top of page
mmu_circRbm39_809
Basic information of circular RNA
PanCircBase ID:
mmu_circRbm39_809
mm39_Chr. Position ID:
chr2|155996158|156006843|-
Gene name:
Rbm39
Transcript:
ENSMUST00000109587.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
7
Exon/intron indexes:
13,12,11,10,9,8,7
Exon/intron offsets:
0,4161,4798,7329,7589,8490,10567
Genomic length:
10685
Exon/intron sizes in nt:
5,17,82,05,66,13,81,53,000
Flanking exon/introns:
chr2:155992736-155996158|chr2:156006843-156009457
Splice length:
809
Other database IDs:
circAtlas: mmu-Rbm39_0049
circBase: hsa_circ_0060136, CIRCpedia: HSA_CIRCpedia_113507
Human Ortholog IDs:
Mature spliced Sequence:
GGAACCTATTGATAATCTCACTCCTGAGGAAAGGGATGCAAGGACTGTTTTCTGCATGCAACTGGCAGCAAGAATTCGACCGAGAGATTTGGAAGAGTTTTTCTCTACAGTTGGAAAGGTTCGAGATGTGAGAATGATTTCTGATAGAAATTCAAGACGTTCCAAAGGAATTGCATATGTGGAATTTGTTGATGTCAGTTCAGTGCCTCTAGCAATTGGATTAACTGGCCAACGAGTTTTAGGAGTGCCAATCATAGTTCAGGCATCACAGGCAGAAAAAAACAGAGCTGCTGCAATGGCAAACAATTTACAAAAGGGAAGTGCTGGACCTATGAGGCTCTATGTAGGCTCATTACACTTTAACATAACTGAAGACATGCTTCGGGGGATCTTTGAACCTTTTGGAAGGATTGAAAGTATTCAGCTCATGATGGATAGTGAAACTGGCCGATCTAAGGGATATGGATTTATTACATTTTCTGACTCAGAATGTGCCAAAAAGGCTTTGGAACAACTGAATGGATTTGAGTTAGCTGGGAGACCAATGAAAGTTGGTCACGTTACTGAACGAACTGATGCTTCGAGTGCTAGTTCATTTTTGGACAGTGACGAACTAGAAAGGACTGGAATTGACTTGGGAACAACTGGACGTCTTCAGTTAATGGCAAGACTTGCGGAGGGTACCGGTTTGCAGATTCCACCTGCCGCACAACAAGCATTACAAATGAGTGGCTCTCTGGCATTTGGTGCTGTGGCAGAATTCTCTTTTGTTATAGATTTGCAAACACGACTTTCCCAACAGACCGAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TGGCTCTCTGGCATTTGGTG
60.61
CTCGGTCGAATTCTTGCTGC
59.63
164
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TGGCTCTCTGGCATTTGGTG
60.61
GGTCGAATTCTTGCTGCCAG
59.55
161
PCR template sequence:
CAACAAGCATTACAAATGAGTGGCTCTCTGGCATTTGGTGCTGTGGCAGAATTCTCTTTTGTTATAGATTTGCAAACACGACTTTCCCAACAGACCGAAGGGAACCTATTGATAATCTCACTCCTGAGGAAAGGGATGCAAGGACTGTTTTCTGCATGCAACTGGCAGCAAGAATTCGACCGAGAGATTTGGAAGAGTTT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
11
Interacting miRNAs (#binding sites)
mmu-miR-155-5p(1), mmu-miR-19b-3p(1), mmu-miR-211-5p(1), mmu-miR-204-5p(1), mmu-miR-19a-3p(1), mmu-miR-96-5p(1), mmu-miR-183-5p(1), mmu-miR-29b-2-5p(1), mmu-miR-5101(1), mmu-miR-3065-5p(1), mmu-miR-7a-1-3p(1)
siRNAs for circular RNA silencing
Junction sequence
CAACAGACCGAAGGGAACCTATTGAT
siRNA sets
ATCAATAGGTTCCCTTCGG, AATAGGTTCCCTTCGGTCT, CAATAGGTTCCCTTCGGTC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCRBM39_809_ORF_1
0.8882
0.010138507
0.94260599
885
ORF sequence:
ATGCAACTGGCAGCAAGAATTCGACCGAGAGATTTGGAAGAGTTTTTCTCTACAGTTGGAAAGGTTCGAGATGTGAGAATGATTTCTGATAGAAATTCAAGACGTTCCAAAGGAATTGCATATGTGGAATTTGTTGATGTCAGTTCAGTGCCTCTAGCAATTGGATTAACTGGCCAACGAGTTTTAGGAGTGCCAATCATAGTTCAGGCATCACAGGCAGAAAAAAACAGAGCTGCTGCAATGGCAAACAATTTACAAAAGGGAAGTGCTGGACCTATGAGGCTCTATGTAGGCTCATTACACTTTAACATAACTGAAGACATGCTTCGGGGGATCTTTGAACCTTTTGGAAGGATTGAAAGTATTCAGCTCATGATGGATAGTGAAACTGGCCGATCTAAGGGATATGGATTTATTACATTTTCTGACTCAGAATGTGCCAAAAAGGCTTTGGAACAACTGAATGGATTTGAGTTAGCTGGGAGACCAATGAAAGTTGGTCACGTTACTGAACGAACTGATGCTTCGAGTGCTAGTTCATTTTTGGACAGTGACGAACTAGAAAGGACTGGAATTGACTTGGGAACAACTGGACGTCTTCAGTTAATGGCAAGACTTGCGGAGGGTACCGGTTTGCAGATTCCACCTGCCGCACAACAAGCATTACAAATGAGTGGCTCTCTGGCATTTGGTGCTGTGGCAGAATTCTCTTTTGTTATAGATTTGCAAACACGACTTTCCCAACAGACCGAAGGGAACCTATTGATAATCTCACTCCTGAGGAAAGGGATGCAAGGACTGTTTTCTGCATGCAACTGGCAGCAAGAATTCGACCGAGAGATTTGGAAGAGTTTTTCTCTACAGTTGGAAAGGTTCGAGATGTGA
Peptide sequence:
MQLAARIRPRDLEEFFSTVGKVRDVRMISDRNSRRSKGIAYVEFVDVSSVPLAIGLTGQRVLGVPIIVQASQAEKNRAAAMANNLQKGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPMKVGHVTERTDASSASSFLDSDELERTGIDLGTTGRLQLMARLAEGTGLQIPPAAQQALQMSGSLAFGAVAEFSFVIDLQTRLSQQTEGNLLIISLLRKGMQGLFSACNWQQEFDREIWKSFSLQLERFEM
IRESfinder result
IRESfinder score
0.651022937
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
bottom of page