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mmu_circSmad4_1433
Basic information of circular RNA
PanCircBase ID:
mmu_circSmad4_1433
mm39_Chr. Position ID:
chr18|73781955|73811110|-
Gene name:
Smad4
Transcript:
ENSMUST00000025393.14
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
9
Exon/intron indexes:
10,9,8,7,6,5,4,3,2
Exon/intron offsets:
0,841,8310,9683,9894,13773,26276,26886,28778
Genomic length:
29155
Exon/intron sizes in nt:
169,184,51,117,120,210,30,175,377
Flanking exon/introns:
chr18:73774992-73781955|chr18:73811110-73836500
Splice length:
1433
Other database IDs:
circBase: mmu_circ_0007492, CIRCpedia: MMU_CIRCpedia_28502, circAtlas: mmu-Smad4_0009
circBase: hsa_circ_0108590, circAtlas: hsa-SMAD4_0004, CIRCpedia: HSA_CIRCpedia_23977
Human Ortholog IDs:
Mature spliced Sequence:
GTCATCCTGCTCACCAGATGTCTTGACAGTTTTTCTTGCAACATTGGCCATTGGTTTTCACTGCCTTCAAAAGATCAAAATTACTCCAGAAATTGGAGAGTTGGATTTAAAAGAAAAAACTTGAACAAATGGACAATATGTCTATAACAAATACACCAACAAGTAACGATGCCTGTCTGAGCATTGTACATAGTTTGATGTGTCATAGACAAGGTGGGGAAAGTGAAACCTTTGCAAAAAGAGCAATTGAGAGTTTGGTAAAGAAGCTGAAAGAGAAAAAAGATGAATTGGATTCTTTAATAACAGCTATAACTACAAATGGAGCTCATCCTAGCAAGTGTGTCACCATACAGAGAACATTGGATGGACGACTTCAGGTGGCTGGTCGGAAAGGATTTCCTCATGTGATCTATGCCCGTCTGTGGAGGTGGCCTGATCTACACAAGAATGAACTAAAGCATGTTAAATATTGTCAGTATGCGTTTGACTTAAAATGTGACAGTGTCTGTGTGAATCCATATCACTATGAGCGGGTTGTCTCACCTGGAATTGATCTCTCAGGATTAACACTGCAGAGTAATGCTCCAAGTATGTTAGTGAAGGATGAGTACGTTCACGACTTTGAAGGACAGCCGTCCTTACCCACTGAAGGACATTCGATTCAAACCATCCAACACCCGCCAAGTAATCGCGCATCAACGGAGACGTACAGCGCCCCGGCTCTGTTAGCCCCGGCAGAGTCTAACGCCACCAGCACCACCAACTTCCCCAACATTCCTGTGGCTTCCACAAGTCAGCCGGCCAGTATTCTGGCGGGCAGCCATAGTGAAGGACTGTTGCAGATAGCTTCAGGGCCTCAGCCAGGACAGCAGCAGAATGGATTTACTGCTCAGCCAGCTACTTACCATCATAACAGCACTACCACCTGGACTGGAAGTAGGACTGCACCATACACACCTAATTTGCCTCACCACCAAAACGGCCATCTTCAGCACCACCCGCCTATGCCGCCCCATCCTGGACATTACTGGCCAGTTCACAATGAGCTTGCATTCCAGCCTCCCATTTCCAATCATCCTGCTCCTGAGTACTGGTGCTCCATTGCTTACTTTGAAATGGACGTTCAGGTAGGAGAGACGTTTAAGGTCCCTTCAAGCTGCCCTGTTGTGACTGTGGATGGCTATGTGGATCCTTCGGGAGGAGATCGCTTTTGCTTGGGTCAACTCTCCAATGTCCACAGGACAGAAGCGATTGAGAGAGCGAGGTTGCACATAGGCAAAGGAGTGCAGTTGGAATGTAAAGGTGAAGGTGACGTTTGGGTCAGGTGCCTTAGTGACCACGCGGTCTTTGTACAGAGTTACTACCTGGACAGAGAAGCTGGCCGAGCACCTGGCGACGCTGTTCATAAGATCTACCCAAGCGCGTATATAAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CCACGCGGTCTTTGTACAGA
60.32
GCAGTGAAAACCAATGGCCA
59.61
161
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
ACCACGCGGTCTTTGTACAG
60.6
GCAGTGAAAACCAATGGCCA
59.61
162
PCR template sequence:
TGACCACGCGGTCTTTGTACAGAGTTACTACCTGGACAGAGAAGCTGGCCGAGCACCTGGCGACGCTGTTCATAAGATCTACCCAAGCGCGTATATAAAGGTCATCCTGCTCACCAGATGTCTTGACAGTTTTTCTTGCAACATTGGCCATTGGTTTTCACTGCCTTCAAAAGATCAAAATTACTCCAGAAATTGGAGAG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
