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mmu_circSsb_706
Basic information of circular RNA
PanCircBase ID:
mmu_circSsb_706
mm39_Chr. Position ID:
chr2|69697795|69701177|+
Gene name:
Ssb
Transcript:
ENSMUST00000090852.11
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
6
Exon/intron indexes:
6,7,8,9,10,11
Exon/intron offsets:
0,1327,1690,2428,2933,3226
Genomic length:
3382
Exon/intron sizes in nt:
1,01,72,40,14,11,96,150
Flanking exon/introns:
chr2:69697723-69697795|chr2:69701177-69701465
Splice length:
706
Other database IDs:
CIRCpedia: MMU_CIRCpedia_27293, circAtlas: mmu-Ssb_0008
Human Ortholog IDs:
Mature spliced Sequence:
GGGTCAATATTTGCTGTGTTTGATAGTATTCAGTCTGCAAAGAAGTTTGTGGAGATCCCTGGCCAGAAGTACAAAGACACTAACCTGCTAATACTCTTTAAGGAAGATTACTTTGCAAAAAAAAATGAAGAAAGAAAGCAGAGCAAAGTGGAAGCTAAATTAAAAGCTAAACAAGAGCATGAAGGAAGACACAAGCCAGGAAGTACTGAAACCAGAGCTCTAGAAGGAAAGATGGGATGCTTACTGAAGTTTTCAGGTGACTTGGATGACCAGACCTGTAGAGAAGATTTACACTTCCTTTTCTCAAATCATGGTGAAATAAAATGGGTCGACTTTGCCAGAGGAGCAAAAGAGGGAATAATTCTCTTCAAAGAAAAGGCTAAGGAAGCACTTGAGAAAGCCAGAAATGCAAATAATGGTAACCTACTGTTAAGGAACAAAAAGGTGACTTGGAAAGTACTAGAAGGACATGCGGAAAAAGAAGCATTGAAAAAAATCACAGATGATCAGCAAGAATCCCTAAACAAATGGAAGTCAAAAGGAGGGCATGCAGGTGGAAGATTTAAAGGAAGCCATGTTTTTACAGCAGCCCGCAGATTTAAAGGAAAAGGGAAGGGTAATAGGCCTGGTTATGCTGGGGCACCCAAAGGAAGAGGACAGTTTCATGGAAGGAGGACAAGATTTGATGATGATGATCGTCGTCGTG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GGGAAGGGTAATAGGCCTGG
59.23
GCCAGGGATCTCCACAAACT
59.67
160
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
ATAGGCCTGGTTATGCTGGG
59.23
GCCAGGGATCTCCACAAACT
59.67
150
PCR template sequence:
AAAGGGAAGGGTAATAGGCCTGGTTATGCTGGGGCACCCAAAGGAAGAGGACAGTTTCATGGAAGGAGGACAAGATTTGATGATGATGATCGTCGTCGTGGGGTCAATATTTGCTGTGTTTGATAGTATTCAGTCTGCAAAGAAGTTTGTGGAGATCCCTGGCCAGAAGTACAAAGACACTAACCTGCTAATACTCTTTA
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-211-5p(1), mmu-miR-136-5p(1), mmu-miR-29b-1-5p(1), mmu-miR-541-5p(1), mmu-miR-224-5p(1), mmu-miR-29b-2-5p(1), mmu-miR-129-5p(1), mmu-miR-669d-5p(1)
siRNAs for circular RNA silencing
Junction sequence
GATCGTCGTCGTGGGGTCAATATTTG
siRNA sets
CAAATATTGACCCCACGAC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSSB_706_ORF_1
0.9115
0.062185268
0.9482456
864
ORF sequence:
ATGCAGGTGGAAGATTTAAAGGAAGCCATGTTTTTACAGCAGCCCGCAGATTTAAAGGAAAAGGGAAGGGTAATAGGCCTGGTTATGCTGGGGCACCCAAAGGAAGAGGACAGTTTCATGGAAGGAGGACAAGATTTGATGATGATGATCGTCGTCGTGGGGTCAATATTTGCTGTGTTTGATAGTATTCAGTCTGCAAAGAAGTTTGTGGAGATCCCTGGCCAGAAGTACAAAGACACTAACCTGCTAATACTCTTTAAGGAAGATTACTTTGCAAAAAAAAATGAAGAAAGAAAGCAGAGCAAAGTGGAAGCTAAATTAAAAGCTAAACAAGAGCATGAAGGAAGACACAAGCCAGGAAGTACTGAAACCAGAGCTCTAGAAGGAAAGATGGGATGCTTACTGAAGTTTTCAGGTGACTTGGATGACCAGACCTGTAGAGAAGATTTACACTTCCTTTTCTCAAATCATGGTGAAATAAAATGGGTCGACTTTGCCAGAGGAGCAAAAGAGGGAATAATTCTCTTCAAAGAAAAGGCTAAGGAAGCACTTGAGAAAGCCAGAAATGCAAATAATGGTAACCTACTGTTAAGGAACAAAAAGGTGACTTGGAAAGTACTAGAAGGACATGCGGAAAAAGAAGCATTGAAAAAAATCACAGATGATCAGCAAGAATCCCTAAACAAATGGAAGTCAAAAGGAGGGCATGCAGGTGGAAGATTTAAAGGAAGCCATGTTTTTACAGCAGCCCGCAGATTTAAAGGAAAAGGGAAGGGTAATAGGCCTGGTTATGCTGGGGCACCCAAAGGAAGAGGACAGTTTCATGGAAGGAGGACAAGATTTGATGATGATGATCGTCGTCGT
Peptide sequence:
MQVEDLKEAMFLQQPADLKEKGRVIGLVMLGHPKEEDSFMEGGQDLMMMIVVVGSIFAVFDSIQSAKKFVEIPGQKYKDTNLLILFKEDYFAKKNEERKQSKVEAKLKAKQEHEGRHKPGSTETRALEGKMGCLLKFSGDLDDQTCREDLHFLFSNHGEIKWVDFARGAKEGIILFKEKAKEALEKARNANNGNLLLRNKKVTWKVLEGHAEKEALKKITDDQQESLNKWKSKGGHAGGRFKGSHVFTAARRFKGKGKGNRPGYAGAPKGRGQFHGRRTRFDDDDRRR
IRESfinder result
IRESfinder score
0.472046771
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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