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mmu_circElk4_1412
Basic information of circular RNA
PanCircBase ID:
mmu_circElk4_1412
mm39_Chr. Position ID:
chr1|131940763|131947204|+
Gene name:
Elk4
Transcript:
ENSMUST00000027696.10
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
2,3,4,5
Exon/intron offsets:
0,1357,4567,6324
Genomic length:
6441
Exon/intron sizes in nt:
209,216,870,117
Flanking exon/introns:
chr1:131935678-131940763|chr1:131947204-131951290
Splice length:
1412
Other database IDs:
circAtlas: mmu-Elk4_0007
Human Ortholog IDs:
Mature spliced Sequence:
GGCTGCCAGTTTGTATGTAAACTACCCTGCTATGACGCTTAACTGTCTGGAGGAGAAGTACAAGTTGGACTAGGAACAGATTGATCCCTCCACGTCAGCCTCCTGGCCACCCGAGACTCACATCTTGTCAGAGAAACACAATGGGCTCATTTAGCTGTACATTGAACTGGTGGTCTTCTAAGAGAATGTGATGATAATAAGACTTTAAGCCCATTGCTATGGACAGTGCCATCACTCTGTGGCAGTTCCTTCTCCAGCTCCTGCAGGAGCCTCAGAATGAGCACATGATCTGCTGGACATCTAACAATGGGGAGTTCAAGCTTCTGCAGGCGGAGGAGGTGGCTCGTCTTTGGGGGATTCGCAAGAACAAGCCTAATATGAATTATGATAAACTCAGCCGAGCCCTGCGATACTACTACGTAAAGAACATCATTAAAAAAGTGAATGGTCAGAAGTTTGTGTACAAGTTTGTCTCCTATCCAGAGATTTTGAAAATGGACCCACTGACGGTAGGCAGGATTGAGGGAGACTGTGAAGCTTTAAATTCCATTGAAACCAGCAGTTCCAAAGATGTTGAGTATGGAGGAAAGGAGAGGCCACCTCAGCCTGGAGCCAAGACCTCTAGTCGCAATGACTACATACACTCTGGTTTGTATTCTTCATTTACTCTTAACTCTCTGAACACCTCCAATAAGAAGCTTTTCAAGTCAATAAAGATAGAGAATCCAGCGGAAAAACTAGCAGAGAAGAAAGCCCAGGAGCCAACACCGTCCGTCATCAAATTTGTGACAACGCCTGCCAAAAAGCCGCCCATCGAGCCTGTCGCTGCTGCCTTTGCAACGAGCCCTAGTCTTTCTCCATCTTCTGAAGAAACTATCCAAGCTTTGGAGACATTAGTCTCTCCCACACTACCTTCCCTGGAAACCCCAGCCTCCATATCCATTCTGGCTACCACCTTTAACCCCACTCCTCCGGTTCCATCCACACCCCTTCCTCTAAAGGAGCCTCCCAGGACACCTTCTCCACCACTGAGTTCTAACCCAGACATTGACACAGACATTGAGTCAGTGGCTTCTCAGCCAATGGAACTTCCAGAGAACTTATCACTGGAGCCTAAAAATGAGGATTCAGCTTTGCCAGAAAAGGACAAAACAAATAACTCATCAAGATCTAAGAAGCCCAAAGGGTTAGAACTGACACCCGCCCTTGTGGTCACAGGCAGTGACCCCAGCCCCTTGGGGATCCTAAGCCCATCTCTCCCGACAGCGTCTCTTACACCAGCACTCTTTTCACAGACTCCCATCTTGCTGACTCCGAGCCCCTTGCTCTCCAGCATCCACTTTTGGAGCACTCTCAGCCCGTTTGCTCCCTTGAGCCCAGCCAGACTGCAAGGTGCTAATACGCTTTTCCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TTTTGGAGCACTCTCAGCCC
60.25
GCTGACGTGGAGGGATCAAT
59.82
171
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
ACTCTCAGCCCGTTTGCTC
60
GCTGACGTGGAGGGATCAAT
59.82
162
PCR template sequence:
TCCGAGCCCCTTGCTCTCCAGCATCCACTTTTGGAGCACTCTCAGCCCGTTTGCTCCCTTGAGCCCAGCCAGACTGCAAGGTGCTAATACGCTTTTCCAGGGCTGCCAGTTTGTATGTAAACTACCCTGCTATGACGCTTAACTGTCTGGAGGAGAAGTACAAGTTGGACTAGGAACAGATTGATCCCTCCACGTCAGCC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
