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mmu_circClip1_1503
Basic information of circular RNA
PanCircBase ID:
mmu_circClip1_1503
mm39_Chr. Position ID:
chr5|123755398|123773341|-
Gene name:
Clip1
Transcript:
ENSMUST00000137363.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
7
Exon/intron indexes:
12,11,10,9,8,7,6
Exon/intron offsets:
0,321,4460,5420,5877,13117,17838
Genomic length:
17943
Exon/intron sizes in nt:
21,61,66,15,78,45,87,10,000
Flanking exon/introns:
chr5:123750001-123755398|chr5:123773341-123778556
Splice length:
1503
Other database IDs:
circBase: mmu_circ_0012104, CIRCpedia: MMU_CIRCpedia_6165, circAtlas: mmu-Clip1_0015
circBase: hsa_circ_0097608, circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_142827
Human Ortholog IDs:
Mature spliced Sequence:
ACGCAGACCAAACTGGAGCATGCCCGCACTAAGGAGCTTGAACAGAGCCTGCTCTTTGAAAAGACCAAAGCTGACAAACTCCAGAGGGAGTTAGAAGACACTAGGGTGGCTACCGTCTCAGAAAAGTCCCGAATAATGGAACTAGAAAAGGACCTAGCATTGAGAGCACAGGAAGTAGCTGAGCTCCGAAGAAGGCTAGAGTCCAGTAAACCTCCTGGGGATGTGGATATGTCTCTCTCCCTTTTGCAAGAAATAAGTGCTTTGCAAGAAAAGCTAGAAGCCATCCATACTGACCACCAGGGCGAGATGACTTCTTTGAAGGAACACTTCGGAGCTCGAGAGGAGGCGTTTCAGAAGGAGATCAAGGCTCTGCACACGGCCACTGAGAAGCTTTCCAAAGAGAACGAGTCCCTGAGAAGCAAGCTCGACCACGCTAATAAGGAGAACTCCGATGTGATAGCTCTATGGAAGTCCAAACTGGAGACCGCCATAGCATCCCACCAGCAGGCAATGGAGGAGCTGAAGGTGTCCTTTAGCAAAGGCATTGGAACGGACTCCGCTGAATTTGCTGAGTTAAAGACACAGATAGAGAGACTGAGACTAGATTACCAGCACGAAATAGAAAGTTTACAGAGTAAACAGGACTCTGAGCGGTCTGCTCATGCTAAAGAGATGGAGACCATGCAGGCCAAGCTGATGAAGATCATTAAAGAGAAGGAGGACAGCCTGGAGGCCGTCAAAGCGAGACTGGACAGTGCAGAAGACCAGCACCTAGTGGAAATGGAGGACACGCTAAACAAACTGCAGGAGGCGGAGATTAAGAAAGAAAAGTTTGCCAGTACTTCAGAGGAGGCGGTCTCTGCTCAGACAAGGATGCAAGATACCGTAAATAAACTGCACCAAAAGGAGGAACAGTTTAACGTGTTGTCGTCTGAACTGGAGAAGTTGAGAGAAAATTTAACAGACATGGAGGCAAAATTTAAAGAGAAGGATGATCGAGAAGATCAGCTGGTAAAGGCAAAGGAAAAATTAGAAAACGACATTGCAGAAATAATGAAGATGTCAGGAGATAACTCTTCTCAGCTGACAAAGATGAATGATGAATTACGTCTGAAGGAAAGATCCGTGGAAGAACTCCAGCTCAAGCTTACAAAGGCCAATGAAAACGCCAGTTTTCTGCAGAAGAGTATTGGCGAAGTGACTCTTAAAGCTGAGCAGAGTCAGCAGCAAGCAGCCAGAAAACATGAAGAAGAAAAGAAAGAGTTGGAGGAAAAACTGTTGGAACTGGAAAAGAAGATGGAAACAAGCTACAACCAGTGTCAGGACCTGAAAGCTAAGTATGAAAAAGCCAGTTCTGAGACTAAAACAAAGCATGAAGAAATCCTGCAGAACCTCCAGAAGATGCTGGCGGACACAGAGGATAAGCTGAAGGCTGCTCAGGAGGCGAACAGAGATCTGATGCAGGACATGGAGGAGCTGAAAACACAGGCCGACAAAGCCAAA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GCGGACACAGAGGATAAGCT
59.54
AGCAGGCTCTGTTCAAGCTC
60.32
149
