top of page
mmu_circSetx_541
Basic information of circular RNA
PanCircBase ID:
mmu_circSetx_541
mm39_Chr. Position ID:
chr2|29020191|29029451|+
Gene name:
Setx
Transcript:
ENSMUST00000061578.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
4,5,6
Exon/intron offsets:
0,3742,9040
Genomic length:
9260
Exon/intron sizes in nt:
21,11,10,220
Flanking exon/introns:
chr2:29017075-29020191|chr2:29029451-29030280
Splice length:
541
Other database IDs:
CIRCpedia: MMU_CIRCpedia_15356, circAtlas: mmu-Setx_0026
circAtlas: hsa-SCAF8_0001
Human Ortholog IDs:
Mature spliced Sequence:
GTTTTATGGGAGCTAGAAACCTTACGCCTCGTAAGTCACTTTGAGAAGTCCATGAAGGCAGAAGCTGAAGATGACGATGATTTATATATAGTAGACAACAATGGAGAGGAACAGCTGTTTGACTGTAGTGGCCAAGATTTTGAAAATAAGCTTCGAGTTCCTCTTTTTGAAATACTGAAGTACCCTTACTTGCTTCTGCATGAGCGTGTTAATGAACTGTGTGTGGAAGCGCTTTGCCGAATGGAACAAAACAATTGCTCCTTTCAGGTTTTTGACAAATATCCAGGCATCTATTTGTTTTTGGTTCATCCCAATGAAATGGTTCGGCGATGGGCTATTCTGACTGCAAGAAACCTGGGGAAGGTGGACAGAGATGACTATTATGACTTACAGGAAGTTTTAACTTGCCTTTTTAAAGTCATTGAGCTGGGGCTTTTGGAAAGTCCAGACATTTACACATCTTCTGTGCTTGAAAAAGGCAAACTGATCCTTTTGCCTGCACACATGTATGATACTACCAACTACAAAAACTATTGGCTAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TCTTCTGTGCTTGAAAAAGGCA
58.98
TCAGCTTCTGCCTTCATGGA
59.01
150
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TCTTCTGTGCTTGAAAAAGGCA
58.98
AGCTTCTGCCTTCATGGACT
59.01
148
PCR template sequence:
AGTCCAGACATTTACACATCTTCTGTGCTTGAAAAAGGCAAACTGATCCTTTTGCCTGCACACATGTATGATACTACCAACTACAAAAACTATTGGCTAGGTTTTATGGGAGCTAGAAACCTTACGCCTCGTAAGTCACTTTGAGAAGTCCATGAAGGCAGAAGCTGAAGATGACGATGATTTATATATAGTAGACAACA
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-17-5p(1), mmu-miR-136-5p(1), mmu-miR-1187(1), mmu-miR-7a-1-3p(1)
siRNAs for circular RNA silencing
Junction sequence
AACTATTGGCTAGGTTTTATGGGAGC
siRNA sets
GCTCCCATAAAACCTAGCC, TAAAACCTAGCCAATAGTT, CTCCCATAAAACCTAGCCA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSETX_541_ORF_1
1.1083
0.068407259
0.716234511
534
ORF sequence:
ATGAAGGCAGAAGCTGAAGATGACGATGATTTATATATAGTAGACAACAATGGAGAGGAACAGCTGTTTGACTGTAGTGGCCAAGATTTTGAAAATAAGCTTCGAGTTCCTCTTTTTGAAATACTGAAGTACCCTTACTTGCTTCTGCATGAGCGTGTTAATGAACTGTGTGTGGAAGCGCTTTGCCGAATGGAACAAAACAATTGCTCCTTTCAGGTTTTTGACAAATATCCAGGCATCTATTTGTTTTTGGTTCATCCCAATGAAATGGTTCGGCGATGGGCTATTCTGACTGCAAGAAACCTGGGGAAGGTGGACAGAGATGACTATTATGACTTACAGGAAGTTTTAACTTGCCTTTTTAAAGTCATTGAGCTGGGGCTTTTGGAAAGTCCAGACATTTACACATCTTCTGTGCTTGAAAAAGGCAAACTGATCCTTTTGCCTGCACACATGTATGATACTACCAACTACAAAAACTATTGGCTAGGTTTTATGGGAGCTAGAAACCTTACGCCTCGTAAGTCACTTTGA
Peptide sequence:
MKAEAEDDDDLYIVDNNGEEQLFDCSGQDFENKLRVPLFEILKYPYLLLHERVNELCVEALCRMEQNNCSFQVFDKYPGIYLFLVHPNEMVRRWAILTARNLGKVDRDDYYDLQEVLTCLFKVIELGLLESPDIYTSSVLEKGKLILLPAHMYDTTNYKNYWLGFMGARNLTPRKSL
IRESfinder result
IRESfinder score
0.715368493
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
bottom of page