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mmu_circRrn3_606
Basic information of circular RNA
PanCircBase ID:
mmu_circRrn3_606
mm39_Chr. Position ID:
chr16|13606641|13613941|+
Gene name:
Rrn3
Transcript:
ENSMUST00000023363.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
7
Exon/intron indexes:
4,5,6,7,8,9,10
Exon/intron offsets:
0,182,755,1843,3142,4170,7207
Genomic length:
7300
Exon/intron sizes in nt:
90,130,60,64,70,99,93
Flanking exon/introns:
chr16:13601993-13606641|chr16:13613941-13616475
Splice length:
606
Other database IDs:
CIRCpedia: MMU_CIRCpedia_220425, circAtlas: mmu-Rrn3_0004
Human Ortholog IDs:
Mature spliced Sequence:
GATGACCAGATCATTAACTGGCTACTAGAATTTCGTTCCTCTGTCATGTACTTGACAAAAGACTTTGAGCAACTTATAAACATCATATTGAGATTGCCCTGGTTGAATAGAAGTCAGAGAGTGGTGGAGGAGTATTTGGCTTTTCTTGGTAATCTTGTGTCTGCACAGACTGTCTTCCTTAGACCATGTCTCAGCATGATTGCGTCTCATTTTGTACCTCCCCGAGTAATTGTCAAGGAAGGTGGCATAGATGTTTCAGATTCTGATGACGAAGATGACAATCTTCCTGCAATTTTTGACACATGTCACAGAGCCTTGCAAATAATAACAAGATATGTCCCATCGACACCATGGTTTCTAATGCCAATACTGGTGGAGAAATTCCCGTTTGTGAGGAAGTCCGAGAGAACATTGGAATGTTATGTTCATAACTTATTAAGGATAAGTTTATATTTCCCAACTTTGAGGCGTGAAATTCTGGAGCTTGTTATTGAAAAGCTACTCAAGTTAGATGTGAGTGTATCGCGGCAGGATATTGAAGATGCTGAAGAGAAAGCAGCTCAGACTTGTGGTGGGACAGATACCACAGAAGGACTGTTTAATATG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AGATGTGAGTGTATCGCGGC
60.25
TCAAGTACATGACAGAGGAACGA
59.18
152
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GATGTGAGTGTATCGCGGCA
60.53
TCAAGTACATGACAGAGGAACGA
59.18
151
PCR template sequence:
GTTAGATGTGAGTGTATCGCGGCAGGATATTGAAGATGCTGAAGAGAAAGCAGCTCAGACTTGTGGTGGGACAGATACCACAGAAGGACTGTTTAATATGGATGACCAGATCATTAACTGGCTACTAGAATTTCGTTCCTCTGTCATGTACTTGACAAAAGACTTTGAGCAACTTATAAACATCATATTGAGATTGCCCT
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-26a-5p(1), mmu-miR-26b-5p(1)
siRNAs for circular RNA silencing
Junction sequence
ACTGTTTAATATGGATGACCAGATCA
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCRRN3_606_ORF_1
0.9177
-0.011947471
0.99190004
1167
ORF sequence:
ATGTACTTGACAAAAGACTTTGAGCAACTTATAAACATCATATTGAGATTGCCCTGGTTGAATAGAAGTCAGAGAGTGGTGGAGGAGTATTTGGCTTTTCTTGGTAATCTTGTGTCTGCACAGACTGTCTTCCTTAGACCATGTCTCAGCATGATTGCGTCTCATTTTGTACCTCCCCGAGTAATTGTCAAGGAAGGTGGCATAGATGTTTCAGATTCTGATGACGAAGATGACAATCTTCCTGCAATTTTTGACACATGTCACAGAGCCTTGCAAATAATAACAAGATATGTCCCATCGACACCATGGTTTCTAATGCCAATACTGGTGGAGAAATTCCCGTTTGTGAGGAAGTCCGAGAGAACATTGGAATGTTATGTTCATAACTTATTAAGGATAAGTTTATATTTCCCAACTTTGAGGCGTGAAATTCTGGAGCTTGTTATTGAAAAGCTACTCAAGTTAGATGTGAGTGTATCGCGGCAGGATATTGAAGATGCTGAAGAGAAAGCAGCTCAGACTTGTGGTGGGACAGATACCACAGAAGGACTGTTTAATATGGATGACCAGATCATTAACTGGCTACTAGAATTTCGTTCCTCTGTCATGTACTTGACAAAAGACTTTGAGCAACTTATAAACATCATATTGAGATTGCCCTGGTTGAATAGAAGTCAGAGAGTGGTGGAGGAGTATTTGGCTTTTCTTGGTAATCTTGTGTCTGCACAGACTGTCTTCCTTAGACCATGTCTCAGCATGATTGCGTCTCATTTTGTACCTCCCCGAGTAATTGTCAAGGAAGGTGGCATAGATGTTTCAGATTCTGATGACGAAGATGACAATCTTCCTGCAATTTTTGACACATGTCACAGAGCCTTGCAAATAATAACAAGATATGTCCCATCGACACCATGGTTTCTAATGCCAATACTGGTGGAGAAATTCCCGTTTGTGAGGAAGTCCGAGAGAACATTGGAATGTTATGTTCATAACTTATTAAGGATAAGTTTATATTTCCCAACTTTGAGGCGTGAAATTCTGGAGCTTGTTATTGAAAAGCTACTCAAGTTAGATGTGAGTGTATCGCGGCAGGATATTGAAGATGCTGAAGAGAAAGCAGCTCAGACTTGTGGTGGGACAGATACCACAGAAGGACTGTTTAATATG
Peptide sequence:
MYLTKDFEQLINIILRLPWLNRSQRVVEEYLAFLGNLVSAQTVFLRPCLSMIASHFVPPRVIVKEGGIDVSDSDDEDDNLPAIFDTCHRALQIITRYVPSTPWFLMPILVEKFPFVRKSERTLECYVHNLLRISLYFPTLRREILELVIEKLLKLDVSVSRQDIEDAEEKAAQTCGGTDTTEGLFNMDDQIINWLLEFRSSVMYLTKDFEQLINIILRLPWLNRSQRVVEEYLAFLGNLVSAQTVFLRPCLSMIASHFVPPRVIVKEGGIDVSDSDDEDDNLPAIFDTCHRALQIITRYVPSTPWFLMPILVEKFPFVRKSERTLECYVHNLLRISLYFPTLRREILELVIEKLLKLDVSVSRQDIEDAEEKAAQTCGGTDTTEGLFNM
IRESfinder result
IRESfinder score
0.637021131
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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