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mmu_circRbm39_586
Basic information of circular RNA
PanCircBase ID:
mmu_circRbm39_586
mm39_Chr. Position ID:
chr2|156004648|156014942|-
Gene name:
Rbm39
Transcript:
ENSMUST00000109587.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
8,7,6,5,4
Exon/intron offsets:
0,2077,4809,4956,10099
Genomic length:
10294
Exon/intron sizes in nt:
15,31,18,54,66,195
Flanking exon/introns:
chr2:156003885-156004648|chr2:156014942-156019255
Splice length:
586
Other database IDs:
circAtlas: mmu-Rbm39_0009
circBase: hsa_circ_0141652, circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_95797
Human Ortholog IDs:
Mature spliced Sequence:
GAGAAAAAAAAGCAAGAGCAGAAGTCGTAGTCATGAGAGAAAAAGAAGCAAAAGTAAAGAACGGAAAAGAAGTAGAGATAGAGAAAGGAAAAAGAGCAAAAGTCGAGAGCGGAAACGAAGTAGAAGCAAAGAAAGGAGACGAAGCCGCTCACGCAGTCGGGATAGAAGATTCCGAGGCCGCTACAGAAGTCCCTACTCCGGACCAAAATTTAACAGTGCCATCCGAGGAAAGATTGGATTGCCTCATAGCATCAAATTAAGCAGAAGACGTTCCCGAAGCAAAAGTCCATTTAGGAAAGACAAGAGCCCTGTGAGGGAACCTATTGATAATCTCACTCCTGAGGAAAGGGATGCAAGGACTGTTTTCTGCATGCAACTGGCAGCAAGAATTCGACCGAGAGATTTGGAAGAGTTTTTCTCTACAGTTGGAAAGGTTCGAGATGTGAGAATGATTTCTGATAGAAATTCAAGACGTTCCAAAGGAATTGCATATGTGGAATTTGTTGATGTCAGTTCAGTGCCTCTAGCAATTGGATTAACTGGCCAACGAGTTTTAGGAGTGCCAATCATAGTTCAGGCATCACAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TGTCAGTTCAGTGCCTCTAGC
59.73
TCCGTTCTTTACTTTTGCTTCT
56.22
144
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TGTCAGTTCAGTGCCTCTAGC
59.73
TCCGTTCTTTACTTTTGCTTCTT
56.92
144
PCR template sequence:
TGCATATGTGGAATTTGTTGATGTCAGTTCAGTGCCTCTAGCAATTGGATTAACTGGCCAACGAGTTTTAGGAGTGCCAATCATAGTTCAGGCATCACAGGAGAAAAAAAAGCAAGAGCAGAAGTCGTAGTCATGAGAGAAAAAGAAGCAAAAGTAAAGAACGGAAAAGAAGTAGAGATAGAGAAAGGAAAAAGAGCAAA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
5
Interacting miRNAs (#binding sites)
mmu-miR-183-5p(2), mmu-miR-434-5p(1), mmu-miR-96-5p(1), mmu-miR-3065-5p(1), mmu-miR-7a-1-3p(1)
siRNAs for circular RNA silencing
Junction sequence
TCAGGCATCACAGGAGAAAAAAAAGC
siRNA sets
TTTTTTTCTCCTGTGATGC, TTTTTTCTCCTGTGATGCC, TTTTCTCCTGTGATGCCTG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCRBM39_586_ORF_1
1.0917
0.004058682
0.190231302
246
ORF sequence:
ATGCAACTGGCAGCAAGAATTCGACCGAGAGATTTGGAAGAGTTTTTCTCTACAGTTGGAAAGGTTCGAGATGTGAGAATGATTTCTGATAGAAATTCAAGACGTTCCAAAGGAATTGCATATGTGGAATTTGTTGATGTCAGTTCAGTGCCTCTAGCAATTGGATTAACTGGCCAACGAGTTTTAGGAGTGCCAATCATAGTTCAGGCATCACAGGAGAAAAAAAAGCAAGAGCAGAAGTCGTAG
Peptide sequence:
MQLAARIRPRDLEEFFSTVGKVRDVRMISDRNSRRSKGIAYVEFVDVSSVPLAIGLTGQRVLGVPIIVQASQEKKKQEQKS
IRESfinder result
IRESfinder score
0.466343916
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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