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mmu_circAgbl2_1940
Basic information of circular RNA
PanCircBase ID:
mmu_circAgbl2_1940
mm39_Chr. Position ID:
chr2|90621803|90641107|+
Gene name:
Agbl2
Transcript:
ENSMUST00000170320.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
10
Exon/intron indexes:
6,7,8,9,10,11,12,13,14,15
Exon/intron offsets:
0,2413,5976,9577,11582,14339,15839,16518,18488,19181
Genomic length:
19304
Exon/intron sizes in nt:
18,61,08,15,47,83,15,70,00,00,00,00,00,000
Flanking exon/introns:
chr2:90620176-90621803|chr2:90641107-90641600
Splice length:
1940
Other database IDs:
CIRCpedia: MMU_CIRCpedia_33846, circAtlas: mmu-Agbl2_0011
circAtlas: hsa-AGBL2_0027
Human Ortholog IDs:
Mature spliced Sequence:
ACTCACTTCTGCTGAGCTCGCCGCTCCTGAGGACCAGGCAGCTGATTTTTGATGAGCTAGATGAAGCAAGCCCACGGCTTCGAGAACCCCGAGAACTCTTCTCATGTTTCTCTAGCAGAGGGCCGCTGCAGGCTCCAAGATGGCCAATCGAATGTGAGGTCATCAAGGAAAACATTCATCACATTGAGTGGGTTCCACATCAACCAGAATATTTCTACCAACCTACAGGAAGCGAGAAGGTGCCAGAGATTGTGGGAGAGGAGCAAGGTACAGTTGTGTACCAGCTAGATTCAGTGCCTGCAGAAGGCACCTATTTCACTAGTTCCAGAATAGGAGGCAAACGAGGGACCATCAAGGAACTTGCTGTCACACTGCAAGGGCCGGACGACAATACTCTATTGTTTGAGTCAAGGTTTGAGAGCGGGAATCTGCAGAAAGCCGTCAGAGTAGGTATCTATGAGTACGAGCTCACCTTGCGGACTGACCTCTACACGGACAAACACACTCAGTGGTTTTACTTCAGAGTTCAGAACACCAGAAAAGACGCTACCTATCGCTTCACCATCGTCAACTTGCTGAAACCCAAGAGCCTTTACGCAGTAGGCATGAAGCCTCTCATGTACTCTCAGCTGGATGCCACCATCTACAACATCGGCTGGAGGAGAGAGGGCCGTGAAATCAAGTACTACAAGAACAATGTGGACGACGGCCAGCAGCCCTTATACTGCCTCACCTGGACCACTCAGTTTCCTCACGACCAGGACACTTGCTTCTTCGCACACTTTTACCCATACACTTATACTGACTTGCAATGCTATCTCTTGTCAGTAGCAAACAACCCCATCCAGTCTCAGTTCTGCAAGCTCCGAGCCCTATGCAGGAGCCTAGCAGGGAACACTGTCTACCTGCTGACCATCACCAACCCATCCAGGACCCCTCAAGAGGCAGCCGCAAAGAAAGCTGTGGTCTTGAGCGCCCGAGTCCACCCTGGAGAGAGTAACAGCTCCTGGATCATGAACGGCTTTTTGGACTTCATCCTTAGCAACTCTCCCGATGCCCAGCTCCTCAGGGATATCTTTGTCTTCAAGGTGATTCCCATGTTAAACCCAGATGGCGTGATAGTGGGGAACTATCGGTGTTCGCTGGCTGGAAGGGACTTGAACAGGCATTATAAAACCGTTCTTAAGGACTCCTTCCCTTGCATTTGGTACACCAAGAACATGATCAAAAGGCTTCTGGAAGAAAGAGAGGTTCTCTTGTACTGTGATTTCCATGGGCATAGCCGCAAGAACAACATCTTCCTGTATGGCTGTCACAGCAACAACCGCAAGCACTGGCTCCATGAGCGTGTCTTTCCTTTAATGTTGAGCAAGAATGCACCAGACAAGTTCTCTTTCGACAGCTGTAACTTTAAGGTCCAAAAATGCAAAGAAGGAACGGGAAGAGTGGTGATGTGGCGGATGGGCATCATCAACAGCTACACCATGGAGTCTACCTTTGGCGGGTCTACCCTGGGTAGTAAAAGAGACACTCACTTTACCATTGAGGACCTGAAGTCCCTAGGGTATCATGTCTGTGACACTCTTCTGGATTTCTGTGATCCTGACCAAACCAAGTACACACAGTGTCTACAAGAGCTTAAGGAGCTCCTACAACAGGAAATCAACAAAAAGTTGAATAACTTTGGACAAGATATGGATTTAGAAGGAAACTGGAGTGACATTCCTTTGTCTGACATTGAATCCAGCACGAGTGGCTCGGACAGCTCCCTCTCCGATGGCCCTCCCATTCGTCTACTGAACATCGTTGCAGATGAGCCAAATCAGAAGACGGTGTTAAAGAATCCAAAAAAGAAGAGACTTCAGACTAGAAAACAGCGGAATGAGCAGTACCAGAAGAGCTACTTGATGCGGGAGTTAAAGTTAACAGAAAACGCCCCA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
ACAGCGGAATGAGCAGTACC
60.11
AGAGTTCTCGGGGTTCTCGA
59.96
166
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CAGCGGAATGAGCAGTACCA
