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mmu_circSetx_375
Basic information of circular RNA
PanCircBase ID:
mmu_circSetx_375
mm39_Chr. Position ID:
chr2|29048852|29051877|+
Gene name:
Setx
Transcript:
ENSMUST00000061578.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
15,16,17
Exon/intron offsets:
0,2631,2909
Genomic length:
3025
Exon/intron sizes in nt:
15,71,02,116
Flanking exon/introns:
chr2:29048277-29048852|chr2:29051877-29052989
Splice length:
375
Other database IDs:
circAtlas: mmu-Setx_0013
Human Ortholog IDs:
Mature spliced Sequence:
AACCAGAGGAAGGGCCATTCAGATGAAAATTTCAATGCCAAAATCAAACAAAATCGAGTCCTCGTGTGTGCACCTTCCAATGCGGCGGTTGATGAACTTATGAAAAAAATTATCCTCGAATTTAAAGAAAAATGTAAAGACAAGAAGAATCCTTTGGGAAACTGTGGAGATATAAATTTAGTACGACTAGGTCCAGAAAAGTCTATTAATACAGAGGTCTTAAAATTCAGTTTGGACAGCCAAGTCAACCATAGAATGAAAAAAGACTTGCCTTCTCATATTCAAGAAATGCTTAGAAGAAAAGAAATTCTAGATGCTCAACTTGATGAGCTTTCTCGTCAGCGAGCTCTGTGCCGAGGTGGGCGGGAGATGCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
ATGAGCTTTCTCGTCAGCGA
59.47
TAAGTTCATCAACCGCCGCA
60.32
150
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
ATGAGCTTTCTCGTCAGCGA
59.47
GTTCATCAACCGCCGCATTG
60.8
147
PCR template sequence:
TCATATTCAAGAAATGCTTAGAAGAAAAGAAATTCTAGATGCTCAACTTGATGAGCTTTCTCGTCAGCGAGCTCTGTGCCGAGGTGGGCGGGAGATGCAGAACCAGAGGAAGGGCCATTCAGATGAAAATTTCAATGCCAAAATCAAACAAAATCGAGTCCTCGTGTGTGCACCTTCCAATGCGGCGGTTGATGAACTTA
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-335-3p(2), mmu-miR-18a-5p(1), mmu-miR-328-3p(1), mmu-miR-5101(1)
siRNAs for circular RNA silencing
Junction sequence
GCGGGAGATGCAGAACCAGAGGAAGG
siRNA sets
TTCCTCTGGTTCTGCATCT,CTCTGGTTCTGCATCTCCC,TCTGGTTCTGCATCTCCCG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSETX_375_ORF_1
0.9454
0.049426294
0.801766668
651
ORF sequence:
ATGAAAAAAATTATCCTCGAATTTAAAGAAAAATGTAAAGACAAGAAGAATCCTTTGGGAAACTGTGGAGATATAAATTTAGTACGACTAGGTCCAGAAAAGTCTATTAATACAGAGGTCTTAAAATTCAGTTTGGACAGCCAAGTCAACCATAGAATGAAAAAAGACTTGCCTTCTCATATTCAAGAAATGCTTAGAAGAAAAGAAATTCTAGATGCTCAACTTGATGAGCTTTCTCGTCAGCGAGCTCTGTGCCGAGGTGGGCGGGAGATGCAGAACCAGAGGAAGGGCCATTCAGATGAAAATTTCAATGCCAAAATCAAACAAAATCGAGTCCTCGTGTGTGCACCTTCCAATGCGGCGGTTGATGAACTTATGAAAAAAATTATCCTCGAATTTAAAGAAAAATGTAAAGACAAGAAGAATCCTTTGGGAAACTGTGGAGATATAAATTTAGTACGACTAGGTCCAGAAAAGTCTATTAATACAGAGGTCTTAAAATTCAGTTTGGACAGCCAAGTCAACCATAGAATGAAAAAAGACTTGCCTTCTCATATTCAAGAAATGCTTAGAAGAAAAGAAATTCTAGATGCTCAACTTGATGAGCTTTCTCGTCAGCGAGCTCTGTGCCGAGGTGGGCGGGAGATGCAG
Peptide sequence:
MKKIILEFKEKCKDKKNPLGNCGDINLVRLGPEKSINTEVLKFSLDSQVNHRMKKDLPSHIQEMLRRKEILDAQLDELSRQRALCRGGREMQNQRKGHSDENFNAKIKQNRVLVCAPSNAAVDELMKKIILEFKEKCKDKKNPLGNCGDINLVRLGPEKSINTEVLKFSLDSQVNHRMKKDLPSHIQEMLRRKEILDAQLDELSRQRALCRGGREMQ
IRESfinder result
IRESfinder score
0.569563677
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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