15
Interacting miRNAs (#binding sites)
mmu-let-7a-5p(1), mmu-miR-1a-3p(1), mmu-miR-429-3p(1), mmu-miR-206-3p(1), mmu-miR-200b-3p(1), mmu-miR-200c-3p(1), mmu-miR-132-3p(1), mmu-miR-138-5p(1), mmu-miR-136-5p(1), mmu-miR-212-3p(1), mmu-miR-483-5p(1), mmu-miR-425-5p(1), mmu-miR-34b-5p(1), mmu-miR-1904(1), mmu-miR-193b-3p(1)
siRNAs for circular RNA silencing
Junction sequence
CGCGTATATAAAGGTCATCCTGCTCA
siRNA sets
GATGACCTTTATATACGCG, GGATGACCTTTATATACGC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSMAD4_1433_ORF_1
0.8249
0.054312293
0.999017172
1452
ORF sequence:
ATGGACAATATGTCTATAACAAATACACCAACAAGTAACGATGCCTGTCTGAGCATTGTACATAGTTTGATGTGTCATAGACAAGGTGGGGAAAGTGAAACCTTTGCAAAAAGAGCAATTGAGAGTTTGGTAAAGAAGCTGAAAGAGAAAAAAGATGAATTGGATTCTTTAATAACAGCTATAACTACAAATGGAGCTCATCCTAGCAAGTGTGTCACCATACAGAGAACATTGGATGGACGACTTCAGGTGGCTGGTCGGAAAGGATTTCCTCATGTGATCTATGCCCGTCTGTGGAGGTGGCCTGATCTACACAAGAATGAACTAAAGCATGTTAAATATTGTCAGTATGCGTTTGACTTAAAATGTGACAGTGTCTGTGTGAATCCATATCACTATGAGCGGGTTGTCTCACCTGGAATTGATCTCTCAGGATTAACACTGCAGAGTAATGCTCCAAGTATGTTAGTGAAGGATGAGTACGTTCACGACTTTGAAGGACAGCCGTCCTTACCCACTGAAGGACATTCGATTCAAACCATCCAACACCCGCCAAGTAATCGCGCATCAACGGAGACGTACAGCGCCCCGGCTCTGTTAGCCCCGGCAGAGTCTAACGCCACCAGCACCACCAACTTCCCCAACATTCCTGTGGCTTCCACAAGTCAGCCGGCCAGTATTCTGGCGGGCAGCCATAGTGAAGGACTGTTGCAGATAGCTTCAGGGCCTCAGCCAGGACAGCAGCAGAATGGATTTACTGCTCAGCCAGCTACTTACCATCATAACAGCACTACCACCTGGACTGGAAGTAGGACTGCACCATACACACCTAATTTGCCTCACCACCAAAACGGCCATCTTCAGCACCACCCGCCTATGCCGCCCCATCCTGGACATTACTGGCCAGTTCACAATGAGCTTGCATTCCAGCCTCCCATTTCCAATCATCCTGCTCCTGAGTACTGGTGCTCCATTGCTTACTTTGAAATGGACGTTCAGGTAGGAGAGACGTTTAAGGTCCCTTCAAGCTGCCCTGTTGTGACTGTGGATGGCTATGTGGATCCTTCGGGAGGAGATCGCTTTTGCTTGGGTCAACTCTCCAATGTCCACAGGACAGAAGCGATTGAGAGAGCGAGGTTGCACATAGGCAAAGGAGTGCAGTTGGAATGTAAAGGTGAAGGTGACGTTTGGGTCAGGTGCCTTAGTGACCACGCGGTCTTTGTACAGAGTTACTACCTGGACAGAGAAGCTGGCCGAGCACCTGGCGACGCTGTTCATAAGATCTACCCAAGCGCGTATATAAAGGTCATCCTGCTCACCAGATGTCTTGACAGTTTTTCTTGCAACATTGGCCATTGGTTTTCACTGCCTTCAAAAGATCAAAATTACTCCAGAAATTGGAGAGTTGGATTTAAAAGAAAAAACTTGAACAAATGGACAATATGTCTATAA
Peptide sequence:
MDNMSITNTPTSNDACLSIVHSLMCHRQGGESETFAKRAIESLVKKLKEKKDELDSLITAITTNGAHPSKCVTIQRTLDGRLQVAGRKGFPHVIYARLWRWPDLHKNELKHVKYCQYAFDLKCDSVCVNPYHYERVVSPGIDLSGLTLQSNAPSMLVKDEYVHDFEGQPSLPTEGHSIQTIQHPPSNRASTETYSAPALLAPAESNATSTTNFPNIPVASTSQPASILAGSHSEGLLQIASGPQPGQQQNGFTAQPATYHHNSTTTWTGSRTAPYTPNLPHHQNGHLQHHPPMPPHPGHYWPVHNELAFQPPISNHPAPEYWCSIAYFEMDVQVGETFKVPSSCPVVTVDGYVDPSGGDRFCLGQLSNVHRTEAIERARLHIGKGVQLECKGEGDVWVRCLSDHAVFVQSYYLDREAGRAPGDAVHKIYPSAYIKVILLTRCLDSFSCNIGHWFSLPSKDQNYSRNWRVGFKRKNLNKWTICL
IRESfinder result
IRESfinder score
0.563697545
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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