60.11
AGAGTTCTCGGGGTTCTCGA
59.96
165
PCR template sequence:
GAATCCAAAAAAGAAGAGACTTCAGACTAGAAAACAGCGGAATGAGCAGTACCAGAAGAGCTACTTGATGCGGGAGTTAAAGTTAACAGAAAACGCCCCAACTCACTTCTGCTGAGCTCGCCGCTCCTGAGGACCAGGCAGCTGATTTTTGATGAGCTAGATGAAGCAAGCCCACGGCTTCGAGAACCCCGAGAACTCTT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
12
Interacting miRNAs (#binding sites)
mmu-miR-31-5p(1), mmu-miR-101a-3p(1), mmu-miR-146a-5p(1), mmu-miR-328-3p(1), mmu-miR-138-5p(1), mmu-miR-381-3p(1), mmu-miR-214-3p(1), mmu-miR-351-5p(1), mmu-miR-300-3p(1), mmu-miR-5101(1), mmu-miR-670-5p(1), mmu-miR-574-5p(1)
siRNAs for circular RNA silencing
Junction sequence
AGAAAACGCCCCAACTCACTTCTGCT
siRNA sets
AGCAGAAGTGAGTTGGGGC,GCAGAAGTGAGTTGGGGCG,CAGAAGTGAGTTGGGGCGT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCAGBL2_1940_ORF_1
0.8359
0.269859482
0.999147137
1350
ORF sequence:
ATGAAGCCTCTCATGTACTCTCAGCTGGATGCCACCATCTACAACATCGGCTGGAGGAGAGAGGGCCGTGAAATCAAGTACTACAAGAACAATGTGGACGACGGCCAGCAGCCCTTATACTGCCTCACCTGGACCACTCAGTTTCCTCACGACCAGGACACTTGCTTCTTCGCACACTTTTACCCATACACTTATACTGACTTGCAATGCTATCTCTTGTCAGTAGCAAACAACCCCATCCAGTCTCAGTTCTGCAAGCTCCGAGCCCTATGCAGGAGCCTAGCAGGGAACACTGTCTACCTGCTGACCATCACCAACCCATCCAGGACCCCTCAAGAGGCAGCCGCAAAGAAAGCTGTGGTCTTGAGCGCCCGAGTCCACCCTGGAGAGAGTAACAGCTCCTGGATCATGAACGGCTTTTTGGACTTCATCCTTAGCAACTCTCCCGATGCCCAGCTCCTCAGGGATATCTTTGTCTTCAAGGTGATTCCCATGTTAAACCCAGATGGCGTGATAGTGGGGAACTATCGGTGTTCGCTGGCTGGAAGGGACTTGAACAGGCATTATAAAACCGTTCTTAAGGACTCCTTCCCTTGCATTTGGTACACCAAGAACATGATCAAAAGGCTTCTGGAAGAAAGAGAGGTTCTCTTGTACTGTGATTTCCATGGGCATAGCCGCAAGAACAACATCTTCCTGTATGGCTGTCACAGCAACAACCGCAAGCACTGGCTCCATGAGCGTGTCTTTCCTTTAATGTTGAGCAAGAATGCACCAGACAAGTTCTCTTTCGACAGCTGTAACTTTAAGGTCCAAAAATGCAAAGAAGGAACGGGAAGAGTGGTGATGTGGCGGATGGGCATCATCAACAGCTACACCATGGAGTCTACCTTTGGCGGGTCTACCCTGGGTAGTAAAAGAGACACTCACTTTACCATTGAGGACCTGAAGTCCCTAGGGTATCATGTCTGTGACACTCTTCTGGATTTCTGTGATCCTGACCAAACCAAGTACACACAGTGTCTACAAGAGCTTAAGGAGCTCCTACAACAGGAAATCAACAAAAAGTTGAATAACTTTGGACAAGATATGGATTTAGAAGGAAACTGGAGTGACATTCCTTTGTCTGACATTGAATCCAGCACGAGTGGCTCGGACAGCTCCCTCTCCGATGGCCCTCCCATTCGTCTACTGAACATCGTTGCAGATGAGCCAAATCAGAAGACGGTGTTAAAGAATCCAAAAAAGAAGAGACTTCAGACTAGAAAACAGCGGAATGAGCAGTACCAGAAGAGCTACTTGATGCGGGAGTTAAAGTTAACAGAAAACGCCCCAACTCACTTCTGCTGA
Peptide sequence:
MKPLMYSQLDATIYNIGWRREGREIKYYKNNVDDGQQPLYCLTWTTQFPHDQDTCFFAHFYPYTYTDLQCYLLSVANNPIQSQFCKLRALCRSLAGNTVYLLTITNPSRTPQEAAAKKAVVLSARVHPGESNSSWIMNGFLDFILSNSPDAQLLRDIFVFKVIPMLNPDGVIVGNYRCSLAGRDLNRHYKTVLKDSFPCIWYTKNMIKRLLEEREVLLYCDFHGHSRKNNIFLYGCHSNNRKHWLHERVFPLMLSKNAPDKFSFDSCNFKVQKCKEGTGRVVMWRMGIINSYTMESTFGGSTLGSKRDTHFTIEDLKSLGYHVCDTLLDFCDPDQTKYTQCLQELKELLQQEINKKLNNFGQDMDLEGNWSDIPLSDIESSTSGSDSSLSDGPPIRLLNIVADEPNQKTVLKNPKKKRLQTRKQRNEQYQKSYLMRELKLTENAPTHFC
IRESfinder result
IRESfinder score
0.578089281
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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