top of page
mmu_circAldh18a1_839
Basic information of circular RNA
PanCircBase ID:
mmu_circAldh18a1_839
mm39_Chr. Position ID:
chr19|40558911|40568520|-
Gene name:
Aldh18a1
Transcript:
ENSMUST00000176939.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
6
Exon/intron indexes:
9,8,7,6,5,4
Exon/intron offsets:
0,3303,3749,7110,7304,9394
Genomic length:
9609
Exon/intron sizes in nt:
12,59,11,53,10,51,50,200
Flanking exon/introns:
chr19:40557621-40558911|chr19:40568520-40573933
Splice length:
839
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
ATCGTGTCCAGCCCTCAGCTATTAGACATGTTCGTTCTTGGAGCAACATCCCCTTTATCACGGTACCCCTCAGTCGTGCCCACGGCAAGCCCTTTGCCCACCGAAGTGAGCTGAAGCACGCCAAGAGAATTGTAGTGAAACTCGGCAGTGCCGTGGTGACCAGAGGAGATGAGTGTGGCCTGGCACTGGGACGCCTGGCATCTATTGTTGAACAGGTCTCGGTGCTGCAGAATCAGGGCCGAGAGATGATGCTGGTGACCAGTGGAGCCGTCGCCTTCGGCAAACAGCGCCTGCGCCATGAGATCCTTCTGTCTCAGAGCGTGCGGCAAGCCCTGCACTCAGGACAGAACCATCTGAAGGAGATGGCAATTCCGGTCTTAGAGGCCCGAGCCTGTGCAGCTGCTGGACAGAGTGGACTGATGGCCTTGTACGAGGCCATGTTTACACAGTACAGCATCTGTGCTGCCCAGATCTTGGTGACCAACCTGGATTTCCACGACGAGCAGAAGCGCAGAAATCTCAACGGTACCCTCCACGAGCTGCTCCGCATGAACATCGTCCCCATCGTCAACACAAACGATGCCGTCGTCCCTCCAGCCGAGCCCAACAGTGATCTTCAGGGGGTGATTAGTGTTAAGGATAATGATAGCCTGGCTGCCCGGCTGGCCGTGGAGATGAAAACCGACCTCTTGATTGTCCTCTCGGACGTAGAAGGCCTCTTTGACAGCCCCCCAGGCTCAGATGATGCAAAGCTCATTGATATATTCTATCCGGGAGATCAGCAGTCTGTGACATTTGGAACCAAGTCTAGAGTGGGCCTAGGGGGCATGGAAGCCAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TATCCGGGAGATCAGCAGTCT
59.85
GGGTACCGTGATAAAGGGGA
58.5
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TCTATCCGGGAGATCAGCAGT
59.85
GGGTACCGTGATAAAGGGGA
58.5
142
PCR template sequence:
AGATGATGCAAAGCTCATTGATATATTCTATCCGGGAGATCAGCAGTCTGTGACATTTGGAACCAAGTCTAGAGTGGGCCTAGGGGGCATGGAAGCCAAGATCGTGTCCAGCCCTCAGCTATTAGACATGTTCGTTCTTGGAGCAACATCCCCTTTATCACGGTACCCCTCAGTCGTGCCCACGGCAAGCCCTTTGCCCA
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-30e-5p(1), mmu-miR-30a-5p(1), mmu-miR-30d-5p(1), mmu-miR-351-5p(1), mmu-miR-5101(1), mmu-miR-484(1), mmu-miR-3470b(1), mmu-miR-1904(1), mmu-miR-338-3p(1)
siRNAs for circular RNA silencing
Junction sequence
CATGGAAGCCAAGATCGTGTCCAGCC
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCALDH18A1_839_ORF_1
1.1414
0.436837124
0.976693986
708
ORF sequence:
ATGATGCTGGTGACCAGTGGAGCCGTCGCCTTCGGCAAACAGCGCCTGCGCCATGAGATCCTTCTGTCTCAGAGCGTGCGGCAAGCCCTGCACTCAGGACAGAACCATCTGAAGGAGATGGCAATTCCGGTCTTAGAGGCCCGAGCCTGTGCAGCTGCTGGACAGAGTGGACTGATGGCCTTGTACGAGGCCATGTTTACACAGTACAGCATCTGTGCTGCCCAGATCTTGGTGACCAACCTGGATTTCCACGACGAGCAGAAGCGCAGAAATCTCAACGGTACCCTCCACGAGCTGCTCCGCATGAACATCGTCCCCATCGTCAACACAAACGATGCCGTCGTCCCTCCAGCCGAGCCCAACAGTGATCTTCAGGGGGTGATTAGTGTTAAGGATAATGATAGCCTGGCTGCCCGGCTGGCCGTGGAGATGAAAACCGACCTCTTGATTGTCCTCTCGGACGTAGAAGGCCTCTTTGACAGCCCCCCAGGCTCAGATGATGCAAAGCTCATTGATATATTCTATCCGGGAGATCAGCAGTCTGTGACATTTGGAACCAAGTCTAGAGTGGGCCTAGGGGGCATGGAAGCCAAGATCGTGTCCAGCCCTCAGCTATTAGACATGTTCGTTCTTGGAGCAACATCCCCTTTATCACGGTACCCCTCAGTCGTGCCCACGGCAAGCCCTTTGCCCACCGAAGTGAGCTGA
Peptide sequence:
MMLVTSGAVAFGKQRLRHEILLSQSVRQALHSGQNHLKEMAIPVLEARACAAAGQSGLMALYEAMFTQYSICAAQILVTNLDFHDEQKRRNLNGTLHELLRMNIVPIVNTNDAVVPPAEPNSDLQGVISVKDNDSLAARLAVEMKTDLLIVLSDVEGLFDSPPGSDDAKLIDIFYPGDQQSVTFGTKSRVGLGGMEAKIVSSPQLLDMFVLGATSPLSRYPSVVPTASPLPTEVS
IRESfinder result
IRESfinder score
0.343573263
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
bottom of page