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mmu_circRmdn3_726
Basic information of circular RNA
PanCircBase ID:
mmu_circRmdn3_726
mm39_Chr. Position ID:
chr2|118976818|118984563|-
Gene name:
Rmdn3
Transcript:
ENSMUST00000094695.12
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
6,5,4,3
Exon/intron offsets:
0,971,7038,7552
Genomic length:
7745
Exon/intron sizes in nt:
1,03,28,61,44,193
Flanking exon/introns:
chr2:118973169-118976818|chr2:118984563-118986838
Splice length:
726
Other database IDs:
circAtlas: mmu-Rmdn3_0007
circBase: hsa_circ_0034627, circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_373760
Human Ortholog IDs:
Mature spliced Sequence:
TGACACAGTTTCGGGCTATCCCAGGTGAAGCTGGAGATGCTGCCATACTGCCCAGCCTCTCACAGGAAGGGCAGGAGAAGGTGCTGGACCGCCTGGACTTTGTGCTGACCAGTCTTATGGCGCTGCGGCGCGAGGTGGAGGAGCTTCAGAGAAGCCTGCAAGGACTAGCTGGGGAGATTGTTGGGGAGGTCCGCTCTCATATAGAAGAGAACCAGAGAGTGGCCCGGCGGCGCAGGTTCCCTTTTGCCAGAGAGAGGAGTGACTCCACGGGCTCCAGCTCTGTCTACTTCACCGCCTCCTCAGGGGCTGCACTCACAGACGCCGAGAGCGAGGGAGGTTATACAACAGCCAACGCGGAGTCTGATTACGAGCGGGACTCCGACAAGGAGAGTGGAGATGCTGAGGACGAAGTGAGCTGCGAGACCGTGAGGATGGGGAGGAAGGACTCTCTGGACCTGGATGTGGAGGCGGCGTCCAGTCCGGCGGCGGCCGCCTTGGAGGAGGATGACTCCTCAGGCCGAGAGGATGTGCAGCTGGTCCTGCTGCAGGCCGATGAGCTGCACCAGGGCAGCAAGCAGGACAAGCGGGAAGGCTTCCAGCTGCTGCTCAACAATAAGCTGGCGTATGGAAGCCGACAAGACTTTCTGTGGCGCCTGGCCCGGGCCTACAGTGACATGTCAGACCTTACTGAGGAGGAGAGCGGGAAGAAGTCCTATGCCCTAAATG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GACAAGACTTTCTGTGGCGC
59.76
CTTCTCCTGCCCTTCCTGTG
60.04
173
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GACAAGACTTTCTGTGGCGC
59.76
GTATGGCAGCATCTCCAGCT
59.89
141
PCR template sequence:
GGAAGCCGACAAGACTTTCTGTGGCGCCTGGCCCGGGCCTACAGTGACATGTCAGACCTTACTGAGGAGGAGAGCGGGAAGAAGTCCTATGCCCTAAATGTGACACAGTTTCGGGCTATCCCAGGTGAAGCTGGAGATGCTGCCATACTGCCCAGCCTCTCACAGGAAGGGCAGGAGAAGGTGCTGGACCGCCTGGACTT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
6
Interacting miRNAs (#binding sites)
mmu-miR-207(2), mmu-miR-9-5p(1), mmu-miR-322-5p(1), mmu-miR-351-5p(1), mmu-miR-499-5p(1), mmu-miR-697(1)
siRNAs for circular RNA silencing
Junction sequence
TATGCCCTAAATGTGACACAGTTTCG
siRNA sets
