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mmu_circMfsd11_697
Basic information of circular RNA
PanCircBase ID:
mmu_circMfsd11_697
mm39_Chr. Position ID:
chr11|116749299|116759485|+
Gene name:
Mfsd11
Transcript:
ENSMUST00000139954.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
8
Exon/intron indexes:
4,5,6,7,8,9,10,11
Exon/intron offsets:
0,850,1023,2585,3049,5432,7417,10060
Genomic length:
10186
Exon/intron sizes in nt:
10,85,59,75,91,45,41,60,000
Flanking exon/introns:
chr11:116745524-116749299|chr11:116759485-116762119
Splice length:
697
Other database IDs:
circAtlas: mmu-Mfsd11_0001
circBase: hsa_circ_0107687, circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_130020
Human Ortholog IDs:
Mature spliced Sequence:
CTTGGCAATTATTTATGGCGTGTTCTCTGCTTCAAATTTGATCACTCCGTCCGTGGTCGCCATTGTTGGACCTCAGATCTCTATGTTTGTCAGTGGTTTGTTTTACAGCCTTTCCCATGGTCCTTCTACACAGCATCTGTCTTCATCGGAATTGCCGCTGCTGTCCTTTGGACAGCACAAGGAAATTGCCTGACGATAAATTCTGATGAGCACACAATCGGGAGAAACAGCGGAATTTTCTGGGCACTCTTACAGTCTAGCTTGTTCTTTGGGAATCTCTACATATATTTTGCATGGCAAGGGAAGACCCAGATCTCAGAGCATGACCGAAGGACAGTGTTTATTGCTCTGACAGTGATAAGCCTCGTGGGGACCGTTCTGTTCTTTCTCATTCGGAAACCAGATCCTGAGAATGTCCTTGGAGAAGAAGAGTCTTGCGATGACCAGGACATGGAAGCCACCGAGTCTGCCCAGAACAACGTGACAAAGGCAGTCGATGCGTTTAAAAAGTCTCTGAGGCTGTGTGTCACCAGGGAGATGCTGCTCCTGAGCGTCACGACTGCCTACACAGGTCTGGAGCTGACCTTCTTCTCTGGGGTGTACGGTACCTGTATTGGGGCCGTAAACAAATTTGGGACAGAAGAGAAAAGCCTCATTGGACTTTCTGGAATTTTCATCGGCATTGGAGAGATTTTAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
ACCTGTATTGGGGCCGTAAA
59.01
CAACAATGGCGACCACGGA
60.96
159
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
ACCTGTATTGGGGCCGTAAA
59.01
AACAATGGCGACCACGGAC
60.96
158
PCR template sequence:
GTGTACGGTACCTGTATTGGGGCCGTAAACAAATTTGGGACAGAAGAGAAAAGCCTCATTGGACTTTCTGGAATTTTCATCGGCATTGGAGAGATTTTAGCTTGGCAATTATTTATGGCGTGTTCTCTGCTTCAAATTTGATCACTCCGTCCGTGGTCGCCATTGTTGGACCTCAGATCTCTATGTTTGTCAGTGGTTTG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
7
Interacting miRNAs (#binding sites)
mmu-miR-200a-3p(1), mmu-miR-141-3p(1), mmu-miR-429-3p(1), mmu-miR-15b-5p(1), mmu-miR-184-3p(1), mmu-miR-503-5p(1), mmu-miR-207(1)
siRNAs for circular RNA silencing
Junction sequence
GGAGAGATTTTAGCTTGGCAATTATT
siRNA sets
TAATTGCCAAGCTAAAATC, ATTGCCAAGCTAAAATCTC, AATAATTGCCAAGCTAAAA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCMFSD11_697_ORF_1
1.0679
0.132506115
0.338561312
288
ORF sequence:
ATGGAAGCCACCGAGTCTGCCCAGAACAACGTGACAAAGGCAGTCGATGCGTTTAAAAAGTCTCTGAGGCTGTGTGTCACCAGGGAGATGCTGCTCCTGAGCGTCACGACTGCCTACACAGGTCTGGAGCTGACCTTCTTCTCTGGGGTGTACGGTACCTGTATTGGGGCCGTAAACAAATTTGGGACAGAAGAGAAAAGCCTCATTGGACTTTCTGGAATTTTCATCGGCATTGGAGAGATTTTAGCTTGGCAATTATTTATGGCGTGTTCTCTGCTTCAAATTTGA
Peptide sequence:
MEATESAQNNVTKAVDAFKKSLRLCVTREMLLLSVTTAYTGLELTFFSGVYGTCIGAVNKFGTEEKSLIGLSGIFIGIGEILAWQLFMACSLLQI
IRESfinder result
IRESfinder score
0.713488009
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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