top of page
mmu_circSetd2_691
Basic information of circular RNA
PanCircBase ID:
mmu_circSetd2_691
mm39_Chr. Position ID:
chr9|110385355|110398879|+
Gene name:
Setd2
Transcript:
ENSMUST00000153838.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
6
Exon/intron indexes:
5,6,7,8,9,10
Exon/intron offsets:
0,4828,6649,8283,11420,13389
Genomic length:
13524
Exon/intron sizes in nt:
1,29,12,47,89,81,27,130
Flanking exon/introns:
chr9:110382302-110385355|chr9:110398879-110401014
Splice length:
691
Other database IDs:
CIRCpedia: MMU_CIRCpedia_2911, circAtlas: mmu-Setd2_0044
Human Ortholog IDs:
Mature spliced Sequence:
TTCCTCTCGATGTCCAAATGGAGATTACTGTTCAAACAGACGGTTTCAGAGAAAACAGCATGCAGATGTAGAAGTCATACTTACAGAAAAGAAAGGCTGGGGCTTAAGGGCTGCTAAGGATCTTCCTTCGAACACCTTTGTCCTGGAATACTGTGGAGAGGTACTTGATCATAAAGAGTTTAAAGCTCGGGTGAAAGAATATGCACGGAACAAAAACATCCACTACTACTTCATGGCCCTGAAAAATGACGAGATAATAGATGCCACTCAAAAAGGGAATTGCTCTCGTTTCATGAATCATAGCTGTGAACCAAACTGTGAAACCCAGAAATGGACTGTGAATGGACAGCTGAGGGTTGGATTTTTTACCACCAAACTAGTTCCTTCAGGCTCAGAATTAACTTTTGACTACCAGTTCCAAAGATATGGCAAAGAAGCTCAGAAGTGTTTCTGTGGGTCAGCCAACTGCCGGGGCTACTTGGGAGGAGAAAACAGAGTCAGTATCAGAGCTGCAGGAGGGAAGATGAAAAAGGAACGCTCTCGAAAGAAGGATTCAGTGGATGGAGAACTTGAAGCACTGATGGAAAATGGTGAAGGCCTCTCTGATAAGAACCAGGTTCTTAGTTTATCCCGGCTCATGGTTAGAATTGAAACTTTGGAACAGAAACTTACCTGTCTTAAGCTCATTCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AGTTTATCCCGGCTCATGGT
58.79
TGACTTCTACATCTGCATGCTGT
60.06
146
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TCCCGGCTCATGGTTAGAAT
58.49
TGACTTCTACATCTGCATGCTGT
60.06
140
PCR template sequence:
TGAAGGCCTCTCTGATAAGAACCAGGTTCTTAGTTTATCCCGGCTCATGGTTAGAATTGAAACTTTGGAACAGAAACTTACCTGTCTTAAGCTCATTCAGTTCCTCTCGATGTCCAAATGGAGATTACTGTTCAAACAGACGGTTTCAGAGAAAACAGCATGCAGATGTAGAAGTCATACTTACAGAAAAGAAAGGCTGG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
6
Interacting miRNAs (#binding sites)
mmu-miR-136-5p(1), mmu-miR-26b-5p(1), mmu-miR-382-3p(1), mmu-miR-29b-2-5p(1), mmu-miR-673-5p(1), mmu-miR-335-3p(1)
siRNAs for circular RNA silencing
Junction sequence
TAAGCTCATTCAGTTCCTCTCGATGT
siRNA sets
ATCGAGAGGAACTGAATGA, CGAGAGGAACTGAATGAGC, TCGAGAGGAACTGAATGAG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSETD2_691_ORF_1
0.518
0.086915879
0.855719644
795
ORF sequence:
ATGGTGAAGGCCTCTCTGATAAGAACCAGGTTCTTAGTTTATCCCGGCTCATGGTTAGAATTGAAACTTTGGAACAGAAACTTACCTGTCTTAAGCTCATTCAGTTCCTCTCGATGTCCAAATGGAGATTACTGTTCAAACAGACGGTTTCAGAGAAAACAGCATGCAGATGTAGAAGTCATACTTACAGAAAAGAAAGGCTGGGGCTTAAGGGCTGCTAAGGATCTTCCTTCGAACACCTTTGTCCTGGAATACTGTGGAGAGGTACTTGATCATAAAGAGTTTAAAGCTCGGGTGAAAGAATATGCACGGAACAAAAACATCCACTACTACTTCATGGCCCTGAAAAATGACGAGATAATAGATGCCACTCAAAAAGGGAATTGCTCTCGTTTCATGAATCATAGCTGTGAACCAAACTGTGAAACCCAGAAATGGACTGTGAATGGACAGCTGAGGGTTGGATTTTTTACCACCAAACTAGTTCCTTCAGGCTCAGAATTAACTTTTGACTACCAGTTCCAAAGATATGGCAAAGAAGCTCAGAAGTGTTTCTGTGGGTCAGCCAACTGCCGGGGCTACTTGGGAGGAGAAAACAGAGTCAGTATCAGAGCTGCAGGAGGGAAGATGAAAAAGGAACGCTCTCGAAAGAAGGATTCAGTGGATGGAGAACTTGAAGCACTGATGGAAAATGGTGAAGGCCTCTCTGATAAGAACCAGGTTCTTAGTTTATCCCGGCTCATGGTTAGAATTGAAACTTTGGAACAGAAACTTACCTGTCTTAAGCTCATTCAG
Peptide sequence:
MVKASLIRTRFLVYPGSWLELKLWNRNLPVLSSFSSSRCPNGDYCSNRRFQRKQHADVEVILTEKKGWGLRAAKDLPSNTFVLEYCGEVLDHKEFKARVKEYARNKNIHYYFMALKNDEIIDATQKGNCSRFMNHSCEPNCETQKWTVNGQLRVGFFTTKLVPSGSELTFDYQFQRYGKEAQKCFCGSANCRGYLGGENRVSIRAAGGKMKKERSRKKDSVDGELEALMENGEGLSDKNQVLSLSRLMVRIETLEQKLTCLKLIQ
IRESfinder result
IRESfinder score
0.592469081
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
bottom of page