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mmu_circMrpl39_549
Basic information of circular RNA
PanCircBase ID:
mmu_circMrpl39_549
mm39_Chr. Position ID:
chr16|84517157|84527815|-
Gene name:
Mrpl39
Transcript:
ENSMUST00000116584.2
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
6
Exon/intron indexes:
9,8,7,6,5,4
Exon/intron offsets:
0,3568,4855,7214,10149,10558
Genomic length:
10658
Exon/intron sizes in nt:
48,15,46,61,13,68,100
Flanking exon/introns:
chr16:84515272-84517157|chr16:84527815-84529229
Splice length:
549
Other database IDs:
circAtlas: mmu-Mrpl39_0001
circBase: hsa_circ_0061321, circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_35099
Human Ortholog IDs:
Mature spliced Sequence:
GCGTATTGGCGTTCTTGTGCCATGATGCTGGGCTGTGTAATCGAAAGGGCATTCAAAGATGACTATGTGGTCAGCCTGGTCAGAGCACCGGAAGTTCCTGTGATTGCTGGGGCCTTCTGCTATGATGTCACTTTGGATAAGAGACTGGATGAGTGGATGCCAACAAAAGAGAACCTGCGTTCTTTCACAAAAGATGCCCATGCTTTAATATATAGGGACCTTCCCTTTGAAACTCTGGACGTTGATGCAAGAGTGGCGCTGGAAATATTTCAACATAACAAGTACAAAGTGGATTTCATAGAGGAGAAGGCATCTCAGAACCCCGAGAGAATAGTCAAGTTACACAGAATCGGTGACTTCATTGATGTAAGTGAAGGCCCCCTTATTCCGAGAACAAGTGTTTGCTTCCAGTATGAAGTGTCAGCGGTCCACAATCTTAACCCCAGCCAGCCGAACCTCATTCGCAGATTTCAGGGCCTGTCTTTACCCACGCACTTGAGAGCACAGTTTACAATATGGGACAAGCTAGTGGAAAGATCTCGGAAAATG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CCTGTCTTTACCCACGCACT
59.97
GAACTTCCGGTGCTCTGACC
60.67
170
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CCTGTCTTTACCCACGCACT
59.97
GGAACTTCCGGTGCTCTGAC
60.67
171
PCR template sequence:
GCCGAACCTCATTCGCAGATTTCAGGGCCTGTCTTTACCCACGCACTTGAGAGCACAGTTTACAATATGGGACAAGCTAGTGGAAAGATCTCGGAAAATGGCGTATTGGCGTTCTTGTGCCATGATGCTGGGCTGTGTAATCGAAAGGGCATTCAAAGATGACTATGTGGTCAGCCTGGTCAGAGCACCGGAAGTTCCTG
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-203-3p(1), mmu-miR-452-3p(1), mmu-miR-338-3p(1)
siRNAs for circular RNA silencing
Junction sequence
ATCTCGGAAAATGGCGTATTGGCGTT
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCMRPL39_549_ORF_1
1.0257
0.155324414
0.993604222
1077
ORF sequence:
ATGATGCTGGGCTGTGTAATCGAAAGGGCATTCAAAGATGACTATGTGGTCAGCCTGGTCAGAGCACCGGAAGTTCCTGTGATTGCTGGGGCCTTCTGCTATGATGTCACTTTGGATAAGAGACTGGATGAGTGGATGCCAACAAAAGAGAACCTGCGTTCTTTCACAAAAGATGCCCATGCTTTAATATATAGGGACCTTCCCTTTGAAACTCTGGACGTTGATGCAAGAGTGGCGCTGGAAATATTTCAACATAACAAGTACAAAGTGGATTTCATAGAGGAGAAGGCATCTCAGAACCCCGAGAGAATAGTCAAGTTACACAGAATCGGTGACTTCATTGATGTAAGTGAAGGCCCCCTTATTCCGAGAACAAGTGTTTGCTTCCAGTATGAAGTGTCAGCGGTCCACAATCTTAACCCCAGCCAGCCGAACCTCATTCGCAGATTTCAGGGCCTGTCTTTACCCACGCACTTGAGAGCACAGTTTACAATATGGGACAAGCTAGTGGAAAGATCTCGGAAAATGGCGTATTGGCGTTCTTGTGCCATGATGCTGGGCTGTGTAATCGAAAGGGCATTCAAAGATGACTATGTGGTCAGCCTGGTCAGAGCACCGGAAGTTCCTGTGATTGCTGGGGCCTTCTGCTATGATGTCACTTTGGATAAGAGACTGGATGAGTGGATGCCAACAAAAGAGAACCTGCGTTCTTTCACAAAAGATGCCCATGCTTTAATATATAGGGACCTTCCCTTTGAAACTCTGGACGTTGATGCAAGAGTGGCGCTGGAAATATTTCAACATAACAAGTACAAAGTGGATTTCATAGAGGAGAAGGCATCTCAGAACCCCGAGAGAATAGTCAAGTTACACAGAATCGGTGACTTCATTGATGTAAGTGAAGGCCCCCTTATTCCGAGAACAAGTGTTTGCTTCCAGTATGAAGTGTCAGCGGTCCACAATCTTAACCCCAGCCAGCCGAACCTCATTCGCAGATTTCAGGGCCTGTCTTTACCCACGCACTTGAGAGCACAGTTTACAATATGGGACAAGCTAGTGGAAAGATCTCGGAAAATG
Peptide sequence:
MMLGCVIERAFKDDYVVSLVRAPEVPVIAGAFCYDVTLDKRLDEWMPTKENLRSFTKDAHALIYRDLPFETLDVDARVALEIFQHNKYKVDFIEEKASQNPERIVKLHRIGDFIDVSEGPLIPRTSVCFQYEVSAVHNLNPSQPNLIRRFQGLSLPTHLRAQFTIWDKLVERSRKMAYWRSCAMMLGCVIERAFKDDYVVSLVRAPEVPVIAGAFCYDVTLDKRLDEWMPTKENLRSFTKDAHALIYRDLPFETLDVDARVALEIFQHNKYKVDFIEEKASQNPERIVKLHRIGDFIDVSEGPLIPRTSVCFQYEVSAVHNLNPSQPNLIRRFQGLSLPTHLRAQFTIWDKLVERSRKM
IRESfinder result
IRESfinder score
0.597218891
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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