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mmu_circAmotl1_1367
Basic information of circular RNA
PanCircBase ID:
mmu_circAmotl1_1367
mm39_Chr. Position ID:
chr9|14461687|14486735|-
Gene name:
Amotl1
Transcript:
ENSMUST00000013220.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
8
Exon/intron indexes:
11,10,9,8,7,6,5,4
Exon/intron offsets:
0,1230,5182,8067,11683,21231,22283,24759
Genomic length:
25048
Exon/intron sizes in nt:
23,01,26,19,11,50,14,60,00,00,000
Flanking exon/introns:
chr9:14460102-14461687|chr9:14486735-14504049
Splice length:
1367
Other database IDs:
CIRCpedia: HSA_CIRCpedia_75126
Human Ortholog IDs:
Mature spliced Sequence:
CCGGCCCTGCCAGCTGCCTTTTCCATCTACGGTGCAGCAGCATAGCCCCATGTCCTCTCAGACCTCCTCCATCGGTGGTACTCTGCACTCCGTCTCCCTGCCTCTTCCACTTCCCATAAGCCTGGCGGCTTCACAGCCCCTACCAGCCTCCCCCAACCAGCAGCTTGGACCGGATGCCTTTGCGATTGTGGAGCGAGCCCAGCAAATGGTAGAGATCCTGACAGAGGAGAACCGTGTGCTTCACCAGGAGCTTCAGGGCTGCTATGACAACGCTGACAAGCTCCACAAGTTTGAAAAAGAGCTGCAGAGTATTTCGGAGGCCTACGAGAGCCTGGTCAAGTCCACCACCAAGCGTGAGTCTCTGGACAAGGCAATGAGAACCAAGCTCGAAGGCGAGATAAGGAGACTTCATGACTTCAACAGAGATCTCCGAGATCGACTGGAGACAGCCAACAGGCAGCTGTCCAGCAGGGAATACGATGGGCATGAAGACAAAGCTGCAGAGAGCCATTACGTGTCCCAGAACAAAGAATTCTTGAAGGAAAAGGAAAAGTTGGAAATGGAGTTGGCAGCAGTGCGTACGGCAAGTGAGGACCATCGGAGGCACATCGAGATCCTGGACCAGGCTTTGAGCAATGCGCAGGCTAGAGTGATCAAACTGGAGGAAGAGTTACGAGAGAAGCAAGCCTATGTGGAAAAGGTGGAGAAGCTGCAGCAGGCCCTGACCCAGCTGCAGTCAGCGTGCGAGAAGCGAGGGCAGATGGAACGCAGGTTGCGGACCTGGCTGGAGAGGGAGCTAGACGCTCTGAGGACACAGCAGAAACATGGCACAGGCCCTCCAGTCAGTCTCCCAGAATGTAATGCTCCTGCCCTCATGGAGCTGGTGAGGGAGAAGGAGGAGCGGATCCTCGCCTTGGAGGCCGACATGACCAAGTGGGAGCAGAAGTACCTGGAAGAGAGCACCATCCGGCACTTTGCCATGAGCGCAGCTGCCGCTGCCACAGCCGAGAGGGACACCACCATCAGCAACCACTCGAGGAATGGCAGCTATGGGGAGAGCTCCCTGGAGGCCCACATCTGGCCAGAGGAAGAAGAAGTGGTGCAGGCCAACAGGAGGTGTCAGGACATGGAGTACACTATTAAAAACCTCCATGCCAAAATCATAGAGAAGGATGCCATGATAAAGGTCCTGCAGCAGCGATCCCGTAAGGATGCTGGGAAGACGGACTCTGCCAGCCTGAGGCCTGCCCGCTCTGTCCCATCCATCGCTGCGGCCACTGGGACACATTCTCGCCAGACTTCTCTTACCAGCAGCCAGCTGACAGAAGAGAAAAAGGAAGAGAAGACGACCTGGAAAGGGAGTATAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TTCTCTTACCAGCAGCCAGC
60.04
CCGATGGAGGAGGTCTGAGA
60.11
143
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GGACACATTCTCGCCAGACT
59.75
GAGAGGACATGGGGCTATGC
59.96
146
PCR template sequence:
GCTGCGGCCACTGGGACACATTCTCGCCAGACTTCTCTTACCAGCAGCCAGCTGACAGAAGAGAAAAAGGAAGAGAAGACGACCTGGAAAGGGAGTATAGCCGGCCCTGCCAGCTGCCTTTTCCATCTACGGTGCAGCAGCATAGCCCCATGTCCTCTCAGACCTCCTCCATCGGTGGTACTCTGCACTCCGTCTCCCTG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
