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mmu_circSync_1150
Basic information of circular RNA
PanCircBase ID:
mmu_circSync_1150
mm39_Chr. Position ID:
chr4|129187019|129188169|+
Gene name:
Sync
Transcript:
ENSMUST00000102599.4
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
1
Exon/intron indexes:
2
Exon/intron offsets:
0
Genomic length:
1150
Exon/intron sizes in nt:
1150
Flanking exon/introns:
chr4:129181581-129187019|chr4:129188169-129200134
Splice length:
1150
Other database IDs:
CIRCpedia: MMU_CIRCpedia_7344, circAtlas: mmu-Sync_0001
circBase: hsa_circ_0004895, circAtlas: hsa-SYNC_0002, CIRCpedia: HSA_CIRCpedia_31454
Human Ortholog IDs:
Mature spliced Sequence:
GGAACCACACACCGAGGCGAGTTTTCCTCTTCAGGAGTCAGAATCCCCGAAGGAGGCCAAGACCTTTAACCCAGAGGCCACTCTGTCTTTGGAGGGGACTGTGAACCTAGAGGACATTCTCTATCTGGGGGCATCGGGGGACTTTGAAGAGAGTTTTTATGAGGAAGAATATGAGAAGCCAGCACTGACACTGTTTATCGACGAATCGAGGCAGCCAGACGAGGCGCTGGGCCTAGAAGAGCCCGTGCGCCCAGAGGAGATGCTGTCTGTGGAGGAATCCGTGACGCCAGATGAGGTGCAAATTTCAGAGCAGCCTGTGGAGCCAGCTAAGAGCCCAACTGCTTGTGAGGGAGAAATGGTGGCCACGGAGGGAAGCCTGCCTGCTCAACCGATTCCCAACACCGAGGAGGATCCCCTCAGCGTGGAGGACCTGGAGCGGCTGGAAGCTCGTTTCCAGCAGTGTGTACAAGCCGTGTCCCAGCTGGAAGAGGAGAGGGACCAGCTAATCCACGAGCTCGTGCTACTCCGGGAGCCAGCCCTGCAGGAGGTGCAGCAAGTCCACCAGGACATCCTGGCTGCCTACAAGCTCCACGCACAGGCAGAGCTGGAGAGGGACGGGCTCAGGGAGGAGATCCGGACGGTGAAGCAGAAGCTGTTCAAGGTGACCAAGGAATGCGTGGCTTACCAATACCAGCTGGAGTGCCGTCAGCAGGATGTGGCTCAGTTTGCCGACTGCAGGGAAGCGCTGACCACTCGGGCAGCCCAGCTCTCGGAAGAACTGACCCAGCTCCGAGATGCCTGTCAGAAGCAGAAGGAGCAGTTACAGCAACAACTAGAAGCACCCCCGACCCAGAGCGATGGGCACTTTCTCCAGGAGAGCCGACGGCTGTCGACACAGTTTGAAAATCTCATGGCCGAGAGCCGCCAGGGCCTGGAGGAGGAGTATGAGCCTCAGCTGCTCCGGCTCCTGGAAAGGAAAGAGGCCGGGACCAAAGCTCTACAGGACACCCAGGCGGAGATCCAGGAGATGAGGGAGGCTCTGCGACCCCTGGAAGCAGAGGCCCGGCAGCTCCAACTTCAGAACAGGAACCTGGAGGACCAGATCACGCTCGTGAGGCAAAAACGCGATGAAGAGGTTCAACAGTACAGG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CGGCAGCTCCAACTTCAGAA
60.6
AAAGGTCTTGGCCTCCTTCG
59.96
154
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GGCAGCTCCAACTTCAGAAC
59.12
AAAGGTCTTGGCCTCCTTCG
59.96
153
PCR template sequence:
GGAAGCAGAGGCCCGGCAGCTCCAACTTCAGAACAGGAACCTGGAGGACCAGATCACGCTCGTGAGGCAAAAACGCGATGAAGAGGTTCAACAGTACAGGGGAACCACACACCGAGGCGAGTTTTCCTCTTCAGGAGTCAGAATCCCCGAAGGAGGCCAAGACCTTTAACCCAGAGGCCACTCTGTCTTTGGAGGGGACT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
