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mmu_circSynrg_349
Basic information of circular RNA
PanCircBase ID:
mmu_circSynrg_349
mm39_Chr. Position ID:
chr11|83869745|83873133|+
Gene name:
Synrg
Transcript:
ENSMUST00000049714.15
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
4,5,6
Exon/intron offsets:
0,2497,3276
Genomic length:
3388
Exon/intron sizes in nt:
13,11,06,112
Flanking exon/introns:
chr11:83868027-83869745|chr11:83873133-83877639
Splice length:
349
Other database IDs:
circBase: hsa_circ_0106731, circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_20417
Human Ortholog IDs:
Mature spliced Sequence:
GCAGGAATACCAATGGGGCCAATGCCAGCAGCGGGTGTGCCTTTCCTGGGTCAGCCACCTTTCTTGAGCATGCGTCCTGCAGGCCCACAGTACACTCCAGACATGCAGAAGCAGTTTGCGGAAGAGCAACAAAAACGATTTGAACAACAACAAAAGCTCTTAGAAGAAGAAAGAAAAAGACGTCAGTTTGAAGAGCAAAAGCAAAAGCTCAGACTTCTCAGCAGCGTGAAGCCCAAGACAGGAGAGAAGAACAGAGACGATGCTTTGGAAGCCATAAAAGGAAACTTGGATGGGTTTTCCAGAGATGCTAAGATGCACCCCACTCCAGCATCACATCCAAAGAAACAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TGCTAAGATGCACCCCACTC
59.75
TGGAGTGTACTGTGGGCCT
60.15
143
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TGCTAAGATGCACCCCACTC
59.75
CTGGAGTGTACTGTGGGCCT
61.19
144
PCR template sequence:
AACAGAGACGATGCTTTGGAAGCCATAAAAGGAAACTTGGATGGGTTTTCCAGAGATGCTAAGATGCACCCCACTCCAGCATCACATCCAAAGAAACAAGGCAGGAATACCAATGGGGCCAATGCCAGCAGCGGGTGTGCCTTTCCTGGGTCAGCCACCTTTCTTGAGCATGCGTCCTGCAGGCCCACAGTACACTCCAG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
2
Interacting miRNAs (#binding sites)
mmu-miR-122-5p(1), mmu-miR-342-5p(1)
siRNAs for circular RNA silencing
Junction sequence
CCAAAGAAACAAGGCAGGAATACCAA
siRNA sets
GTATTCCTGCCTTGTTTCT, TTCCTGCCTTGTTTCTTTG, TATTCCTGCCTTGTTTCTT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSYNRG_349_ORF_1
0.7557
0.105364993
0.510126053
480
ORF sequence:
ATGGGGCCAATGCCAGCAGCGGGTGTGCCTTTCCTGGGTCAGCCACCTTTCTTGAGCATGCGTCCTGCAGGCCCACAGTACACTCCAGACATGCAGAAGCAGTTTGCGGAAGAGCAACAAAAACGATTTGAACAACAACAAAAGCTCTTAGAAGAAGAAAGAAAAAGACGTCAGTTTGAAGAGCAAAAGCAAAAGCTCAGACTTCTCAGCAGCGTGAAGCCCAAGACAGGAGAGAAGAACAGAGACGATGCTTTGGAAGCCATAAAAGGAAACTTGGATGGGTTTTCCAGAGATGCTAAGATGCACCCCACTCCAGCATCACATCCAAAGAAACAAGGCAGGAATACCAATGGGGCCAATGCCAGCAGCGGGTGTGCCTTTCCTGGGTCAGCCACCTTTCTTGAGCATGCGTCCTGCAGGCCCACAGTACACTCCAGACATGCAGAAGCAGTTTGCGGAAGAGCAACAAAAACGATTTGA
Peptide sequence:
MGPMPAAGVPFLGQPPFLSMRPAGPQYTPDMQKQFAEEQQKRFEQQQKLLEEERKRRQFEEQKQKLRLLSSVKPKTGEKNRDDALEAIKGNLDGFSRDAKMHPTPASHPKKQGRNTNGANASSGCAFPGSATFLEHASCRPTVHSRHAEAVCGRATKTI
IRESfinder result
IRESfinder score
0.367483134
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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