10
Interacting miRNAs (#binding sites)
mmu-miR-27b-3p(1), mmu-miR-7a-5p(1), mmu-miR-185-5p(1), mmu-miR-29b-1-5p(1), mmu-miR-183-5p(1), mmu-miR-297a-5p(1), mmu-miR-27a-5p(1), mmu-miR-384-3p(1), mmu-miR-29b-2-5p(1), mmu-miR-574-5p(1)
siRNAs for circular RNA silencing
Junction sequence
TACGCTTTTCCAGGGCTGCCAGTTTG
siRNA sets
CTGGCAGCCCTGGAAAAGC, AAACTGGCAGCCCTGGAAA, TGGCAGCCCTGGAAAAGCG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCELK4_1412_ORF_1
0.9972
0.18062333
0.997981142
1236
ORF sequence:
ATGGACAGTGCCATCACTCTGTGGCAGTTCCTTCTCCAGCTCCTGCAGGAGCCTCAGAATGAGCACATGATCTGCTGGACATCTAACAATGGGGAGTTCAAGCTTCTGCAGGCGGAGGAGGTGGCTCGTCTTTGGGGGATTCGCAAGAACAAGCCTAATATGAATTATGATAAACTCAGCCGAGCCCTGCGATACTACTACGTAAAGAACATCATTAAAAAAGTGAATGGTCAGAAGTTTGTGTACAAGTTTGTCTCCTATCCAGAGATTTTGAAAATGGACCCACTGACGGTAGGCAGGATTGAGGGAGACTGTGAAGCTTTAAATTCCATTGAAACCAGCAGTTCCAAAGATGTTGAGTATGGAGGAAAGGAGAGGCCACCTCAGCCTGGAGCCAAGACCTCTAGTCGCAATGACTACATACACTCTGGTTTGTATTCTTCATTTACTCTTAACTCTCTGAACACCTCCAATAAGAAGCTTTTCAAGTCAATAAAGATAGAGAATCCAGCGGAAAAACTAGCAGAGAAGAAAGCCCAGGAGCCAACACCGTCCGTCATCAAATTTGTGACAACGCCTGCCAAAAAGCCGCCCATCGAGCCTGTCGCTGCTGCCTTTGCAACGAGCCCTAGTCTTTCTCCATCTTCTGAAGAAACTATCCAAGCTTTGGAGACATTAGTCTCTCCCACACTACCTTCCCTGGAAACCCCAGCCTCCATATCCATTCTGGCTACCACCTTTAACCCCACTCCTCCGGTTCCATCCACACCCCTTCCTCTAAAGGAGCCTCCCAGGACACCTTCTCCACCACTGAGTTCTAACCCAGACATTGACACAGACATTGAGTCAGTGGCTTCTCAGCCAATGGAACTTCCAGAGAACTTATCACTGGAGCCTAAAAATGAGGATTCAGCTTTGCCAGAAAAGGACAAAACAAATAACTCATCAAGATCTAAGAAGCCCAAAGGGTTAGAACTGACACCCGCCCTTGTGGTCACAGGCAGTGACCCCAGCCCCTTGGGGATCCTAAGCCCATCTCTCCCGACAGCGTCTCTTACACCAGCACTCTTTTCACAGACTCCCATCTTGCTGACTCCGAGCCCCTTGCTCTCCAGCATCCACTTTTGGAGCACTCTCAGCCCGTTTGCTCCCTTGAGCCCAGCCAGACTGCAAGGTGCTAATACGCTTTTCCAGGGCTGCCAGTTTGTATGTAAACTACCCTGCTATGACGCTTAA
Peptide sequence:
MDSAITLWQFLLQLLQEPQNEHMICWTSNNGEFKLLQAEEVARLWGIRKNKPNMNYDKLSRALRYYYVKNIIKKVNGQKFVYKFVSYPEILKMDPLTVGRIEGDCEALNSIETSSSKDVEYGGKERPPQPGAKTSSRNDYIHSGLYSSFTLNSLNTSNKKLFKSIKIENPAEKLAEKKAQEPTPSVIKFVTTPAKKPPIEPVAAAFATSPSLSPSSEETIQALETLVSPTLPSLETPASISILATTFNPTPPVPSTPLPLKEPPRTPSPPLSSNPDIDTDIESVASQPMELPENLSLEPKNEDSALPEKDKTNNSSRSKKPKGLELTPALVVTGSDPSPLGILSPSLPTASLTPALFSQTPILLTPSPLLSSIHFWSTLSPFAPLSPARLQGANTLFQGCQFVCKLPCYDA
IRESfinder result
IRESfinder score
0.708239431
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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