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mmu_circLimch1_1351
Basic information of circular RNA
PanCircBase ID:
mmu_circLimch1_1351
mm39_Chr. Position ID:
chr5|67150485|67183455|+
Gene name:
Limch1
Transcript:
ENSMUST00000101164.11
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
9
Exon/intron indexes:
9,10,11,12,13,14,15,16,17
Exon/intron offsets:
0,3977,5504,5837,9285,23322,24474,28749,32929
Genomic length:
32970
Exon/intron sizes in nt:
36,127,158,409,222,91,161,106,41
Flanking exon/introns:
chr5:67132005-67150485|chr5:67183455-67184830
Splice length:
1351
Other database IDs:
circBase: hsa_circ_0069582, circAtlas: hsa-SCAF8_0001
Human Ortholog IDs:
Mature spliced Sequence:
ATACGGTCCCAGAACTCCTGTGTCAGATGACGCAGAGAGCACGAGTATGTTTGACATGCGGTGTGAGGAGGAGGCAGCGGTGCTGCCGCACAGCAGGGCCCGCCAGGAGCAGCTGCAGCTGATAAATAACCAGCTGAGGGAAGAGGACGACAAATGGCAAGATGACCTGGCTCGCTGGAAGAGCCGGAGAAGAAGCGCTTCTCAGGACTTGATCAAGAAAGAGGAAGAAAGGAAAAAAATGGAGAAGCTGATGTCTGGGGAAGATGGGACAAGTGAGCGGAGGAAAAGCATCAAAACTTACAGAGAAATCGTCCAAGAAAAAGAGCGGAGAGAGAGGGAACTTCATGAGGCGTACAAGAACGCAAGGTCGCAGGAGGAGGCCGAGGGGATCCTCCAGCAGTACATCGAGAGGTTCACCATCAGTGAGGCTGTCCTCGAACGCTTGGAGATGCCAAAAATCCTGGAAAGAAGCCATTCAACAGAGCCAAACGTGTCCTCCTTCCCAAACGACCCCAGCCCCATGAAGTACCTGCGGCAGCAGTCACTGCCCCCACCCAAGTTCACTGCCACGGTTGAGACCACCATAGCTCGCACCAGTGTCCCAGAGAGCATTGCGTCAGCAGGCACTGGGTCTCCAAGCAAAATCATCACTCCAAACACAGTGCCTATGCTGACACCCAGGCCTTACTCCCAGCCCAAAAACTCTCAAGAGGTTCTGAAGACTTTTAAGGTAGATGGGAAGGTCAGCATGAATGGGGAAATGGCCCCTGGAGATGAGGAAGGAAAGGAAAAAGAAGGCCCTGCAGCTGCAGCCCCTGGCCCTTCCTTAACCAAGTCCCAGATGTTTGAAGGTGTGGCCACGGTGCACGACTCTCCTGTGCAGGTGAAACAAGGCAGCAACAGCATCGAGATCAACATCAAGAAGCCAAATTCTGCTCCCCAGGAACTGACAGCAGCCTCTGAGGAAACTGAATCGAACGGCCAAGAGGATGAAGACGGTGAAGAAAGGCCAGGGACAGGGGATTTGGAGCCTGACTCGGCAGAACCCCAGCACTTTACGACAACTGTGACTCGGTGCAGCCCAACAGTGGCCTTGGTGGAGTTTTCATCCAACCCGCAGCTGAAGAATGAGGTGCCAGAACAAGGCCAGAAGAAGCCAGAAGATGAGATGAGTGGGAAGGTGGAGTTAGTGTTGTCACAGAAGGTGGCAAAGCCAAAATCCCCAGAGCCTGAAGCAACCCTGACGTTTCCATTTCTCGACAAAATGCCTGAAACCAACCAACTACATTTGCCAAATCCCAGTTCTCAAGCGGATTCTCCAAGCAGTGAAAAGTCCCCTGGGAGCACACCC
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
ATGCCTGAAACCAACCAACT
57.91
TCCTCACACCGCATGTCAAA
59.89
156
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
ATGCCTGAAACCAACCAACT
57.91
CCTCACACCGCATGTCAAAC
59.76
155
PCR template sequence:
ATTTCTCGACAAAATGCCTGAAACCAACCAACTACATTTGCCAAATCCCAGTTCTCAAGCGGATTCTCCAAGCAGTGAAAAGTCCCCTGGGAGCACACCCATACGGTCCCAGAACTCCTGTGTCAGATGACGCAGAGAGCACGAGTATGTTTGACATGCGGTGTGAGGAGGAGGCAGCGGTGCTGCCGCACAGCAGGGCC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
