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mmu_circSec24a_801
Basic information of circular RNA
PanCircBase ID:
mmu_circSec24a_801
mm39_Chr. Position ID:
chr11|51608550|51624391|-
Gene name:
Sec24a
Transcript:
ENSMUST00000109097.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
7
Exon/intron indexes:
12,11,10,9,8,7,6
Exon/intron offsets:
0,4091,5860,8761,11728,14079,15668
Genomic length:
15841
Exon/intron sizes in nt:
5,61,19,11,31,10,12,71,00,000
Flanking exon/introns:
chr11:51607472-51608550|chr11:51624391-51624596
Splice length:
801
Other database IDs:
circAtlas: mmu-Sec24a_0031
circAtlas: hsa-SCAF8_0001
Human Ortholog IDs:
Mature spliced Sequence:
ACTCCCTTAGGTGCTAATCATTTAACTGCAAGCATGAGTGGATTAAGTCTGCATCCAGAGGGACTAAGAGTTGTCAATCTTCTTCAAGAAAGGAACATGCTTCCTTCCACACCACTGCAGCCTCCAGTCCCAAATCTGCTTGAAGACATCCAGAAACTCAACTGTAACCCAGAGTTGTTCCGATGCACGCTGACGAGTGTCCCTCAGACTCAGGCCTTACTGAATAAAGCCAAGCTTCCTCTGGGGCTGCTGCTCCACCCCTTCAAGGACCTAGTGCAGTTGCCCGTGGTCACCTCCAGCACAATTGTGAGATGCCGTTCATGCAGGACTTACATTAACCCTTTCGTCAACTTCCTTGATCAAAGAAGGTGGAAATGTAACTTATGTTATCGAGTCAATGATGTTCCTGAAGAATTCATGTACAACCCTTTAACCAGAGTTTATGGAGAACCTCACAAAAGACCTGAAGTCCAGAATGCTACTATTGAGTTTATGGCTCCTTCAGAATACATGTTACGACCACCACAACCTCCAGTGTACCTCTTTGTATTTGATGTATCTCACAACGCAATAGAAACTGGATACTTGAATTCAGTTTGCCAGAGTTTGTTAGACAATCTGGATCTGCTTCCTGGCAACACTAGGACAAAAATCGGTTTCATAACATTTGATAGCACTATCCATTTCTACAGTCTTCAGGAAGGTCTCTCCCAGCCTCAGATGCTAATAGTTTCAGATATTGACGATGTTTTTATCCCTATGCCAGAGAACTTACTAGTAAACTTAAATGAAAGTAAAGAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TCTCCCAGCCTCAGATGCTA
59.74
AGTCCCTCTGGATGCAGACT
59.96
160
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GGTCTCTCCCAGCCTCAGAT
60.4
AGTCCCTCTGGATGCAGACT
59.96
164
PCR template sequence:
AGGTCTCTCCCAGCCTCAGATGCTAATAGTTTCAGATATTGACGATGTTTTTATCCCTATGCCAGAGAACTTACTAGTAAACTTAAATGAAAGTAAAGAGACTCCCTTAGGTGCTAATCATTTAACTGCAAGCATGAGTGGATTAAGTCTGCATCCAGAGGGACTAAGAGTTGTCAATCTTCTTCAAGAAAGGAACATGC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
3
Interacting miRNAs (#binding sites)
mmu-miR-26a-5p(1), mmu-miR-495-3p(1), mmu-miR-26b-5p(1)
siRNAs for circular RNA silencing
Junction sequence
TGAAAGTAAAGAGACTCCCTTAGGTG
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSEC24A_801_ORF_1
0.8572
0.06175988
0.999625092
1569
ORF sequence:
