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mmu_circClip1_1197
Basic information of circular RNA
PanCircBase ID:
mmu_circClip1_1197
mm39_Chr. Position ID:
chr5|123765356|123780679|-
Gene name:
Clip1
Transcript:
ENSMUST00000111564.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
10,9,8,7,6
Exon/intron offsets:
0,3159,13200,14484,15125
Genomic length:
15323
Exon/intron sizes in nt:
1,17,71,76,11,04,198
Flanking exon/introns:
chr5:123761333-123765356|chr5:123780679-123784145
Splice length:
1197
Other database IDs:
circAtlas: mmu-Clip1_0049
CIRCpedia: HSA_CIRCpedia_7293
Human Ortholog IDs:
Mature spliced Sequence:
TTGACTGAAACCTCCTCCCGCTACGCCCGCAAGATCTCGGGCACCACTGCCCTCCAGGAGGCGCTGAAGGAGAAGCAGCAGCACATTGAGCAGCTGCTGGCTGAGCGGGACCTGGAGCGGGCCGAGGTGGCCAAGGCTACCAGCCACGTGGGGGAAATAGAGCAGGAGCTAGCCCTGGCCCGAGATGGGCATGACCAGCATGTCCTGGAACTAGAGGCCAAGATGGACCAGCTACGGACCATGGTGGAAGCTGCTGACAGGGAGAAAGTGGAGCTGCTCAACCAGCTGGAAGAGGAGAAGAGGAAGGTTGAGGACCTTCAGTTCCGAGTTGAAGAAGAATCAATTACCAAAGGCGATCTTGAGGTGGCTACCGTCTCAGAAAAGTCCCGAATAATGGAACTAGAAAAGGACCTAGCATTGAGAGCACAGGAAGTAGCTGAGCTCCGAAGAAGGCTAGAGTCCAGTAAACCTCCTGGGGATGTGGATATGTCTCTCTCCCTTTTGCAAGAAATAAGTGCTTTGCAAGAAAAGCTAGAAGCCATCCATACTGACCACCAGGGCGAGATGACTTCTTTGAAGGAACACTTCGGAGCTCGAGAGGAGGCGTTTCAGAAGGAGATCAAGGCTCTGCACACGGCCACTGAGAAGCTTTCCAAAGAGAACGAGTCCCTGAGAAGCAAGCTCGACCACGCTAATAAGGAGAACTCCGATGTGATAGCTCTATGGAAGTCCAAACTGGAGACCGCCATAGCATCCCACCAGCAGGCAATGGAGGAGCTGAAGGTGTCCTTTAGCAAAGGCATTGGAACGGACTCCGCTGAATTTGCTGAGTTAAAGACACAGATAGAGAGACTGAGACTAGATTACCAGCACGAAATAGAAAGTTTACAGAGTAAACAGGACTCTGAGCGGTCTGCTCATGCTAAAGAGATGGAGACCATGCAGGCCAAGCTGATGAAGATCATTAAAGAGAAGGAGGACAGCCTGGAGGCCGTCAAAGCGAGACTGGACAGTGCAGAAGACCAGCACCTAGTGGAAATGGAGGACACGCTAAACAAACTGCAGGAGGCGGAGATTAAGGCTAATAGCATTACCAAAGAGCTCCAGGAGAAAGAGCTAGTGCTCACTGGTCTGCAGGACAGTTTGAATCAAGTCAATCAAGTGAAGGAGACTTTGGAGAAAGAACTTCAGACTTTG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TAGTGCTCACTGGTCTGCAG
59.39
ATGTGCTGCTGCTTCTCCTT
59.96
166
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TAGTGCTCACTGGTCTGCAG
59.39
AATGTGCTGCTGCTTCTCCT
59.96
167
PCR template sequence:
AGAGCTCCAGGAGAAAGAGCTAGTGCTCACTGGTCTGCAGGACAGTTTGAATCAAGTCAATCAAGTGAAGGAGACTTTGGAGAAAGAACTTCAGACTTTGTTGACTGAAACCTCCTCCCGCTACGCCCGCAAGATCTCGGGCACCACTGCCCTCCAGGAGGCGCTGAAGGAGAAGCAGCAGCACATTGAGCAGCTGCTGG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
8
Interacting miRNAs (#binding sites)
mmu-miR-9-5p(1), mmu-miR-155-5p(1), mmu-miR-135a-5p(1), mmu-miR-185-5p(1), mmu-miR-136-5p(1), mmu-miR-370-3p(1), mmu-miR-207(1), mmu-miR-532-5p(1)
siRNAs for circular RNA silencing
Junction sequence
ACTTCAGACTTTGTTGACTGAAACCT
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCCLIP1_1197_ORF_1
1.1956
0.462324841
0.99999949
2172
ORF sequence:
ATGGACCAGCTACGGACCATGGTGGAAGCTGCTGACAGGGAGAAAGTGGAGCTGCTCAACCAGCTGGAAGAGGAGAAGAGGAAGGTTGAGGACCTTCAGTTCCGAGTTGAAGAAGAATCAATTACCAAAGGCGATCTTGAGGTGGCTACCGTCTCAGAAAAGTCCCGAATAATGGAACTAGAAAAGGACCTAGCATTGAGAGCACAGGAAGTAGCTGAGCTCCGAAGAAGGCTAGAGTCCAGTAAACCTCCTGGGGATGTGGATATGTCTCTCTCCCTTTTGCAAGAAATAAGTGCTTTGCAAGAAAAGCTAGAAGCCATCCATACTGACCACCAGGGCGAGATGACTTCTTTGAAGGAACACTTCGGAGCTCGAGAGGAGGCGTTTCAGAAGGAGATCAAGGCTCTGCACACGGCCACTGAGAAGCTTTCCAAAGAGAACGAGTCCCTGAGAAGCAAGCTCGACCACGCTAATAAGGAGAACTCCGATGTGATAGCTCTATGGAAGTCCAAACTGGAGACCGCCATAGCATCCCACCAGCAGGCAATGGAGGAGCTGAAGGTGTCCTTTAGCAAAGGCATTGGAACGGACTCCGCTGAATTTGCTGAGTTAAAGACACAGATAGAGAGACTGAGACTAGATTACCAGCACGAAATAGAAAGTTTACAGAGTAAACAGGACTCTGAGCGGTCTGCTCATGCTAAAGAGATGGAGACCATGCAGGCCAAGCTGATGAAGATCATTAAAGAGAAGGAGGACAGCCTGGAGGCCGTCAAAGCGAGACTGGACAGTGCAGAAGACCAGCACCTAGTGGAAATGGAGGACACGCTAAACAAACTGCAGGAGGCGGAGATTAAGGCTAATAGCATTACCAAAGAGCTCCAGGAGAAAGAGCTAGTGCTCACTGGTCTGCAGGACAGTTTGAATCAAGTCAATCAAGTGAAGGAGACTTTGGAGAAAGAACTTCAGACTTTGTTGACTGAAACCTCCTCCCGCTACGCCCGCAAGATCTCGGGCACCACTGCCCTCCAGGAGGCGCTGAAGGAGAAGCAGCAGCACATTGAGCAGCTGCTGGCTGAGCGGGACCTGGAGCGGGCCGAGGTGGCCAAGGCTACCAGCCACGTGGGGGAAATAGAGCAGGAGCTAGCCCTGGCCCGAGATGGGCATGACCAGCATGTCCTGGAACTAGAGGCCAAGATGGACCAGCTACGGACCATGGTGGAAGCTGCTGACAGGGAGAAAGTGGAGCTGCTCAACCAGCTGGAAGAGGAGAAGAGGAAGGTTGAGGACCTTCAGTTCCGAGTTGAAGAAGAATCAATTACCAAAGGCGATCTTGAGGTGGCTACCGTCTCAGAAAAGTCCCGAATAATGGAACTAGAAAAGGACCTAGCATTGAGAGCACAGGAAGTAGCTGAGCTCCGAAGAAGGCTAGAGTCCAGTAAACCTCCTGGGGATGTGGATATGTCTCTCTCCCTTTTGCAAGAAATAAGTGCTTTGCAAGAAAAGCTAGAAGCCATCCATACTGACCACCAGGGCGAGATGACTTCTTTGAAGGAACACTTCGGAGCTCGAGAGGAGGCGTTTCAGAAGGAGATCAAGGCTCTGCACACGGCCACTGAGAAGCTTTCCAAAGAGAACGAGTCCCTGAGAAGCAAGCTCGACCACGCTAATAAGGAGAACTCCGATGTGATAGCTCTATGGAAGTCCAAACTGGAGACCGCCATAGCATCCCACCAGCAGGCAATGGAGGAGCTGAAGGTGTCCTTTAGCAAAGGCATTGGAACGGACTCCGCTGAATTTGCTGAGTTAAAGACACAGATAGAGAGACTGAGACTAGATTACCAGCACGAAATAGAAAGTTTACAGAGTAAACAGGACTCTGAGCGGTCTGCTCATGCTAAAGAGATGGAGACCATGCAGGCCAAGCTGATGAAGATCATTAAAGAGAAGGAGGACAGCCTGGAGGCCGTCAAAGCGAGACTGGACAGTGCAGAAGACCAGCACCTAGTGGAAATGGAGGACACGCTAAACAAACTGCAGGAGGCGGAGATTAAGGCTAATAGCATTACCAAAGAGCTCCAGGAGAAAGAGCTAGTGCTCACTGGTCTGCAGGACAGTTTGAATCAAGTCAATCAAGTGAAGGAGACTTTGGAGAAAGAACTTCAGACTTTG
Peptide sequence:
MDQLRTMVEAADREKVELLNQLEEEKRKVEDLQFRVEEESITKGDLEVATVSEKSRIMELEKDLALRAQEVAELRRRLESSKPPGDVDMSLSLLQEISALQEKLEAIHTDHQGEMTSLKEHFGAREEAFQKEIKALHTATEKLSKENESLRSKLDHANKENSDVIALWKSKLETAIASHQQAMEELKVSFSKGIGTDSAEFAELKTQIERLRLDYQHEIESLQSKQDSERSAHAKEMETMQAKLMKIIKEKEDSLEAVKARLDSAEDQHLVEMEDTLNKLQEAEIKANSITKELQEKELVLTGLQDSLNQVNQVKETLEKELQTLLTETSSRYARKISGTTALQEALKEKQQHIEQLLAERDLERAEVAKATSHVGEIEQELALARDGHDQHVLELEAKMDQLRTMVEAADREKVELLNQLEEEKRKVEDLQFRVEEESITKGDLEVATVSEKSRIMELEKDLALRAQEVAELRRRLESSKPPGDVDMSLSLLQEISALQEKLEAIHTDHQGEMTSLKEHFGAREEAFQKEIKALHTATEKLSKENESLRSKLDHANKENSDVIALWKSKLETAIASHQQAMEELKVSFSKGIGTDSAEFAELKTQIERLRLDYQHEIESLQSKQDSERSAHAKEMETMQAKLMKIIKEKEDSLEAVKARLDSAEDQHLVEMEDTLNKLQEAEIKANSITKELQEKELVLTGLQDSLNQVNQVKETLEKELQTL
IRESfinder result
IRESfinder score
0.346050824
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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