10
Interacting miRNAs (#binding sites)
mmu-miR-20b-5p(1), mmu-miR-93-5p(1), mmu-miR-20a-5p(1), mmu-miR-106b-5p(1), mmu-miR-709(1), mmu-miR-22-3p(1), mmu-miR-370-3p(1), mmu-miR-666-5p(1), mmu-miR-207(1), mmu-miR-1904(1)
siRNAs for circular RNA silencing
Junction sequence
AAAGGGAGTATAGCCGGCCCTGCCAG
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCAMOTL1_1367_ORF_1
1.2207
0.421284554
0.999883253
1437
ORF sequence:
ATGTCCTCTCAGACCTCCTCCATCGGTGGTACTCTGCACTCCGTCTCCCTGCCTCTTCCACTTCCCATAAGCCTGGCGGCTTCACAGCCCCTACCAGCCTCCCCCAACCAGCAGCTTGGACCGGATGCCTTTGCGATTGTGGAGCGAGCCCAGCAAATGGTAGAGATCCTGACAGAGGAGAACCGTGTGCTTCACCAGGAGCTTCAGGGCTGCTATGACAACGCTGACAAGCTCCACAAGTTTGAAAAAGAGCTGCAGAGTATTTCGGAGGCCTACGAGAGCCTGGTCAAGTCCACCACCAAGCGTGAGTCTCTGGACAAGGCAATGAGAACCAAGCTCGAAGGCGAGATAAGGAGACTTCATGACTTCAACAGAGATCTCCGAGATCGACTGGAGACAGCCAACAGGCAGCTGTCCAGCAGGGAATACGATGGGCATGAAGACAAAGCTGCAGAGAGCCATTACGTGTCCCAGAACAAAGAATTCTTGAAGGAAAAGGAAAAGTTGGAAATGGAGTTGGCAGCAGTGCGTACGGCAAGTGAGGACCATCGGAGGCACATCGAGATCCTGGACCAGGCTTTGAGCAATGCGCAGGCTAGAGTGATCAAACTGGAGGAAGAGTTACGAGAGAAGCAAGCCTATGTGGAAAAGGTGGAGAAGCTGCAGCAGGCCCTGACCCAGCTGCAGTCAGCGTGCGAGAAGCGAGGGCAGATGGAACGCAGGTTGCGGACCTGGCTGGAGAGGGAGCTAGACGCTCTGAGGACACAGCAGAAACATGGCACAGGCCCTCCAGTCAGTCTCCCAGAATGTAATGCTCCTGCCCTCATGGAGCTGGTGAGGGAGAAGGAGGAGCGGATCCTCGCCTTGGAGGCCGACATGACCAAGTGGGAGCAGAAGTACCTGGAAGAGAGCACCATCCGGCACTTTGCCATGAGCGCAGCTGCCGCTGCCACAGCCGAGAGGGACACCACCATCAGCAACCACTCGAGGAATGGCAGCTATGGGGAGAGCTCCCTGGAGGCCCACATCTGGCCAGAGGAAGAAGAAGTGGTGCAGGCCAACAGGAGGTGTCAGGACATGGAGTACACTATTAAAAACCTCCATGCCAAAATCATAGAGAAGGATGCCATGATAAAGGTCCTGCAGCAGCGATCCCGTAAGGATGCTGGGAAGACGGACTCTGCCAGCCTGAGGCCTGCCCGCTCTGTCCCATCCATCGCTGCGGCCACTGGGACACATTCTCGCCAGACTTCTCTTACCAGCAGCCAGCTGACAGAAGAGAAAAAGGAAGAGAAGACGACCTGGAAAGGGAGTATAGCCGGCCCTGCCAGCTGCCTTTTCCATCTACGGTGCAGCAGCATAGCCCCATGTCCTCTCAGACCTCCTCCATCGGTGGTACTCTGCACTCCGTCTCCCTGCCTCTTCCACTTCCCATAA
Peptide sequence:
MSSQTSSIGGTLHSVSLPLPLPISLAASQPLPASPNQQLGPDAFAIVERAQQMVEILTEENRVLHQELQGCYDNADKLHKFEKELQSISEAYESLVKSTTKRESLDKAMRTKLEGEIRRLHDFNRDLRDRLETANRQLSSREYDGHEDKAAESHYVSQNKEFLKEKEKLEMELAAVRTASEDHRRHIEILDQALSNAQARVIKLEEELREKQAYVEKVEKLQQALTQLQSACEKRGQMERRLRTWLERELDALRTQQKHGTGPPVSLPECNAPALMELVREKEERILALEADMTKWEQKYLEESTIRHFAMSAAAAATAERDTTISNHSRNGSYGESSLEAHIWPEEEEVVQANRRCQDMEYTIKNLHAKIIEKDAMIKVLQQRSRKDAGKTDSASLRPARSVPSIAAATGTHSRQTSLTSSQLTEEKKEEKTTWKGSIAGPASCLFHLRCSSIAPCPLRPPPSVVLCTPSPCLFHFP
IRESfinder result
IRESfinder score
0.228884596
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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