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mmu_circXrn2_450
Basic information of circular RNA
PanCircBase ID:
mmu_circXrn2_450
mm39_Chr. Position ID:
chr2|146893632|146910775|+
Gene name:
Xrn2
Transcript:
ENSMUST00000028921.6
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
24,25,26,27,28
Exon/intron offsets:
0,9536,9693,11520,17079
Genomic length:
17143
Exon/intron sizes in nt:
57,69,132,128,64
Flanking exon/introns:
chr2:146891982-146893632|chr2:146910775-146916804
Splice length:
450
Other database IDs:
circAtlas: mmu-Xrn2_0035
circBase: hsa_circ_0059606
Human Ortholog IDs:
Mature spliced Sequence:
AACAGTATGTTCCCCTGTGCCCATGTTGCGGGACCTGACACAGAACACTGCAGTCAGTATTAATTTTAAAGATCCACAGTTTGCTGAAGATTATGTTTTTAAAGCTGCAATGCTTCCAGGAGCAAGAAAGCCAGCAACAGTTCTGAAACCTGGTGACTGGGAAAAATCCAGCAATGGGCGGCAATGGAAACCTCAGCTTGGCTTTAACCGGGACCGGCGGCCTGTTCACCTGGACCAGGCAGCCTTTAGAACTTTAGGCCATGTTACACCAAGAGGCTCGGGGACGAGTGTTTATACGAACACTGCACTACCACCTGCCAATTACCAGGGGAACAATTACAGGCCACTGCTGAGAGGTCAAGCTCAGATCCCAAAACTTATGTCAAATATGAGGCCCCAAGATTCCTGGCGAGGCCCTCCTCCTCTTTTCCAGCAGCATAGATTTGAGAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GAGGTCAAGCTCAGATCCCA
58.8
TGCAGTGTTCTGTGTCAGGT
59.46
149
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GAGGTCAAGCTCAGATCCCA
58.8
GTGTTCTGTGTCAGGTCCCG
60.6
145
PCR template sequence:
TGAGAGGTCAAGCTCAGATCCCAAAACTTATGTCAAATATGAGGCCCCAAGATTCCTGGCGAGGCCCTCCTCCTCTTTTCCAGCAGCATAGATTTGAGAGAACAGTATGTTCCCCTGTGCCCATGTTGCGGGACCTGACACAGAACACTGCAGTCAGTATTAATTTTAAAGATCCACAGTTTGCTGAAGATTATGTTTTT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
4
Interacting miRNAs (#binding sites)
mmu-miR-429-3p(1), mmu-miR-200b-3p(1), mmu-miR-200c-3p(1), mmu-miR-670-5p(1)
siRNAs for circular RNA silencing
Junction sequence
ATAGATTTGAGAGAACAGTATGTTCC
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCXRN2_450_ORF_1
0.8669
0.063081261
0.949183544
876
ORF sequence:
ATGTTGCGGGACCTGACACAGAACACTGCAGTCAGTATTAATTTTAAAGATCCACAGTTTGCTGAAGATTATGTTTTTAAAGCTGCAATGCTTCCAGGAGCAAGAAAGCCAGCAACAGTTCTGAAACCTGGTGACTGGGAAAAATCCAGCAATGGGCGGCAATGGAAACCTCAGCTTGGCTTTAACCGGGACCGGCGGCCTGTTCACCTGGACCAGGCAGCCTTTAGAACTTTAGGCCATGTTACACCAAGAGGCTCGGGGACGAGTGTTTATACGAACACTGCACTACCACCTGCCAATTACCAGGGGAACAATTACAGGCCACTGCTGAGAGGTCAAGCTCAGATCCCAAAACTTATGTCAAATATGAGGCCCCAAGATTCCTGGCGAGGCCCTCCTCCTCTTTTCCAGCAGCATAGATTTGAGAGAACAGTATGTTCCCCTGTGCCCATGTTGCGGGACCTGACACAGAACACTGCAGTCAGTATTAATTTTAAAGATCCACAGTTTGCTGAAGATTATGTTTTTAAAGCTGCAATGCTTCCAGGAGCAAGAAAGCCAGCAACAGTTCTGAAACCTGGTGACTGGGAAAAATCCAGCAATGGGCGGCAATGGAAACCTCAGCTTGGCTTTAACCGGGACCGGCGGCCTGTTCACCTGGACCAGGCAGCCTTTAGAACTTTAGGCCATGTTACACCAAGAGGCTCGGGGACGAGTGTTTATACGAACACTGCACTACCACCTGCCAATTACCAGGGGAACAATTACAGGCCACTGCTGAGAGGTCAAGCTCAGATCCCAAAACTTATGTCAAATATGAGGCCCCAAGATTCCTGGCGAGGCCCTCCTCCTCTTTTCCAGCAGCATAGATTTGAG
Peptide sequence:
MLRDLTQNTAVSINFKDPQFAEDYVFKAAMLPGARKPATVLKPGDWEKSSNGRQWKPQLGFNRDRRPVHLDQAAFRTLGHVTPRGSGTSVYTNTALPPANYQGNNYRPLLRGQAQIPKLMSNMRPQDSWRGPPPLFQQHRFERTVCSPVPMLRDLTQNTAVSINFKDPQFAEDYVFKAAMLPGARKPATVLKPGDWEKSSNGRQWKPQLGFNRDRRPVHLDQAAFRTLGHVTPRGSGTSVYTNTALPPANYQGNNYRPLLRGQAQIPKLMSNMRPQDSWRGPPPLFQQHRFE
IRESfinder result
IRESfinder score
0.642214428
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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