16
Interacting miRNAs (#binding sites)
mmu-miR-34a-5p(2), mmu-miR-296-3p(2), mmu-miR-134-5p(1), mmu-miR-27b-3p(1), mmu-miR-93-5p(1), mmu-miR-135a-5p(1), mmu-miR-34c-5p(1), mmu-miR-106b-5p(1), mmu-miR-136-5p(1), mmu-miR-182-5p(1), mmu-miR-370-3p(1), mmu-miR-34b-5p(1), mmu-miR-29b-2-5p(1), mmu-miR-342-3p(1), mmu-miR-207(1), mmu-miR-484(1)
siRNAs for circular RNA silencing
Junction sequence
TGGGAGCACACCCATACGGTCCCAGA
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCLIMCH1_1351_ORF_1
0.9981
0.378043939
0.999560441
1335
ORF sequence:
ATGTTTGACATGCGGTGTGAGGAGGAGGCAGCGGTGCTGCCGCACAGCAGGGCCCGCCAGGAGCAGCTGCAGCTGATAAATAACCAGCTGAGGGAAGAGGACGACAAATGGCAAGATGACCTGGCTCGCTGGAAGAGCCGGAGAAGAAGCGCTTCTCAGGACTTGATCAAGAAAGAGGAAGAAAGGAAAAAAATGGAGAAGCTGATGTCTGGGGAAGATGGGACAAGTGAGCGGAGGAAAAGCATCAAAACTTACAGAGAAATCGTCCAAGAAAAAGAGCGGAGAGAGAGGGAACTTCATGAGGCGTACAAGAACGCAAGGTCGCAGGAGGAGGCCGAGGGGATCCTCCAGCAGTACATCGAGAGGTTCACCATCAGTGAGGCTGTCCTCGAACGCTTGGAGATGCCAAAAATCCTGGAAAGAAGCCATTCAACAGAGCCAAACGTGTCCTCCTTCCCAAACGACCCCAGCCCCATGAAGTACCTGCGGCAGCAGTCACTGCCCCCACCCAAGTTCACTGCCACGGTTGAGACCACCATAGCTCGCACCAGTGTCCCAGAGAGCATTGCGTCAGCAGGCACTGGGTCTCCAAGCAAAATCATCACTCCAAACACAGTGCCTATGCTGACACCCAGGCCTTACTCCCAGCCCAAAAACTCTCAAGAGGTTCTGAAGACTTTTAAGGTAGATGGGAAGGTCAGCATGAATGGGGAAATGGCCCCTGGAGATGAGGAAGGAAAGGAAAAAGAAGGCCCTGCAGCTGCAGCCCCTGGCCCTTCCTTAACCAAGTCCCAGATGTTTGAAGGTGTGGCCACGGTGCACGACTCTCCTGTGCAGGTGAAACAAGGCAGCAACAGCATCGAGATCAACATCAAGAAGCCAAATTCTGCTCCCCAGGAACTGACAGCAGCCTCTGAGGAAACTGAATCGAACGGCCAAGAGGATGAAGACGGTGAAGAAAGGCCAGGGACAGGGGATTTGGAGCCTGACTCGGCAGAACCCCAGCACTTTACGACAACTGTGACTCGGTGCAGCCCAACAGTGGCCTTGGTGGAGTTTTCATCCAACCCGCAGCTGAAGAATGAGGTGCCAGAACAAGGCCAGAAGAAGCCAGAAGATGAGATGAGTGGGAAGGTGGAGTTAGTGTTGTCACAGAAGGTGGCAAAGCCAAAATCCCCAGAGCCTGAAGCAACCCTGACGTTTCCATTTCTCGACAAAATGCCTGAAACCAACCAACTACATTTGCCAAATCCCAGTTCTCAAGCGGATTCTCCAAGCAGTGAAAAGTCCCCTGGGAGCACACCCATACGGTCCCAGAACTCCTGTGTCAGATGA
Peptide sequence:
MFDMRCEEEAAVLPHSRARQEQLQLINNQLREEDDKWQDDLARWKSRRRSASQDLIKKEEERKKMEKLMSGEDGTSERRKSIKTYREIVQEKERRERELHEAYKNARSQEEAEGILQQYIERFTISEAVLERLEMPKILERSHSTEPNVSSFPNDPSPMKYLRQQSLPPPKFTATVETTIARTSVPESIASAGTGSPSKIITPNTVPMLTPRPYSQPKNSQEVLKTFKVDGKVSMNGEMAPGDEEGKEKEGPAAAAPGPSLTKSQMFEGVATVHDSPVQVKQGSNSIEINIKKPNSAPQELTAASEETESNGQEDEDGEERPGTGDLEPDSAEPQHFTTTVTRCSPTVALVEFSSNPQLKNEVPEQGQKKPEDEMSGKVELVLSQKVAKPKSPEPEATLTFPFLDKMPETNQLHLPNPSSQADSPSSEKSPGSTPIRSQNSCVR
IRESfinder result
IRESfinder score
0.273933965
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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