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mmu_circSmurf2_1187
Basic information of circular RNA
PanCircBase ID:
mmu_circSmurf2_1187
mm39_Chr. Position ID:
chr11|106732425|106766765|-
Gene name:
Smurf2
Transcript:
ENSMUST00000139297.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
10
Exon/intron indexes:
11,10,9,8,7,6,5,4,3,2
Exon/intron offsets:
0,4383,8148,10847,14581,23112,26935,27397,29902,34301
Genomic length:
34340
Exon/intron sizes in nt:
196,159,85,203,84,66,134,112,109,39
Flanking exon/introns:
chr11:106730117-106732425|chr11:106766765-106811006
Splice length:
1187
Other database IDs:
circAtlas: mmu-Smurf2_0043
Human Ortholog IDs:
Mature spliced Sequence:
TACTCTGTGCAAAAAACTTGGTGAAAAAGGATTTTTTCCGTCTTCCTGATCCATTTGCTAAGGTGGTAGTTGATGGTTCTGGGCAGTGCCATTCTACAGATACTGTGAAGAACACACTTGATCCAAAGTGGAATCAGCATTATGACCTGCAGTGAAGTGAAATCTACAAGAGTCCTGCTCGCTCAAGGCCTGCATATAGGGAAGAAGCAGGGGAAAAGCGTTACAAACAGCTTTGTTCTGCAGCATTAAAAATGTAACAGGTATATCGGAAAGTCTGATTCAGTTACGATCAGCGTATGGAATCATAAGAAGATCCATAAGAAGCAAGGTGCTGGATTTCTTGGTTGTGTTCGTCTTCTTTCCAATGCCATCAACCGCCTCAAGGACACTGGTTATCAGAGGTTGGATTTATGCAAACTGGGGCCAAATGACAATGATACAGTTCGAGGACAAATTGTAGTTGGGAAGAAAGGCGGACTGCCTCGGGAAGAATCCAGTATCTAAACCACATCACAAGAACTACACAGTGGGAACGCCCAACACGACCGGCGTCAGAATATTCTAGTCCTGGCAGACCCCTCAGCTGCTTTGTGGATGAGAATACTCCAATTACTGGAACAAATGGTGCAACGTGTGGACATTCTTCAGACCCCAGACTAGCAGAGAGAAGAGTCAGGTCCCAGCGACATAGAAATTACATGAGCAGGACACACTTACACACTCCTCCAGACCTACCGGAAGGCTATGAACAAAGGACAACGCAGCAGGGTCAGGTATATTTCTTACATACTCAGACTGGTGTGAGCACATGGCATGATCCACGAGTGCCTAGGGATCTTAGCAACATCAATTGTGAAGAGCTCGGTCCTTTGCCTCCTGGATGGGAGATCCGCAATACCGCAACAGGAAGAGTTTATTTCGTTGACCATAACAACAGAACAACACAATTTACAGATCCCCGGCTCTCTGCTAACTTGCATTTAGTTTTAAATCGTCAGAACCAGTTGAAAGACCAACAGCAACAGCAAGTGGTGCCATTGTGTCCCGATGACACTGAGTGTCTGACAGTGCCAAGATACAAGCGAGATTTGGTTCAAAAACTAAAAATCTTGCGGCAAGAACTTTCCCAACAGCAGCCTCAAGCTGGCCACTGCCGTATTGAGGTGTCTAGGGAAGAGATTTTTGAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CTTGCGGCAAGAACTTTCCC
60.04
ACTGCCCAGAACCATCAACT
59.23
166
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AACTTTCCCAACAGCAGCCT
60.11
ACTGCCCAGAACCATCAACT
59.23
155
PCR template sequence:
TTTGGTTCAAAAACTAAAAATCTTGCGGCAAGAACTTTCCCAACAGCAGCCTCAAGCTGGCCACTGCCGTATTGAGGTGTCTAGGGAAGAGATTTTTGAGTACTCTGTGCAAAAAACTTGGTGAAAAAGGATTTTTTCCGTCTTCCTGATCCATTTGCTAAGGTGGTAGTTGATGGTTCTGGGCAGTGCCATTCTACAGA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
11
Interacting miRNAs (#binding sites)
mmu-miR-183-5p(2), mmu-miR-155-5p(1), mmu-miR-34c-5p(1), mmu-miR-34a-5p(1), mmu-miR-122-5p(1), mmu-miR-7a-5p(1), mmu-miR-181b-5p(1), mmu-miR-434-3p(1), mmu-miR-96-5p(1), mmu-miR-574-5p(1), mmu-miR-181d-5p(1)
siRNAs for circular RNA silencing
Junction sequence
AGAGATTTTTGAGTACTCTGTGCAAA
siRNA sets
CAGAGTACTCAAAAATCTC, ACAGAGTACTCAAAAATCT, TTTGCACAGAGTACTCAAA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSMURF2_1187_ORF_1
0.9197
0.056559296
0.585390767
513
ORF sequence:
ATGAGCAGGACACACTTACACACTCCTCCAGACCTACCGGAAGGCTATGAACAAAGGACAACGCAGCAGGGTCAGGTATATTTCTTACATACTCAGACTGGTGTGAGCACATGGCATGATCCACGAGTGCCTAGGGATCTTAGCAACATCAATTGTGAAGAGCTCGGTCCTTTGCCTCCTGGATGGGAGATCCGCAATACCGCAACAGGAAGAGTTTATTTCGTTGACCATAACAACAGAACAACACAATTTACAGATCCCCGGCTCTCTGCTAACTTGCATTTAGTTTTAAATCGTCAGAACCAGTTGAAAGACCAACAGCAACAGCAAGTGGTGCCATTGTGTCCCGATGACACTGAGTGTCTGACAGTGCCAAGATACAAGCGAGATTTGGTTCAAAAACTAAAAATCTTGCGGCAAGAACTTTCCCAACAGCAGCCTCAAGCTGGCCACTGCCGTATTGAGGTGTCTAGGGAAGAGATTTTTGAGTACTCTGTGCAAAAAACTTGGTGA
Peptide sequence:
MSRTHLHTPPDLPEGYEQRTTQQGQVYFLHTQTGVSTWHDPRVPRDLSNINCEELGPLPPGWEIRNTATGRVYFVDHNNRTTQFTDPRLSANLHLVLNRQNQLKDQQQQQVVPLCPDDTECLTVPRYKRDLVQKLKILRQELSQQQPQAGHCRIEVSREEIFEYSVQKTW
IRESfinder result
IRESfinder score
0.508596501
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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