AAACTGTGTCACATTTAGG, AACTGTGTCACATTTAGGG, GAAACTGTGTCACATTTAG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCRMDN3_726_ORF_1
1.1188
0.557824189
0.999836414
1335
ORF sequence:
ATGGCGCTGCGGCGCGAGGTGGAGGAGCTTCAGAGAAGCCTGCAAGGACTAGCTGGGGAGATTGTTGGGGAGGTCCGCTCTCATATAGAAGAGAACCAGAGAGTGGCCCGGCGGCGCAGGTTCCCTTTTGCCAGAGAGAGGAGTGACTCCACGGGCTCCAGCTCTGTCTACTTCACCGCCTCCTCAGGGGCTGCACTCACAGACGCCGAGAGCGAGGGAGGTTATACAACAGCCAACGCGGAGTCTGATTACGAGCGGGACTCCGACAAGGAGAGTGGAGATGCTGAGGACGAAGTGAGCTGCGAGACCGTGAGGATGGGGAGGAAGGACTCTCTGGACCTGGATGTGGAGGCGGCGTCCAGTCCGGCGGCGGCCGCCTTGGAGGAGGATGACTCCTCAGGCCGAGAGGATGTGCAGCTGGTCCTGCTGCAGGCCGATGAGCTGCACCAGGGCAGCAAGCAGGACAAGCGGGAAGGCTTCCAGCTGCTGCTCAACAATAAGCTGGCGTATGGAAGCCGACAAGACTTTCTGTGGCGCCTGGCCCGGGCCTACAGTGACATGTCAGACCTTACTGAGGAGGAGAGCGGGAAGAAGTCCTATGCCCTAAATGTGACACAGTTTCGGGCTATCCCAGGTGAAGCTGGAGATGCTGCCATACTGCCCAGCCTCTCACAGGAAGGGCAGGAGAAGGTGCTGGACCGCCTGGACTTTGTGCTGACCAGTCTTATGGCGCTGCGGCGCGAGGTGGAGGAGCTTCAGAGAAGCCTGCAAGGACTAGCTGGGGAGATTGTTGGGGAGGTCCGCTCTCATATAGAAGAGAACCAGAGAGTGGCCCGGCGGCGCAGGTTCCCTTTTGCCAGAGAGAGGAGTGACTCCACGGGCTCCAGCTCTGTCTACTTCACCGCCTCCTCAGGGGCTGCACTCACAGACGCCGAGAGCGAGGGAGGTTATACAACAGCCAACGCGGAGTCTGATTACGAGCGGGACTCCGACAAGGAGAGTGGAGATGCTGAGGACGAAGTGAGCTGCGAGACCGTGAGGATGGGGAGGAAGGACTCTCTGGACCTGGATGTGGAGGCGGCGTCCAGTCCGGCGGCGGCCGCCTTGGAGGAGGATGACTCCTCAGGCCGAGAGGATGTGCAGCTGGTCCTGCTGCAGGCCGATGAGCTGCACCAGGGCAGCAAGCAGGACAAGCGGGAAGGCTTCCAGCTGCTGCTCAACAATAAGCTGGCGTATGGAAGCCGACAAGACTTTCTGTGGCGCCTGGCCCGGGCCTACAGTGACATGTCAGACCTTACTGAGGAGGAGAGCGGGAAGAAGTCCTATGCCCTAAAT
Peptide sequence:
MALRREVEELQRSLQGLAGEIVGEVRSHIEENQRVARRRRFPFARERSDSTGSSSVYFTASSGAALTDAESEGGYTTANAESDYERDSDKESGDAEDEVSCETVRMGRKDSLDLDVEAASSPAAAALEEDDSSGREDVQLVLLQADELHQGSKQDKREGFQLLLNNKLAYGSRQDFLWRLARAYSDMSDLTEEESGKKSYALNVTQFRAIPGEAGDAAILPSLSQEGQEKVLDRLDFVLTSLMALRREVEELQRSLQGLAGEIVGEVRSHIEENQRVARRRRFPFARERSDSTGSSSVYFTASSGAALTDAESEGGYTTANAESDYERDSDKESGDAEDEVSCETVRMGRKDSLDLDVEAASSPAAAALEEDDSSGREDVQLVLLQADELHQGSKQDKREGFQLLLNNKLAYGSRQDFLWRLARAYSDMSDLTEEESGKKSYALN
IRESfinder result
IRESfinder score
0.149025794
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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