top of page
mmu_circArl13b_641
Basic information of circular RNA
PanCircBase ID:
mmu_circArl13b_641
mm39_Chr. Position ID:
chr16|62624199|62633627|-
Gene name:
Arl13b
Transcript:
ENSMUST00000089289.6
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
7,6,5,4
Exon/intron offsets:
0,2705,8012,9322
Genomic length:
9428
Exon/intron sizes in nt:
2,26,10,62,03,106
Flanking exon/introns:
chr16:62623199-62624199|chr16:62633627-62647526
Splice length:
641
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GCTGGCCAACAAGCAAGACAAGGAGGGGGCTTTAGGCGAAGCGGATGTGATTGAGTGTCTCTCGCTGGAGAAGCTGGTCAACGAGCACAAGTGCCTGTGTCAGATCGAACCTTGTTCAGCAGTCTTGGGATATGGAAAGAAAATTGACAAGTCCATTAAAAAGGGGCTTTATTGGCTACTGCATATCATTGCAAAGGACTTTGATGCCTTAAGTGAACGCATCCAGAAAGACACAACTGAACAGCGAGCTCTTGAGGAACAAGAGAAACGTGAGAGGGCTGAACGAGTCCGGAAGTTAAGGGAAGAAAGAGAACGAGAGCAGACGGAACTTGATGGGACCAGTGGTCTGGCTGAGATTGACTCAGGACCAGTTCTTGCGAATCCTTTCCAACCCATTGCAGCTGTAATCATTGAGAATGAAAAGAAGCAGGAAAAAGAGAAAAAGAAGCAGACCGTGGAGAAGGACAGTGATGTTGGTCTCCTAGAACATAAAGTGGAGCCAGAGCAAGCAGCGCCTCAGAGTGAGGCAGATTGCTGCCTCCAAAACCCTGACGAGCGAGTGGTGGACAGTTACAGGGAGGCACTGTCGCAGCAGCTGGACAGTGAGGATGAGCAGGACCAGCGAGGGTCAGAGTCCGGGG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GCGAGTGGTGGACAGTTACA
59.97
TCTCCAGCGAGAGACACTCA
59.96
157
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GGACAGTTACAGGGAGGCAC
60.04
TCTCCAGCGAGAGACACTCA
59.96
148
PCR template sequence:
CAAAACCCTGACGAGCGAGTGGTGGACAGTTACAGGGAGGCACTGTCGCAGCAGCTGGACAGTGAGGATGAGCAGGACCAGCGAGGGTCAGAGTCCGGGGGCTGGCCAACAAGCAAGACAAGGAGGGGGCTTTAGGCGAAGCGGATGTGATTGAGTGTCTCTCGCTGGAGAAGCTGGTCAACGAGCACAAGTGCCTGTGT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
5
Interacting miRNAs (#binding sites)
mmu-miR-216a-5p(1), mmu-miR-149-5p(1), mmu-miR-207(1), mmu-miR-335-3p(1), mmu-miR-338-3p(1)
siRNAs for circular RNA silencing
Junction sequence
TCAGAGTCCGGGGGCTGGCCAACAAG
siRNA sets
CTTGTTGGCCAGCCCCCGG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCARL13B_641_ORF_1
0.9854
-0.07790955
0.041834779
87
ORF sequence:
ATGAGCAGGACCAGCGAGGGTCAGAGTCCGGGGGCTGGCCAACAAGCAAGACAAGGAGGGGGCTTTAGGCGAAGCGGATGTGATTGA
Peptide sequence:
MSRTSEGQSPGAGQQARQGGGFRRSGCD
IRESfinder result
IRESfinder score
0.431808895
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
bottom of page