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mmu_circLin9_523
Basic information of circular RNA
PanCircBase ID:
mmu_circLin9_523
mm39_Chr. Position ID:
chr1|180479426|180493505|+
Gene name:
Lin9
Transcript:
ENSMUST00000192561.6
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
4,5,6,7
Exon/intron offsets:
0,7201,9615,13921
Genomic length:
14079
Exon/intron sizes in nt:
1,05,13,41,26,158
Flanking exon/introns:
chr1:180478401-180479426|chr1:180493505-180494889
Splice length:
523
Other database IDs:
circBase: mmu_circ_0008516, CIRCpedia: MMU_CIRCpedia_12287, circAtlas: mmu-Lin9_0002
circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_69311
Human Ortholog IDs:
Mature spliced Sequence:
CCTTTCAGAAATTCAAAAAGAAGTCGACTCTTTTCTGATGAAGATGACAGACAAATAAATACAAAGTCACCTAAAAGAAACCAGAGAGTGGCAATGATCCCACAGAAATTTACAGCAACGATGTCAACACCAGATAAGAAAGCATCACAGAAGATTGGTTTTCGATTACGGAACCTACTCAAGCTTCCCAAAGCACATAAGTGGTGCATATATGAGTGGTTCTACTCAAACATAGACAAGCCACTTTTTGAAGGAGATAATGACTTTTGTGTATGCCTAAAGGAATCCTTTCCTAATTTGAAAACAAGAAAATTAACAAGAGTAGAATGGGGAAAAATCAGGAGACTGATGGGAAAACCTCGGAGATGTTCTTCTGCATTTTTTGAGGAAGAGAGATCAGCCTTAAAACAGAAGCGGCAGAAAATCAGGCTGTTACAACAAAGGAAAGTTGCAGATGTTTCACAGTTCAAAGATCTCCCCGATGAAATCCCTCTACCCCTGGTTATTGGAACCAAAGTTACAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TCTCCCCGATGAAATCCCTCT
60.06
GGATCATTGCCACTCTCTGGT
59.79
150
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TGAAATCCCTCTACCCCTGGT
59.92
GGATCATTGCCACTCTCTGGT
59.79
141
PCR template sequence:
ATCAGGCTGTTACAACAAAGGAAAGTTGCAGATGTTTCACAGTTCAAAGATCTCCCCGATGAAATCCCTCTACCCCTGGTTATTGGAACCAAAGTTACAGCCTTTCAGAAATTCAAAAAGAAGTCGACTCTTTTCTGATGAAGATGACAGACAAATAAATACAAAGTCACCTAAAAGAAACCAGAGAGTGGCAATGATCC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
3
Interacting miRNAs (#binding sites)
mmu-miR-9-5p(1), mmu-miR-29b-1-5p(1), mmu-miR-29b-2-5p(1)
siRNAs for circular RNA silencing
Junction sequence
ACCAAAGTTACAGCCTTTCAGAAATT
siRNA sets
ATTTCTGAAAGGCTGTAAC, TTTCTGAAAGGCTGTAACT, AATTTCTGAAAGGCTGTAA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCLIN9_523_ORF_1
0.5095
-0.036228091
0.449329663
591
ORF sequence:
ATGTTTCACAGTTCAAAGATCTCCCCGATGAAATCCCTCTACCCCTGGTTATTGGAACCAAAGTTACAGCCTTTCAGAAATTCAAAAAGAAGTCGACTCTTTTCTGATGAAGATGACAGACAAATAAATACAAAGTCACCTAAAAGAAACCAGAGAGTGGCAATGATCCCACAGAAATTTACAGCAACGATGTCAACACCAGATAAGAAAGCATCACAGAAGATTGGTTTTCGATTACGGAACCTACTCAAGCTTCCCAAAGCACATAAGTGGTGCATATATGAGTGGTTCTACTCAAACATAGACAAGCCACTTTTTGAAGGAGATAATGACTTTTGTGTATGCCTAAAGGAATCCTTTCCTAATTTGAAAACAAGAAAATTAACAAGAGTAGAATGGGGAAAAATCAGGAGACTGATGGGAAAACCTCGGAGATGTTCTTCTGCATTTTTTGAGGAAGAGAGATCAGCCTTAAAACAGAAGCGGCAGAAAATCAGGCTGTTACAACAAAGGAAAGTTGCAGATGTTTCACAGTTCAAAGATCTCCCCGATGAAATCCCTCTACCCCTGGTTATTGGAACCAAAGTTACA
Peptide sequence:
MFHSSKISPMKSLYPWLLEPKLQPFRNSKRSRLFSDEDDRQINTKSPKRNQRVAMIPQKFTATMSTPDKKASQKIGFRLRNLLKLPKAHKWCIYEWFYSNIDKPLFEGDNDFCVCLKESFPNLKTRKLTRVEWGKIRRLMGKPRRCSSAFFEEERSALKQKRQKIRLLQQRKVADVSQFKDLPDEIPLPLVIGTKVT
IRESfinder result
IRESfinder score
0.566371131
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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