ATGAGTGGATTAAGTCTGCATCCAGAGGGACTAAGAGTTGTCAATCTTCTTCAAGAAAGGAACATGCTTCCTTCCACACCACTGCAGCCTCCAGTCCCAAATCTGCTTGAAGACATCCAGAAACTCAACTGTAACCCAGAGTTGTTCCGATGCACGCTGACGAGTGTCCCTCAGACTCAGGCCTTACTGAATAAAGCCAAGCTTCCTCTGGGGCTGCTGCTCCACCCCTTCAAGGACCTAGTGCAGTTGCCCGTGGTCACCTCCAGCACAATTGTGAGATGCCGTTCATGCAGGACTTACATTAACCCTTTCGTCAACTTCCTTGATCAAAGAAGGTGGAAATGTAACTTATGTTATCGAGTCAATGATGTTCCTGAAGAATTCATGTACAACCCTTTAACCAGAGTTTATGGAGAACCTCACAAAAGACCTGAAGTCCAGAATGCTACTATTGAGTTTATGGCTCCTTCAGAATACATGTTACGACCACCACAACCTCCAGTGTACCTCTTTGTATTTGATGTATCTCACAACGCAATAGAAACTGGATACTTGAATTCAGTTTGCCAGAGTTTGTTAGACAATCTGGATCTGCTTCCTGGCAACACTAGGACAAAAATCGGTTTCATAACATTTGATAGCACTATCCATTTCTACAGTCTTCAGGAAGGTCTCTCCCAGCCTCAGATGCTAATAGTTTCAGATATTGACGATGTTTTTATCCCTATGCCAGAGAACTTACTAGTAAACTTAAATGAAAGTAAAGAGACTCCCTTAGGTGCTAATCATTTAACTGCAAGCATGAGTGGATTAAGTCTGCATCCAGAGGGACTAAGAGTTGTCAATCTTCTTCAAGAAAGGAACATGCTTCCTTCCACACCACTGCAGCCTCCAGTCCCAAATCTGCTTGAAGACATCCAGAAACTCAACTGTAACCCAGAGTTGTTCCGATGCACGCTGACGAGTGTCCCTCAGACTCAGGCCTTACTGAATAAAGCCAAGCTTCCTCTGGGGCTGCTGCTCCACCCCTTCAAGGACCTAGTGCAGTTGCCCGTGGTCACCTCCAGCACAATTGTGAGATGCCGTTCATGCAGGACTTACATTAACCCTTTCGTCAACTTCCTTGATCAAAGAAGGTGGAAATGTAACTTATGTTATCGAGTCAATGATGTTCCTGAAGAATTCATGTACAACCCTTTAACCAGAGTTTATGGAGAACCTCACAAAAGACCTGAAGTCCAGAATGCTACTATTGAGTTTATGGCTCCTTCAGAATACATGTTACGACCACCACAACCTCCAGTGTACCTCTTTGTATTTGATGTATCTCACAACGCAATAGAAACTGGATACTTGAATTCAGTTTGCCAGAGTTTGTTAGACAATCTGGATCTGCTTCCTGGCAACACTAGGACAAAAATCGGTTTCATAACATTTGATAGCACTATCCATTTCTACAGTCTTCAGGAAGGTCTCTCCCAGCCTCAGATGCTAATAGTTTCAGATATTGACGATGTTTTTATCCCTATGCCAGAGAACTTACTAGTAAACTTAAATGAAAGTAAAGAG
Peptide sequence:
MSGLSLHPEGLRVVNLLQERNMLPSTPLQPPVPNLLEDIQKLNCNPELFRCTLTSVPQTQALLNKAKLPLGLLLHPFKDLVQLPVVTSSTIVRCRSCRTYINPFVNFLDQRRWKCNLCYRVNDVPEEFMYNPLTRVYGEPHKRPEVQNATIEFMAPSEYMLRPPQPPVYLFVFDVSHNAIETGYLNSVCQSLLDNLDLLPGNTRTKIGFITFDSTIHFYSLQEGLSQPQMLIVSDIDDVFIPMPENLLVNLNESKETPLGANHLTASMSGLSLHPEGLRVVNLLQERNMLPSTPLQPPVPNLLEDIQKLNCNPELFRCTLTSVPQTQALLNKAKLPLGLLLHPFKDLVQLPVVTSSTIVRCRSCRTYINPFVNFLDQRRWKCNLCYRVNDVPEEFMYNPLTRVYGEPHKRPEVQNATIEFMAPSEYMLRPPQPPVYLFVFDVSHNAIETGYLNSVCQSLLDNLDLLPGNTRTKIGFITFDSTIHFYSLQEGLSQPQMLIVSDIDDVFIPMPENLLVNLNESKE
IRESfinder result
IRESfinder score
0.756571425
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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