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GCGGACACAGAGGATAAGCT
59.54
GAGCAGGCTCTGTTCAAGCT
60.32
150
PCR template sequence:
GCTGGCGGACACAGAGGATAAGCTGAAGGCTGCTCAGGAGGCGAACAGAGATCTGATGCAGGACATGGAGGAGCTGAAAACACAGGCCGACAAAGCCAAAACGCAGACCAAACTGGAGCATGCCCGCACTAAGGAGCTTGAACAGAGCCTGCTCTTTGAAAAGACCAAAGCTGACAAACTCCAGAGGGAGTTAGAAGACA
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-7b-5p(1), mmu-miR-135a-5p(1), mmu-miR-185-5p(1), mmu-miR-181b-5p(1), mmu-miR-136-5p(1), mmu-miR-370-3p(1), mmu-miR-335-3p(1), mmu-miR-532-5p(1), mmu-miR-484(1), mmu-miR-181d-5p(1)
siRNAs for circular RNA silencing
Junction sequence
CGACAAAGCCAAAACGCAGACCAAAC
siRNA sets
GTTTGGTCTGCGTTTTGGC, CTGCGTTTTGGCTTTGTCG, TCTGCGTTTTGGCTTTGTC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCCLIP1_1503_ORF_1
1.1061
0.412681688
0.999999995
2871
ORF sequence:
ATGGAACTAGAAAAGGACCTAGCATTGAGAGCACAGGAAGTAGCTGAGCTCCGAAGAAGGCTAGAGTCCAGTAAACCTCCTGGGGATGTGGATATGTCTCTCTCCCTTTTGCAAGAAATAAGTGCTTTGCAAGAAAAGCTAGAAGCCATCCATACTGACCACCAGGGCGAGATGACTTCTTTGAAGGAACACTTCGGAGCTCGAGAGGAGGCGTTTCAGAAGGAGATCAAGGCTCTGCACACGGCCACTGAGAAGCTTTCCAAAGAGAACGAGTCCCTGAGAAGCAAGCTCGACCACGCTAATAAGGAGAACTCCGATGTGATAGCTCTATGGAAGTCCAAACTGGAGACCGCCATAGCATCCCACCAGCAGGCAATGGAGGAGCTGAAGGTGTCCTTTAGCAAAGGCATTGGAACGGACTCCGCTGAATTTGCTGAGTTAAAGACACAGATAGAGAGACTGAGACTAGATTACCAGCACGAAATAGAAAGTTTACAGAGTAAACAGGACTCTGAGCGGTCTGCTCATGCTAAAGAGATGGAGACCATGCAGGCCAAGCTGATGAAGATCATTAAAGAGAAGGAGGACAGCCTGGAGGCCGTCAAAGCGAGACTGGACAGTGCAGAAGACCAGCACCTAGTGGAAATGGAGGACACGCTAAACAAACTGCAGGAGGCGGAGATTAAGAAAGAAAAGTTTGCCAGTACTTCAGAGGAGGCGGTCTCTGCTCAGACAAGGATGCAAGATACCGTAAATAAACTGCACCAAAAGGAGGAACAGTTTAACGTGTTGTCGTCTGAACTGGAGAAGTTGAGAGAAAATTTAACAGACATGGAGGCAAAATTTAAAGAGAAGGATGATCGAGAAGATCAGCTGGTAAAGGCAAAGGAAAAATTAGAAAACGACATTGCAGAAATAATGAAGATGTCAGGAGATAACTCTTCTCAGCTGACAAAGATGAATGATGAATTACGTCTGAAGGAAAGATCCGTGGAAGAACTCCAGCTCAAGCTTACAAAGGCCAATGAAAACGCCAGTTTTCTGCAGAAGAGTATTGGCGAAGTGACTCTTAAAGCTGAGCAGAGTCAGCAGCAAGCAGCCAGAAAACATGAAGAAGAAAAGAAAGAGTTGGAGGAAAAACTGTTGGAACTGGAAAAGAAGATGGAAACAAGCTACAACCAGTGTCAGGACCTGAAAGCTAAGTATGAAAAAGCCAGTTCTGAGACTAAAACAAAGCATGAAGAAATCCTGCAGAACCTCCAGAAGATGCTGGCGGACACAGAGGATAAGCTGAAGGCTGCTCAGGAGGCGAACAGAGATCTGATGCAGGACATGGAGGAGCTGAAAACACAGGCCGACAAAGCCAAAACGCAGACCAAACTGGAGCATGCCCGCACTAAGGAGCTTGAACAGAGCCTGCTCTTTGAAAAGACCAAAGCTGACAAACTCCAGAGGGAGTTAGAAGACACTAGGGTGGCTACCGTCTCAGAAAAGTCCCGAATAATGGAACTAGAAAAGGACCTAGCATTGAGAGCACAGGAAGTAGCTGAGCTCCGAAGAAGGCTAGAGTCCAGTAAACCTCCTGGGGATGTGGATATGTCTCTCTCCCTTTTGCAAGAAATAAGTGCTTTGCAAGAAAAGCTAGAAGCCATCCATACTGACCACCAGGGCGAGATGACTTCTTTGAAGGAACACTTCGGAGCTCGAGAGGAGGCGTTTCAGAAGGAGATCAAGGCTCTGCACACGGCCACTGAGAAGCTTTCCAAAGAGAACGAGTCCCTGAGAAGCAAGCTCGACCACGCTAATAAGGAGAACTCCGATGTGATAGCTCTATGGAAGTCCAAACTGGAGACCGCCATAGCATCCCACCAGCAGGCAATGGAGGAGCTGAAGGTGTCCTTTAGCAAAGGCATTGGAACGGACTCCGCTGAATTTGCTGAGTTAAAGACACAGATAGAGAGACTGAGACTAGATTACCAGCACGAAATAGAAAGTTTACAGAGTAAACAGGACTCTGAGCGGTCTGCTCATGCTAAAGAGATGGAGACCATGCAGGCCAAGCTGATGAAGATCATTAAAGAGAAGGAGGACAGCCTGGAGGCCGTCAAAGCGAGACTGGACAGTGCAGAAGACCAGCACCTAGTGGAAATGGAGGACACGCTAAACAAACTGCAGGAGGCGGAGATTAAGAAAGAAAAGTTTGCCAGTACTTCAGAGGAGGCGGTCTCTGCTCAGACAAGGATGCAAGATACCGTAAATAAACTGCACCAAAAGGAGGAACAGTTTAACGTGTTGTCGTCTGAACTGGAGAAGTTGAGAGAAAATTTAACAGACATGGAGGCAAAATTTAAAGAGAAGGATGATCGAGAAGATCAGCTGGTAAAGGCAAAGGAAAAATTAGAAAACGACATTGCAGAAATAATGAAGATGTCAGGAGATAACTCTTCTCAGCTGACAAAGATGAATGATGAATTACGTCTGAAGGAAAGATCCGTGGAAGAACTCCAGCTCAAGCTTACAAAGGCCAATGAAAACGCCAGTTTTCTGCAGAAGAGTATTGGCGAAGTGACTCTTAAAGCTGAGCAGAGTCAGCAGCAAGCAGCCAGAAAACATGAAGAAGAAAAGAAAGAGTTGGAGGAAAAACTGTTGGAACTGGAAAAGAAGATGGAAACAAGCTACAACCAGTGTCAGGACCTGAAAGCTAAGTATGAAAAAGCCAGTTCTGAGACTAAAACAAAGCATGAAGAAATCCTGCAGAACCTCCAGAAGATGCTGGCGGACACAGAGGATAAGCTGAAGGCTGCTCAGGAGGCGAACAGAGATCTGATGCAGGACATGGAGGAGCTGAAAACACAGGCCGACAAAGCCAAA
Peptide sequence:
MELEKDLALRAQEVAELRRRLESSKPPGDVDMSLSLLQEISALQEKLEAIHTDHQGEMTSLKEHFGAREEAFQKEIKALHTATEKLSKENESLRSKLDHANKENSDVIALWKSKLETAIASHQQAMEELKVSFSKGIGTDSAEFAELKTQIERLRLDYQHEIESLQSKQDSERSAHAKEMETMQAKLMKIIKEKEDSLEAVKARLDSAEDQHLVEMEDTLNKLQEAEIKKEKFASTSEEAVSAQTRMQDTVNKLHQKEEQFNVLSSELEKLRENLTDMEAKFKEKDDREDQLVKAKEKLENDIAEIMKMSGDNSSQLTKMNDELRLKERSVEELQLKLTKANENASFLQKSIGEVTLKAEQSQQQAARKHEEEKKELEEKLLELEKKMETSYNQCQDLKAKYEKASSETKTKHEEILQNLQKMLADTEDKLKAAQEANRDLMQDMEELKTQADKAKTQTKLEHARTKELEQSLLFEKTKADKLQRELEDTRVATVSEKSRIMELEKDLALRAQEVAELRRRLESSKPPGDVDMSLSLLQEISALQEKLEAIHTDHQGEMTSLKEHFGAREEAFQKEIKALHTATEKLSKENESLRSKLDHANKENSDVIALWKSKLETAIASHQQAMEELKVSFSKGIGTDSAEFAELKTQIERLRLDYQHEIESLQSKQDSERSAHAKEMETMQAKLMKIIKEKEDSLEAVKARLDSAEDQHLVEMEDTLNKLQEAEIKKEKFASTSEEAVSAQTRMQDTVNKLHQKEEQFNVLSSELEKLRENLTDMEAKFKEKDDREDQLVKAKEKLENDIAEIMKMSGDNSSQLTKMNDELRLKERSVEELQLKLTKANENASFLQKSIGEVTLKAEQSQQQAARKHEEEKKELEEKLLELEKKMETSYNQCQDLKAKYEKASSETKTKHEEILQNLQKMLADTEDKLKAAQEANRDLMQDMEELKTQADKAK
IRESfinder result
IRESfinder score
0.341227161
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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