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mmu_circDdx1_437
Basic information of circular RNA
PanCircBase ID:
mmu_circDdx1_437
mm39_Chr. Position ID:
chr12|13273793|13279145|-
Gene name:
Ddx1
Transcript:
ENSMUST00000071103.10
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
22,21,20,19,18
Exon/intron offsets:
0,149,1606,3512,5300
Genomic length:
5352
Exon/intron sizes in nt:
73,73,92,147,52
Flanking exon/introns:
chr12:13273719-13273793|chr12:13279145-13279242
Splice length:
437
Other database IDs:
circAtlas: mmu-Ddx1_0011
Human Ortholog IDs:
Mature spliced Sequence:
ACTGATGATGTACACGCAAAGGATAACACAAGACCTGGTGCTAACAGTCCAGAGATGTGGTCTGAAGCTATTAAAATACTGAAGGGGGAGTATGCTGTCCGAGCAATCAAGGAACACAAGATGGATCAAGCAATTATCTTCTGTAGAACTAAAATTGACTGTGATAACTTGGAGCAGTACTTTATGCAGCAAGGAGGAGGACCTGACAAAAAAGGACACCAGTTCTCATGTGTATGTCTTCATGGTGACAGAAAGCCTCATGAGAGAAAGCAAAACTTGGAACGATTTAAGAAAGGAGACGTAAGATTCTTGATTTGCACAGATGTAGCTGCTAGAGGGATTGATATCCATGGCGTTCCTTATGTGATCAACGTCACCCTGCCTGATGAGAAGCAGAATTATGTGCACCGGATCGGCAGAGTGGGACGAGCTGAAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TGTGATCAACGTCACCCTGC
60.6
GGACAGCATACTCCCCCTTC
59.53
175
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GTCACCCTGCCTGATGAGAA
59.38
GGACAGCATACTCCCCCTTC
59.53
165
PCR template sequence:
GGATTGATATCCATGGCGTTCCTTATGTGATCAACGTCACCCTGCCTGATGAGAAGCAGAATTATGTGCACCGGATCGGCAGAGTGGGACGAGCTGAAAGACTGATGATGTACACGCAAAGGATAACACAAGACCTGGTGCTAACAGTCCAGAGATGTGGTCTGAAGCTATTAAAATACTGAAGGGGGAGTATGCTGTCC
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-27b-3p(1), mmu-miR-19b-3p(1), mmu-miR-146a-5p(1), mmu-miR-19a-3p(1), mmu-miR-222-3p(1), mmu-miR-1198-5p(1), mmu-miR-669d-5p(1), mmu-miR-3470b(1), mmu-miR-1904(1), mmu-miR-146b-5p(1)
siRNAs for circular RNA silencing
Junction sequence
GACGAGCTGAAAGACTGATGATGTAC
siRNA sets
TACATCATCAGTCTTTCAG, ATCATCAGTCTTTCAGCTC, ATCAGTCTTTCAGCTCGTC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCDDX1_437_ORF_1
0.9679
0.106800556
0.58143265
465
ORF sequence:
ATGTGGTCTGAAGCTATTAAAATACTGAAGGGGGAGTATGCTGTCCGAGCAATCAAGGAACACAAGATGGATCAAGCAATTATCTTCTGTAGAACTAAAATTGACTGTGATAACTTGGAGCAGTACTTTATGCAGCAAGGAGGAGGACCTGACAAAAAAGGACACCAGTTCTCATGTGTATGTCTTCATGGTGACAGAAAGCCTCATGAGAGAAAGCAAAACTTGGAACGATTTAAGAAAGGAGACGTAAGATTCTTGATTTGCACAGATGTAGCTGCTAGAGGGATTGATATCCATGGCGTTCCTTATGTGATCAACGTCACCCTGCCTGATGAGAAGCAGAATTATGTGCACCGGATCGGCAGAGTGGGACGAGCTGAAAGACTGATGATGTACACGCAAAGGATAACACAAGACCTGGTGCTAACAGTCCAGAGATGTGGTCTGAAGCTATTAAAATACTGA
Peptide sequence:
MWSEAIKILKGEYAVRAIKEHKMDQAIIFCRTKIDCDNLEQYFMQQGGGPDKKGHQFSCVCLHGDRKPHERKQNLERFKKGDVRFLICTDVAARGIDIHGVPYVINVTLPDEKQNYVHRIGRVGRAERLMMYTQRITQDLVLTVQRCGLKLLKY
IRESfinder result
IRESfinder score
0.408936132
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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