic information of circular RNA
PanCircBase ID:
mmu_circSec24a_885
mm39_Chr. Position ID:
chr11|51604357|51617421|-
Gene name:
Sec24a
Transcript:
ENSMUST00000109097.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
7
Exon/intron indexes:
15,14,13,12,11,10,9
Exon/intron offsets:
0,1594,2908,4193,8284,10053,12954
Genomic length:
13064
Exon/intron sizes in nt:
1,59,12,12,07,56,11,91,00,000
Flanking exon/introns:
chr11:51603189-51604357|chr11:51617421-51620278
Splice length:
885
Other database IDs:
CIRCpedia: MMU_CIRCpedia_22154, circAtlas: mmu-Sec24a_0012
circBase: hsa_circ_0128006, circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_123689
Human Ortholog IDs:
Mature spliced Sequence:
TTCCTGAAGAATTCATGTACAACCCTTTAACCAGAGTTTATGGAGAACCTCACAAAAGACCTGAAGTCCAGAATGCTACTATTGAGTTTATGGCTCCTTCAGAATACATGTTACGACCACCACAACCTCCAGTGTACCTCTTTGTATTTGATGTATCTCACAACGCAATAGAAACTGGATACTTGAATTCAGTTTGCCAGAGTTTGTTAGACAATCTGGATCTGCTTCCTGGCAACACTAGGACAAAAATCGGTTTCATAACATTTGATAGCACTATCCATTTCTACAGTCTTCAGGAAGGTCTCTCCCAGCCTCAGATGCTAATAGTTTCAGATATTGACGATGTTTTTATCCCTATGCCAGAGAACTTACTAGTAAACTTAAATGAAAGTAAAGAGCTTGTTCAAGATTTACTGAAAACGCTGCCACAAATGTTTACGAAGACGCTGGAGACCCAGAGTGCCTTGGGTCCTGCACTTCAGGCTGCATTCAAGCTGATATCACCAACTGGTGGTCGAATGTCTGTCTTCCAAACACAACTCCCAACGCTTGGTGTAGGAGCTCTGAAACCACGAGAGGAACCCAACCAAAGGTCATCTGCTAAGGAAATACATCTGACACCATCCACTGACTTCTATAAGAAATTAGCCTTGGACTGTTCTGGGCAGCAAGCAGCTGTTGACTTATTCCTTCTCAGTGGACAGTATTCTGATTTGGCTTCCCTAGGCTGCATCTCTCGGTACTCAGCGGGTAGTGTGTATTACTATCCCTCGTACCATCACCAGCACAACCCAGTGCAAGTACAGAAACTACAGAAGGAACTACACAGGTACCTCACTCGGAAGATTGGATTTGAGGCAGTCATGAGGATCCGGTGCACCAAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
ACACAGGTACCTCACTCGGA
59.89
AGTAGCATTCTGGACTTCAGGT
58.82
142
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
ACACAGGTACCTCACTCGGA
59.89
GTAGCATTCTGGACTTCAGGTCT
59.8
141
PCR template sequence:
CACAACCCAGTGCAAGTACAGAAACTACAGAAGGAACTACACAGGTACCTCACTCGGAAGATTGGATTTGAGGCAGTCATGAGGATCCGGTGCACCAAAGTTCCTGAAGAATTCATGTACAACCCTTTAACCAGAGTTTATGGAGAACCTCACAAAAGACCTGAAGTCCAGAATGCTACTATTGAGTTTATGGCTCCTTC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
11
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-29b-2-5p(1)
siRNAs for circular RNA silencing
Junction sequence
CGGTGCACCAAAGTTCCTGAAGAATT
siRNA sets
AATTCTTCAGGAACTTTGG, TCTTCAGGAACTTTGGTGC, ATTCTTCAGGAACTTTGGT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSEC24A_885_ORF_1
0.8297
0.086759977
0.999906536
1755
ORF sequence:
ATGTACAACCCTTTAACCAGAGTTTATGGAGAACCTCACAAAAGACCTGAAGTCCAGAATGCTACTATTGAGTTTATGGCTCCTTCAGAATACATGTTACGACCACCACAACCTCCAGTGTACCTCTTTGTATTTGATGTATCTCACAACGCAATAGAAACTGGATACTTGAATTCAGTTTGCCAGAGTTTGTTAGACAATCTGGATCTGCTTCCTGGCAACACTAGGACAAAAATCGGTTTCATAACATTTGATAGCACTATCCATTTCTACAGTCTTCAGGAAGGTCTCTCCCAGCCTCAGATGCTAATAGTTTCAGATATTGACGATGTTTTTATCCCTATGCCAGAGAACTTACTAGTAAACTTAAATGAAAGTAAAGAGCTTGTTCAAGATTTACTGAAAACGCTGCCACAAATGTTTACGAAGACGCTGGAGACCCAGAGTGCCTTGGGTCCTGCACTTCAGGCTGCATTCAAGCTGATATCACCAACTGGTGGTCGAATGTCTGTCTTCCAAACACAACTCCCAACGCTTGGTGTAGGAGCTCTGAAACCACGAGAGGAACCCAACCAAAGGTCATCTGCTAAGGAAATACATCTGACACCATCCACTGACTTCTATAAGAAATTAGCCTTGGACTGTTCTGGGCAGCAAGCAGCTGTTGACTTATTCCTTCTCAGTGGACAGTATTCTGATTTGGCTTCCCTAGGCTGCATCTCTCGGTACTCAGCGGGTAGTGTGTATTACTATCCCTCGTACCATCACCAGCACAACCCAGTGCAAGTACAGAAACTACAGAAGGAACTACACAGGTACCTCACTCGGAAGATTGGATTTGAGGCAGTCATGAGGATCCGGTGCACCAAAGTTCCTGAAGAATTCATGTACAACCCTTTAACCAGAGTTTATGGAGAACCTCACAAAAGACCTGAAGTCCAGAATGCTACTATTGAGTTTATGGCTCCTTCAGAATACATGTTACGACCACCACAACCTCCAGTGTACCTCTTTGTATTTGATGTATCTCACAACGCAATAGAAACTGGATACTTGAATTCAGTTTGCCAGAGTTTGTTAGACAATCTGGATCTGCTTCCTGGCAACACTAGGACAAAAATCGGTTTCATAACATTTGATAGCACTATCCATTTCTACAGTCTTCAGGAAGGTCTCTCCCAGCCTCAGATGCTAATAGTTTCAGATATTGACGATGTTTTTATCCCTATGCCAGAGAACTTACTAGTAAACTTAAATGAAAGTAAAGAGCTTGTTCAAGATTTACTGAAAACGCTGCCACAAATGTTTACGAAGACGCTGGAGACCCAGAGTGCCTTGGGTCCTGCACTTCAGGCTGCATTCAAGCTGATATCACCAACTGGTGGTCGAATGTCTGTCTTCCAAACACAACTCCCAACGCTTGGTGTAGGAGCTCTGAAACCACGAGAGGAACCCAACCAAAGGTCATCTGCTAAGGAAATACATCTGACACCATCCACTGACTTCTATAAGAAATTAGCCTTGGACTGTTCTGGGCAGCAAGCAGCTGTTGACTTATTCCTTCTCAGTGGACAGTATTCTGATTTGGCTTCCCTAGGCTGCATCTCTCGGTACTCAGCGGGTAGTGTGTATTACTATCCCTCGTACCATCACCAGCACAACCCAGTGCAAGTACAGAAACTACAGAAGGAACTACACAGGTACCTCACTCGGAAGATTGGATTTGAGGCAGTCATGAGGATCCGGTGCACCAAA
Peptide sequence:
MYNPLTRVYGEPHKRPEVQNATIEFMAPSEYMLRPPQPPVYLFVFDVSHNAIETGYLNSVCQSLLDNLDLLPGNTRTKIGFITFDSTIHFYSLQEGLSQPQMLIVSDIDDVFIPMPENLLVNLNESKELVQDLLKTLPQMFTKTLETQSALGPALQAAFKLISPTGGRMSVFQTQLPTLGVGALKPREEPNQRSSAKEIHLTPSTDFYKKLALDCSGQQAAVDLFLLSGQYSDLASLGCISRYSAGSVYYYPSYHHQHNPVQVQKLQKELHRYLTRKIGFEAVMRIRCTKVPEEFMYNPLTRVYGEPHKRPEVQNATIEFMAPSEYMLRPPQPPVYLFVFDVSHNAIETGYLNSVCQSLLDNLDLLPGNTRTKIGFITFDSTIHFYSLQEGLSQPQMLIVSDIDDVFIPMPENLLVNLNESKELVQDLLKTLPQMFTKTLETQSALGPALQAAFKLISPTGGRMSVFQTQLPTLGVGALKPREEPNQRSSAKEIHLTPSTDFYKKLALDCSGQQAAVDLFLLSGQYSDLASLGCISRYSAGSVYYYPSYHHQHNPVQVQKLQKELHRYLTRKIGFEAVMRIRCTK
IRESfinder result
IRESfinder score
0.715809114
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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