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mmu_ciTimm21_1254
Basic information of circular RNA
PanCircBase ID:
mmu_ciTimm21_1254
mm39_Chr. Position ID:
chr18|84966064|84967318|-
Gene name:
Timm21
Transcript:
ENSMUST00000235548.2
CircRNA type:
Circular intronic (ci)RNA
Exon/Intron count:
1
Exon/intron indexes:
2
Exon/intron offsets:
0
Genomic length:
1254
Exon/intron sizes in nt:
1254
Flanking exon/introns:
chr18:84965870-84967318
Splice length:
1254
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GTTAGTTTTCTGATGATTGTATTGGGAAGGAGGTGTGCATCCCTTCTGAAGCCCATGCTGAGCTGTTTTTCTGTTTTCAGGTCTCATTCTTTGATGCACTTTGACCCTGGCACTGTGTCATACATACACTTTTCAGTGGTGTTAAGTGCACCTGCATCATCAGGTCTCAGGCATCCTTCCTACAAAACTATCCTAAACCAGAATGTCGCCAAGAGAGTTGAAAGTTGGCAGAGACTACACTTAGGGCACTATATTGTATACAGAATTCAGGGGATTCTATGTGGTCCTCAGTAGGCATCCCAACTGTGTTTGGATGCAATGGTAATCACAGGCTCGGGCTCTCAGGCATTTTCACATTGAGACAAATAGAACTGCACAAAATACATGAAAGAATAGAATATTGCTAGAGTCAGCTTCCTAGCTGTTCCATAAACAGGTATGTTTTGTCATACTTTTACAGGTCCCACTTTTTGCCAGGCCAACTGCCTGCCTTACAATAAATAGGTAATCTGGCACTGCTAGGATGGACCTATTTTTTTGCTTATTCCTTTCTTTTAGCTCTTAGGTCTTAGATATCTGACAACTTTCTTTCTCATAATAAAGACACTCAGCAAAAAGACAAAACATGGTATTTAATTGTATGTATGTTTTTAAGAAAAGTATTTGCTTTGAAAATTCAAAACAGTTTCTACGTCAAATGGATTTTCTCATAAAAGATTTGCACCTGGTTTATTTTAACAATGTCATTACTATTGCCCATCCATTTTATCTTCTCAGTATGAGTGTCAATAGAGAAATACATTCAAACTTCTGCTTAATTGTTTCTTGTCAAGGAGAGAGCCTCCGCTCATCCTGTATCATTGTAAAGCTACCAGTGACAGGGTGACCCATCTCTGTCCCTGTGTGTGACATATTTATTTTCGCATAATGCCCTTTCTCTAGTTTTCTTGTTTGAGTCAAGGGCCCTCACAGATTATTTTTCTCTCCTAAAATCACTTGCCATATGTAAACAAATAATGTCACTTGACCATCAGAAAATACTTACATAGGAGCCATGAAAAGAATCACACTAAATAAGTGTAGTCTCTATTCTGCAGGTGATTGGTGTATTTGGTGAGCCTTTGAAAGGCTACGGGGAAATGTCGAGACGTGGGCGGAGACAGCATGTCCGGTAATGCGGTGTCCCCGGGGGAACTCTAGGGTAATCTCTGAGTACAGGGAATTTGGATGTGCAACATTGTATTTTCTCTACAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
ATGTCCGGTAATGCGGTGTC
60.46
ATGGGCTTCAGAAGGGATGC
60.11
146
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
ATGTCCGGTAATGCGGTGTC
60.46
GCATGGGCTTCAGAAGGGAT
60.11
148
PCR template sequence:
CGGAGACAGCATGTCCGGTAATGCGGTGTCCCCGGGGGAACTCTAGGGTAATCTCTGAGTACAGGGAATTTGGATGTGCAACATTGTATTTTCTCTACAGGTTAGTTTTCTGATGATTGTATTGGGAAGGAGGTGTGCATCCCTTCTGAAGCCCATGCTGAGCTGTTTTTCTGTTTTCAGGTCTCATTCTTTGATGCACT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
13
Interacting miRNAs (#binding sites)
mmu-miR-20b-5p(1), mmu-miR-106a-5p(1), mmu-miR-17-5p(1), mmu-miR-19b-3p(1), mmu-miR-19a-3p(1), mmu-miR-148b-3p(1), mmu-miR-125b-5p(1), mmu-miR-185-5p(1), mmu-miR-29b-1-5p(1), mmu-miR-297a-5p(1), mmu-miR-466d-3p(1), mmu-miR-377-3p(1), mmu-miR-335-3p(1)
siRNAs for circular RNA silencing
Junction sequence
ATTTTCTCTACAGGTTAGTTTTCTGA
siRNA sets
GAAAACTAACCTGTAGAGA, AAAACTAACCTGTAGAGAA, AAACTAACCTGTAGAGAAA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CITIMM21_1254_ORF_1
0.4406
-0.235258346
0.041974153
321
ORF sequence:
ATGTGCAACATTGTATTTTCTCTACAGGTTAGTTTTCTGATGATTGTATTGGGAAGGAGGTGTGCATCCCTTCTGAAGCCCATGCTGAGCTGTTTTTCTGTTTTCAGGTCTCATTCTTTGATGCACTTTGACCCTGGCACTGTGTCATACATACACTTTTCAGTGGTGTTAAGTGCACCTGCATCATCAGGTCTCAGGCATCCTTCCTACAAAACTATCCTAAACCAGAATGTCGCCAAGAGAGTTGAAAGTTGGCAGAGACTACACTTAGGGCACTATATTGTATACAGAATTCAGGGGATTCTATGTGGTCCTCAGTAG
Peptide sequence:
MCNIVFSLQVSFLMIVLGRRCASLLKPMLSCFSVFRSHSLMHFDPGTVSYIHFSVVLSAPASSGLRHPSYKTILNQNVAKRVESWQRLHLGHYIVYRIQGILCGPQ
IRESfinder result
IRESfinder score
0.833296043
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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