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mmu_circErn1_728
Basic information of circular RNA
PanCircBase ID:
mmu_circErn1_728
mm39_Chr. Position ID:
chr11|106305176|106314314|-
Gene name:
Ern1
Transcript:
ENSMUST00000001059.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
11,10,9,8,7
Exon/intron offsets:
0,4473,5668,7355,9036
Genomic length:
9138
Exon/intron sizes in nt:
1,19,16,67,92,62,102
Flanking exon/introns:
chr11:106302640-106305176|chr11:106314314-106317638
Splice length:
728
Other database IDs:
CIRCpedia: MMU_CIRCpedia_1761, circAtlas: mmu-Ern1_0025
Human Ortholog IDs:
Mature spliced Sequence:
AATACACCATCACCATGTATGACACCAAGACCCGGGAGCTCCGCTGGAATGCCACCTATTTTGACTATGCAGCCTCACTGCCGGAAGACGACGTGGACTACAAGATGTCCCACTTTGTGTCCAATGGCGATGGACTGGTGGTAACTGTGGACAGTGAATCTGGGGATGTCCTGTGGATCCAAAACTATGCCTCTCCTGTGGTGGCCTTCTACGTCTGGCAGGGGGAGGTCCTGAGAAAGGTGGTGCACATCAACGTTGCTGTGGAGACTCTACGCTACTTGACCTTCATGTCTGGGGAAGTGGGGCGCATCACCAAGTGGAAGTATCCATTCCCCAAGGAGACAGAGGCCAAGAGCAAGCTAACGCCTACTCTGTATGTTGGGAAGTATTCCACCAGCCTCTATGCCTCTCCCTCAATGGTGCATGAGGGGGTTGCTGTCGTGCCTCGAGGCAGCACTCTTCCTTTGCTGGAAGGCCCCCAGACAGATGGCGTCACCATTGGAGACAAAGGAGAGTGTGTGATCACTCCCAGCACAGACCTCAAGTTTGACCCTGGACTCAAAGGGAAGAGCAAGCTGAACTACTTGAGGAATTACTGGCTTCTCATAGGACACCATGAAACTCCTCTGTCTGCATCCACCAAGATGCTGGAGAGATTTCCTAACAACCTGCCCAAACATCGAGAAAATGTGATTCCTGCTGATTCAGAAAAAAGGAGCTTTGAGGAA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
ACAACCTGCCCAAACATCGA
60.18
TAGTCCACGTCGTCTTCCGG
61.3
165
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
ACAACCTGCCCAAACATCGA
60.18
GTCGTCTTCCGGCAGTGAG
60.44
157
PCR template sequence:
GTCTGCATCCACCAAGATGCTGGAGAGATTTCCTAACAACCTGCCCAAACATCGAGAAAATGTGATTCCTGCTGATTCAGAAAAAAGGAGCTTTGAGGAAAATACACCATCACCATGTATGACACCAAGACCCGGGAGCTCCGCTGGAATGCCACCTATTTTGACTATGCAGCCTCACTGCCGGAAGACGACGTGGACTA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
4
Interacting miRNAs (#binding sites)
mmu-miR-26a-5p(1), mmu-miR-298-5p(1), mmu-miR-153-3p(1), mmu-miR-26b-5p(1)
siRNAs for circular RNA silencing
Junction sequence
GAGCTTTGAGGAAAATACACCATCAC
siRNA sets
TGTATTTTCCTCAAAGCTC, GTGTATTTTCCTCAAAGCT, GGTGTATTTTCCTCAAAGC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCERN1_728_ORF_1
1.0002
0.284988497
0.980916618
858
ORF sequence:
ATGTATGACACCAAGACCCGGGAGCTCCGCTGGAATGCCACCTATTTTGACTATGCAGCCTCACTGCCGGAAGACGACGTGGACTACAAGATGTCCCACTTTGTGTCCAATGGCGATGGACTGGTGGTAACTGTGGACAGTGAATCTGGGGATGTCCTGTGGATCCAAAACTATGCCTCTCCTGTGGTGGCCTTCTACGTCTGGCAGGGGGAGGTCCTGAGAAAGGTGGTGCACATCAACGTTGCTGTGGAGACTCTACGCTACTTGACCTTCATGTCTGGGGAAGTGGGGCGCATCACCAAGTGGAAGTATCCATTCCCCAAGGAGACAGAGGCCAAGAGCAAGCTAACGCCTACTCTGTATGTTGGGAAGTATTCCACCAGCCTCTATGCCTCTCCCTCAATGGTGCATGAGGGGGTTGCTGTCGTGCCTCGAGGCAGCACTCTTCCTTTGCTGGAAGGCCCCCAGACAGATGGCGTCACCATTGGAGACAAAGGAGAGTGTGTGATCACTCCCAGCACAGACCTCAAGTTTGACCCTGGACTCAAAGGGAAGAGCAAGCTGAACTACTTGAGGAATTACTGGCTTCTCATAGGACACCATGAAACTCCTCTGTCTGCATCCACCAAGATGCTGGAGAGATTTCCTAACAACCTGCCCAAACATCGAGAAAATGTGATTCCTGCTGATTCAGAAAAAAGGAGCTTTGAGGAAAATACACCATCACCATGTATGACACCAAGACCCGGGAGCTCCGCTGGAATGCCACCTATTTTGACTATGCAGCCTCACTGCCGGAAGACGACGTGGACTACAAGATGTCCCACTTTGTGTCCAATGGCGATGGACTGGTGGTAA
Peptide sequence:
MYDTKTRELRWNATYFDYAASLPEDDVDYKMSHFVSNGDGLVVTVDSESGDVLWIQNYASPVVAFYVWQGEVLRKVVHINVAVETLRYLTFMSGEVGRITKWKYPFPKETEAKSKLTPTLYVGKYSTSLYASPSMVHEGVAVVPRGSTLPLLEGPQTDGVTIGDKGECVITPSTDLKFDPGLKGKSKLNYLRNYWLLIGHHETPLSASTKMLERFPNNLPKHRENVIPADSEKRSFEENTPSPCMTPRPGSSAGMPPILTMQPHCRKTTWTTRCPTLCPMAMDWW
IRESfinder result
IRESfinder score
0.372614767
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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