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mmu_circAgtpbp1_536
Basic information of circular RNA
PanCircBase ID:
mmu_circAgtpbp1_536
mm39_Chr. Position ID:
chr13|59676200|59684187|-
Gene name:
Agtpbp1
Transcript:
ENSMUST00000022040.14
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
7,6,5,4,3
Exon/intron offsets:
0,2670,3626,4785,7862
Genomic length:
7987
Exon/intron sizes in nt:
13,21,47,64,68,125
Flanking exon/introns:
chr13:59673053-59676200|chr13:59684187-59692200
Splice length:
536
Other database IDs:
circAtlas: mmu-Agtpbp1_0038
circBase: hsa_circ_0139224, circAtlas: hsa-AGTPBP1_0039, CIRCpedia: HSA_CIRCpedia_125602
Human Ortholog IDs:
Mature spliced Sequence:
CCTTACCAATAGTTCTCGGGTTGTGGGACTCCTGGCTCAGCTGGAGAAGATCAATACGGATTCCACAGAGTCAGATACTGCCAGATATGTTACATCCAAAATTCTTCATTTGGCTCAAAGTCAAGAAAAAACAAGAAGGGAAATGACAACCAAAGGTTCTACAGGCATGGAAGTTCTGTTGTCAACATTGGAGAACACGAAAGATCTTCAGACTGTACTTAATATCCTAAGCATTCTCATTGAGCTGGTGTCATCGGGTGGGGGTCGAAGAGCGAGTTTCTTAGTTGCCAAAGGTGGTTCACAAATACTGTTGCAACTGCTTATGAATGCCAGCAAAGACTCTCCTCCACATGAGGAGGTGATGGTGCAGACTCACTCCATTCTTGCCAAGATTGGGCCAAAAGATAAGAAATTTGGAGTGAAAGCTCGAGTTAACGGGGCACTGACTGTGACTCTGAACTTGGTAAAGCAGCACTTTCAGAACTACCGCTTGGTTCTTCCTTGTCTTCAGCTCTTGCGAGTCTATTCTACCAACT
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AGCACTTTCAGAACTACCGCT
59.66
TGGCAGTATCTGACTCTGTGG
59.17
149
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AGCACTTTCAGAACTACCGCT
59.66
TCTGACTCTGTGGAATCCGT
58.08
141
PCR template sequence:
GGGGCACTGACTGTGACTCTGAACTTGGTAAAGCAGCACTTTCAGAACTACCGCTTGGTTCTTCCTTGTCTTCAGCTCTTGCGAGTCTATTCTACCAACTCCTTACCAATAGTTCTCGGGTTGTGGGACTCCTGGCTCAGCTGGAGAAGATCAATACGGATTCCACAGAGTCAGATACTGCCAGATATGTTACATCCAAA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
9
Interacting miRNAs (#binding sites)
mmu-miR-182-5p(2), mmu-miR-9-5p(1), mmu-miR-20b-5p(1), mmu-miR-106a-5p(1), mmu-miR-93-5p(1), mmu-miR-20a-5p(1), mmu-miR-17-5p(1), mmu-miR-106b-5p(1), mmu-miR-335-5p(1)
siRNAs for circular RNA silencing
Junction sequence
TATTCTACCAACTCCTTACCAATAGT
siRNA sets
ATTGGTAAGGAGTTGGTAG, TATTGGTAAGGAGTTGGTA, ACTATTGGTAAGGAGTTGG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCAGTPBP1_536_ORF_1
0.9609
0.052777489
0.652798672
540
ORF sequence:
ATGACAACCAAAGGTTCTACAGGCATGGAAGTTCTGTTGTCAACATTGGAGAACACGAAAGATCTTCAGACTGTACTTAATATCCTAAGCATTCTCATTGAGCTGGTGTCATCGGGTGGGGGTCGAAGAGCGAGTTTCTTAGTTGCCAAAGGTGGTTCACAAATACTGTTGCAACTGCTTATGAATGCCAGCAAAGACTCTCCTCCACATGAGGAGGTGATGGTGCAGACTCACTCCATTCTTGCCAAGATTGGGCCAAAAGATAAGAAATTTGGAGTGAAAGCTCGAGTTAACGGGGCACTGACTGTGACTCTGAACTTGGTAAAGCAGCACTTTCAGAACTACCGCTTGGTTCTTCCTTGTCTTCAGCTCTTGCGAGTCTATTCTACCAACTCCTTACCAATAGTTCTCGGGTTGTGGGACTCCTGGCTCAGCTGGAGAAGATCAATACGGATTCCACAGAGTCAGATACTGCCAGATATGTTACATCCAAAATTCTTCATTTGGCTCAAAGTCAAGAAAAAACAAGAAGGGAAATGA
Peptide sequence:
MTTKGSTGMEVLLSTLENTKDLQTVLNILSILIELVSSGGGRRASFLVAKGGSQILLQLLMNASKDSPPHEEVMVQTHSILAKIGPKDKKFGVKARVNGALTVTLNLVKQHFQNYRLVLPCLQLLRVYSTNSLPIVLGLWDSWLSWRRSIRIPQSQILPDMLHPKFFIWLKVKKKQEGK
IRESfinder result
IRESfinder score
0.628951438
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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