18
Interacting miRNAs (#binding sites)
mmu-miR-20b-5p(1), mmu-miR-200a-3p(1), mmu-miR-106a-5p(1), mmu-miR-93-5p(1), mmu-miR-20a-5p(1), mmu-miR-17-5p(1), mmu-miR-223-3p(1), mmu-miR-125b-5p(1), mmu-miR-138-5p(1), mmu-miR-149-5p(1), mmu-miR-351-5p(1), mmu-miR-125a-5p(1), mmu-miR-342-5p(1), mmu-miR-680(1), mmu-miR-129-5p(1), mmu-miR-207(1), mmu-miR-1904(1), mmu-miR-542-5p(1)
siRNAs for circular RNA silencing
Junction sequence
TCAACAGTACAGGGGAACCACACACC
siRNA sets
TGTGGTTCCCCTGTACTGT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSYNC_1150_ORF_1
1.2537
0.528029064
0.999528071
1173
ORF sequence:
ATGAAGAGGTTCAACAGTACAGGGGAACCACACACCGAGGCGAGTTTTCCTCTTCAGGAGTCAGAATCCCCGAAGGAGGCCAAGACCTTTAACCCAGAGGCCACTCTGTCTTTGGAGGGGACTGTGAACCTAGAGGACATTCTCTATCTGGGGGCATCGGGGGACTTTGAAGAGAGTTTTTATGAGGAAGAATATGAGAAGCCAGCACTGACACTGTTTATCGACGAATCGAGGCAGCCAGACGAGGCGCTGGGCCTAGAAGAGCCCGTGCGCCCAGAGGAGATGCTGTCTGTGGAGGAATCCGTGACGCCAGATGAGGTGCAAATTTCAGAGCAGCCTGTGGAGCCAGCTAAGAGCCCAACTGCTTGTGAGGGAGAAATGGTGGCCACGGAGGGAAGCCTGCCTGCTCAACCGATTCCCAACACCGAGGAGGATCCCCTCAGCGTGGAGGACCTGGAGCGGCTGGAAGCTCGTTTCCAGCAGTGTGTACAAGCCGTGTCCCAGCTGGAAGAGGAGAGGGACCAGCTAATCCACGAGCTCGTGCTACTCCGGGAGCCAGCCCTGCAGGAGGTGCAGCAAGTCCACCAGGACATCCTGGCTGCCTACAAGCTCCACGCACAGGCAGAGCTGGAGAGGGACGGGCTCAGGGAGGAGATCCGGACGGTGAAGCAGAAGCTGTTCAAGGTGACCAAGGAATGCGTGGCTTACCAATACCAGCTGGAGTGCCGTCAGCAGGATGTGGCTCAGTTTGCCGACTGCAGGGAAGCGCTGACCACTCGGGCAGCCCAGCTCTCGGAAGAACTGACCCAGCTCCGAGATGCCTGTCAGAAGCAGAAGGAGCAGTTACAGCAACAACTAGAAGCACCCCCGACCCAGAGCGATGGGCACTTTCTCCAGGAGAGCCGACGGCTGTCGACACAGTTTGAAAATCTCATGGCCGAGAGCCGCCAGGGCCTGGAGGAGGAGTATGAGCCTCAGCTGCTCCGGCTCCTGGAAAGGAAAGAGGCCGGGACCAAAGCTCTACAGGACACCCAGGCGGAGATCCAGGAGATGAGGGAGGCTCTGCGACCCCTGGAAGCAGAGGCCCGGCAGCTCCAACTTCAGAACAGGAACCTGGAGGACCAGATCACGCTCGTGAGGCAAAAACGCGATGAAGAGGTTCAACAGTACAGG
Peptide sequence:
MKRFNSTGEPHTEASFPLQESESPKEAKTFNPEATLSLEGTVNLEDILYLGASGDFEESFYEEEYEKPALTLFIDESRQPDEALGLEEPVRPEEMLSVEESVTPDEVQISEQPVEPAKSPTACEGEMVATEGSLPAQPIPNTEEDPLSVEDLERLEARFQQCVQAVSQLEEERDQLIHELVLLREPALQEVQQVHQDILAAYKLHAQAELERDGLREEIRTVKQKLFKVTKECVAYQYQLECRQQDVAQFADCREALTTRAAQLSEELTQLRDACQKQKEQLQQQLEAPPTQSDGHFLQESRRLSTQFENLMAESRQGLEEEYEPQLLRLLERKEAGTKALQDTQAEIQEMREALRPLEAEARQLQLQNRNLEDQITLVRQKRDEEVQQYR
IRESfinder result
IRESfinder score
0.339497191
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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