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mmu_circClip1_606
Basic information of circular RNA
PanCircBase ID:
mmu_circClip1_606
mm39_Chr. Position ID:
chr5|123747301|123755885|-
Gene name:
Clip1
Transcript:
ENSMUST00000111564.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
17,16,15,14
Exon/intron offsets:
0,2583,8097,8418
Genomic length:
8584
Exon/intron sizes in nt:
1,07,11,72,16,166
Flanking exon/introns:
chr5:123741782-123747301|chr5:123755885-123759858
Splice length:
606
Other database IDs:
circAtlas: mmu-Clip1_0037
circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_166939
Human Ortholog IDs:
Mature spliced Sequence:
ATCCGTGGAAGAACTCCAGCTCAAGCTTACAAAGGCCAATGAAAACGCCAGTTTTCTGCAGAAGAGTATTGGCGAAGTGACTCTTAAAGCTGAGCAGAGTCAGCAGCAAGCAGCCAGAAAACATGAAGAAGAAAAGAAAGAGTTGGAGGAAAAACTGTTGGAACTGGAAAAGAAGATGGAAACAAGCTACAACCAGTGTCAGGACCTGAAAGCTAAGTATGAAAAAGCCAGTTCTGAGACTAAAACAAAGCATGAAGAAATCCTGCAGAACCTCCAGAAGATGCTGGCGGACACAGAGGATAAGCTGAAGGCTGCTCAGGAGGCGAACAGAGATCTGATGCAGGACATGGAGGAGCTGAAAACACAGGCCGACAAAGCCAAAGCTGCTCAGACTGCAGAAGACGCCATGCAGATCATGGAACAGATGACCAAAGAGAAAACAGAAACGCTGGCCTCCTTGGAGGACACCAAGCAAACAAATGCAAGACTACAGAATGAATTGGACACACTTAAGGAAAACAACTTGAAAACTGTGGAAGAGCTGAACAAGTCAAAAGAACTGCTGAGTGTAGAGAACCAAAAAATGGAAGAATTCAAGAAAGAAAT
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
ACTGTGGAAGAGCTGAACAAGT
59.83
CTTCTGCAGAAAACTGGCGT
59.05
141
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TGTGGAAGAGCTGAACAAGTCA
59.83
CTCTTCTGCAGAAAACTGGCG
59.8
141
PCR template sequence:
CACTTAAGGAAAACAACTTGAAAACTGTGGAAGAGCTGAACAAGTCAAAAGAACTGCTGAGTGTAGAGAACCAAAAAATGGAAGAATTCAAGAAAGAAATATCCGTGGAAGAACTCCAGCTCAAGCTTACAAAGGCCAATGAAAACGCCAGTTTTCTGCAGAAGAGTATTGGCGAAGTGACTCTTAAAGCTGAGCAGAGT
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-9-5p(1), mmu-miR-7b-5p(1), mmu-miR-5101(1), mmu-miR-335-3p(1)
siRNAs for circular RNA silencing
Junction sequence
TCAAGAAAGAAATATCCGTGGAAGAA
siRNA sets
TTCTTCCACGGATATTTCT, TTCCACGGATATTTCTTTC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCCLIP1_606_ORF_1
1.0683
0.465741633
0.997735919
1035
ORF sequence:
ATGGAAACAAGCTACAACCAGTGTCAGGACCTGAAAGCTAAGTATGAAAAAGCCAGTTCTGAGACTAAAACAAAGCATGAAGAAATCCTGCAGAACCTCCAGAAGATGCTGGCGGACACAGAGGATAAGCTGAAGGCTGCTCAGGAGGCGAACAGAGATCTGATGCAGGACATGGAGGAGCTGAAAACACAGGCCGACAAAGCCAAAGCTGCTCAGACTGCAGAAGACGCCATGCAGATCATGGAACAGATGACCAAAGAGAAAACAGAAACGCTGGCCTCCTTGGAGGACACCAAGCAAACAAATGCAAGACTACAGAATGAATTGGACACACTTAAGGAAAACAACTTGAAAACTGTGGAAGAGCTGAACAAGTCAAAAGAACTGCTGAGTGTAGAGAACCAAAAAATGGAAGAATTCAAGAAAGAAATATCCGTGGAAGAACTCCAGCTCAAGCTTACAAAGGCCAATGAAAACGCCAGTTTTCTGCAGAAGAGTATTGGCGAAGTGACTCTTAAAGCTGAGCAGAGTCAGCAGCAAGCAGCCAGAAAACATGAAGAAGAAAAGAAAGAGTTGGAGGAAAAACTGTTGGAACTGGAAAAGAAGATGGAAACAAGCTACAACCAGTGTCAGGACCTGAAAGCTAAGTATGAAAAAGCCAGTTCTGAGACTAAAACAAAGCATGAAGAAATCCTGCAGAACCTCCAGAAGATGCTGGCGGACACAGAGGATAAGCTGAAGGCTGCTCAGGAGGCGAACAGAGATCTGATGCAGGACATGGAGGAGCTGAAAACACAGGCCGACAAAGCCAAAGCTGCTCAGACTGCAGAAGACGCCATGCAGATCATGGAACAGATGACCAAAGAGAAAACAGAAACGCTGGCCTCCTTGGAGGACACCAAGCAAACAAATGCAAGACTACAGAATGAATTGGACACACTTAAGGAAAACAACTTGAAAACTGTGGAAGAGCTGAACAAGTCAAAAGAACTGCTGAGTGTAGAGAACCAAAAAATGGAAGAATTCAAGAAAGAA
Peptide sequence:
METSYNQCQDLKAKYEKASSETKTKHEEILQNLQKMLADTEDKLKAAQEANRDLMQDMEELKTQADKAKAAQTAEDAMQIMEQMTKEKTETLASLEDTKQTNARLQNELDTLKENNLKTVEELNKSKELLSVENQKMEEFKKEISVEELQLKLTKANENASFLQKSIGEVTLKAEQSQQQAARKHEEEKKELEEKLLELEKKMETSYNQCQDLKAKYEKASSETKTKHEEILQNLQKMLADTEDKLKAAQEANRDLMQDMEELKTQADKAKAAQTAEDAMQIMEQMTKEKTETLASLEDTKQTNARLQNELDTLKENNLKTVEELNKSKELLSVENQKMEEFKKE
IRESfinder result
IRESfinder score
0.244858877
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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