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mmu_circRbm41_1067
Basic information of circular RNA
PanCircBase ID:
mmu_circRbm41_1067
mm39_Chr. Position ID:
chrX|138855655|138895977|-
Gene name:
Rbm41
Transcript:
ENSMUST00000087400.12
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
6,5,4,3,2
Exon/intron offsets:
0,13289,38391,39005,40205
Genomic length:
40322
Exon/intron sizes in nt:
148,404,205,193,117
Flanking exon/introns:
chrX:138791325-138855655|chrX:138895977-138899248
Splice length:
1067
Other database IDs:
CIRCpedia: MMU_CIRCpedia_8870, circAtlas: mmu-Rbm41_0006
CIRCpedia: HSA_CIRCpedia_64968
Human Ortholog IDs:
Mature spliced Sequence:
GGTAAATAGCTGTGTGAAGGATGAAGAACATGTCCTGGAGGAACTGGAAACAGAAGGTGAGAGGCAGCTCAAGAGCCTCCTTCAACATCAACTCGATACCTCTGTCTCCATTGAAGAATGTGTCTCTAAGAAAAAGAGCTTTGCGCCTGGGACTATGTACAAGCCCTTTGGGAAGGAAGCAGCTGGGACAATGACTTTGTCCCAGTTCCAGACACTACATGAAAAAGACCAGGAAACTGCTTCTCTCAGGGAATTAGGGCTCAATGAAACTGAAATATTGATCTGGAAAAGCCATGTTTCCGGTGAAAAGAGGACAAAGCTGAGGGCAACTCCCGAAGCAATACAGAAACGGCTTGAAGATATTAAAGAAAGAATCTCAGAGCGCCAGCGCATCCTTTGCCTGCCACAGAGGTTTTCAAAGAGCAAACAGCTGACCCGAAGAGAAATGGAAATTGAGAAGTCTTTATTTCAGGGAACTGATCGTCACTCCTTCCTTAAGGCTCTTTATTACCAAGATGAACCCCCAAAGAAGAACAAAGGTGACCCCATGAACAACCTGGAACATTTTTACCGCGAGACTATAATGAAAAAGCGTCTTGAAGAGTTCCAACTTTTGAGAGGTGAATCCTTTGCTTGCCACTCACTGGTCTCAGCTGCATCCGTGAGTGGTAGTGGCACAGCTGAGAAGCCATCACTCCTCCAGGACAAGGGAAAACAGGCAGCACAGGGTAAAGGCCCCAGGCTCCATGTGGCAAAGCTTATTGATTTTCCAACTGAGCAATATTGGACTGGGCCTAAGACGCTGAAGCAACCAATAGAATTTATCCCAGAAGATGAGATCCAGAGAAATCGTTTGTCAGAGGAGGAGATCCGAAACATTCCTATGTTTTCTTCATATAATCCAGGGGAACCAAACAAGGTGCTATATCTGAAGAACCTTAGTCCTCGGGTGAAAGAAAGAGACCTTATCTCATTATTCGCTCGATTCCAGGAGAAGAAAGGACCACCCATTCAGTTCCGAATGATGACTGGACGCATGAGGGGGCAAGCTTTCCTCACCTTTCCCA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GACCACCCATTCAGTTCCGA
59.68
CTCTTGAGCTGCCTCTCACC
60.11
141
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CGCTCGATTCCAGGAGAAGA
59.26
GCTGCCTCTCACCTTCTGTT
59.96
157
PCR template sequence:
ATCTCATTATTCGCTCGATTCCAGGAGAAGAAAGGACCACCCATTCAGTTCCGAATGATGACTGGACGCATGAGGGGGCAAGCTTTCCTCACCTTTCCCAGGTAAATAGCTGTGTGAAGGATGAAGAACATGTCCTGGAGGAACTGGAAACAGAAGGTGAGAGGCAGCTCAAGAGCCTCCTTCAACATCAACTCGATACC
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-135a-5p(2), mmu-miR-335-3p(2), mmu-miR-351-5p(1), mmu-miR-207(1), mmu-miR-5101(1), mmu-miR-670-5p(1)
siRNAs for circular RNA silencing
Junction sequence
CTCACCTTTCCCAGGTAAATAGCTGT
siRNA sets
GCTATTTACCTGGGAAAGG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCRBM41_1067_ORF_1
0.8997
0.157898563
0.974674617
918
ORF sequence:
ATGTACAAGCCCTTTGGGAAGGAAGCAGCTGGGACAATGACTTTGTCCCAGTTCCAGACACTACATGAAAAAGACCAGGAAACTGCTTCTCTCAGGGAATTAGGGCTCAATGAAACTGAAATATTGATCTGGAAAAGCCATGTTTCCGGTGAAAAGAGGACAAAGCTGAGGGCAACTCCCGAAGCAATACAGAAACGGCTTGAAGATATTAAAGAAAGAATCTCAGAGCGCCAGCGCATCCTTTGCCTGCCACAGAGGTTTTCAAAGAGCAAACAGCTGACCCGAAGAGAAATGGAAATTGAGAAGTCTTTATTTCAGGGAACTGATCGTCACTCCTTCCTTAAGGCTCTTTATTACCAAGATGAACCCCCAAAGAAGAACAAAGGTGACCCCATGAACAACCTGGAACATTTTTACCGCGAGACTATAATGAAAAAGCGTCTTGAAGAGTTCCAACTTTTGAGAGGTGAATCCTTTGCTTGCCACTCACTGGTCTCAGCTGCATCCGTGAGTGGTAGTGGCACAGCTGAGAAGCCATCACTCCTCCAGGACAAGGGAAAACAGGCAGCACAGGGTAAAGGCCCCAGGCTCCATGTGGCAAAGCTTATTGATTTTCCAACTGAGCAATATTGGACTGGGCCTAAGACGCTGAAGCAACCAATAGAATTTATCCCAGAAGATGAGATCCAGAGAAATCGTTTGTCAGAGGAGGAGATCCGAAACATTCCTATGTTTTCTTCATATAATCCAGGGGAACCAAACAAGGTGCTATATCTGAAGAACCTTAGTCCTCGGGTGAAAGAAAGAGACCTTATCTCATTATTCGCTCGATTCCAGGAGAAGAAAGGACCACCCATTCAGTTCCGAATGATGACTGGACGCATGAGGGGGCAAGCTTTCCTCACCTTTCCCAGGTAA
Peptide sequence:
MYKPFGKEAAGTMTLSQFQTLHEKDQETASLRELGLNETEILIWKSHVSGEKRTKLRATPEAIQKRLEDIKERISERQRILCLPQRFSKSKQLTRREMEIEKSLFQGTDRHSFLKALYYQDEPPKKNKGDPMNNLEHFYRETIMKKRLEEFQLLRGESFACHSLVSAASVSGSGTAEKPSLLQDKGKQAAQGKGPRLHVAKLIDFPTEQYWTGPKTLKQPIEFIPEDEIQRNRLSEEEIRNIPMFSSYNPGEPNKVLYLKNLSPRVKERDLISLFARFQEKKGPPIQFRMMTGRMRGQAFLTFPR
IRESfinder result
IRESfinder score
0.597639544
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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