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mmu_circAgap1_328
Basic information of circular RNA
PanCircBase ID:
mmu_circAgap1_328
mm39_Chr. Position ID:
chr1|89671449|89694186|+
Gene name:
Agap1
Transcript:
ENSMUST00000027521.15
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
2
Exon/intron indexes:
11,12
Exon/intron offsets:
0,22578
Genomic length:
22737
Exon/intron sizes in nt:
1,69,159
Flanking exon/introns:
chr1:89653787-89671449|chr1:89694186-89716884
Splice length:
328
Other database IDs:
circBase: mmu_circ_0009061, CIRCpedia: MMU_CIRCpedia_33509, circAtlas: mmu-Agap1_0011
circBase: hsa_circ_0119381, circAtlas: hsa-AGAP1_0007, CIRCpedia: HSA_CIRCpedia_40125
Human Ortholog IDs:
Mature spliced Sequence:
GATTACATGCAGAATGTCCACGGCAAAGAGATAGACCTCTTGAGGACCACTGTGAAGGTGCCGGGGAAGAGGCCGCCCCGAGCCACGTCTGCCTGTGCACCGATCTCCAGTCCCAAAACCAACGGCCTGGCCAAGGACATGAGCAGTTTACACATCTCACCAAATTCAGGGAATGTCACTAGTGCGTCTGGGTCTCAGATGGCAAGCGGCATCAGCCTGGTCTCCTTCAACAGCCGACCCGATGGCATGCACCAGCGCTCCTACTCAGTCTCCAGTGCCGACCAGTGGAGTGACGCTACAGTCATTGCAAACTCAGCCATCAGCAGTG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CACCAGCGCTCCTACTCAG
59.86
GCACCTTCACAGTGGTCCTC
60.6
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CACCAGCGCTCCTACTCAGT
61.6
GCACCTTCACAGTGGTCCTC
60.6
140
PCR template sequence:
AACAGCCGACCCGATGGCATGCACCAGCGCTCCTACTCAGTCTCCAGTGCCGACCAGTGGAGTGACGCTACAGTCATTGCAAACTCAGCCATCAGCAGTGGATTACATGCAGAATGTCCACGGCAAAGAGATAGACCTCTTGAGGACCACTGTGAAGGTGCCGGGGAAGAGGCCGCCCCGAGCCACGTCTGCCTGTGCAC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
4
Interacting miRNAs (#binding sites)
mmu-miR-27b-3p(1), mmu-miR-27a-3p(1), mmu-miR-138-5p(1), mmu-miR-670-5p(1)
siRNAs for circular RNA silencing
Junction sequence
GCCATCAGCAGTGGATTACATGCAGA
siRNA sets
GTAATCCACTGCTGATGGC, TGTAATCCACTGCTGATGG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCAGAP1_328_ORF_1
0.6709
0.251503779
0.658016489
504
ORF sequence:
ATGCAGAATGTCCACGGCAAAGAGATAGACCTCTTGAGGACCACTGTGAAGGTGCCGGGGAAGAGGCCGCCCCGAGCCACGTCTGCCTGTGCACCGATCTCCAGTCCCAAAACCAACGGCCTGGCCAAGGACATGAGCAGTTTACACATCTCACCAAATTCAGGGAATGTCACTAGTGCGTCTGGGTCTCAGATGGCAAGCGGCATCAGCCTGGTCTCCTTCAACAGCCGACCCGATGGCATGCACCAGCGCTCCTACTCAGTCTCCAGTGCCGACCAGTGGAGTGACGCTACAGTCATTGCAAACTCAGCCATCAGCAGTGGATTACATGCAGAATGTCCACGGCAAAGAGATAGACCTCTTGAGGACCACTGTGAAGGTGCCGGGGAAGAGGCCGCCCCGAGCCACGTCTGCCTGTGCACCGATCTCCAGTCCCAAAACCAACGGCCTGGCCAAGGACATGAGCAGTTTACACATCTCACCAAATTCAGGGAATGTCACTAG
Peptide sequence:
MQNVHGKEIDLLRTTVKVPGKRPPRATSACAPISSPKTNGLAKDMSSLHISPNSGNVTSASGSQMASGISLVSFNSRPDGMHQRSYSVSSADQWSDATVIANSAISSGLHAECPRQRDRPLEDHCEGAGEEAAPSHVCLCTDLQSQNQRPGQGHEQFTHLTKFRECH
IRESfinder result
IRESfinder score
0.319785059
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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