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mmu_circSynj1_1677
Basic information of circular RNA
PanCircBase ID:
mmu_circSynj1_1677
mm39_Chr. Position ID:
chr16|90757131|90775658|-
Gene name:
Synj1
Transcript:
ENSMUST00000121759.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
12
Exon/intron indexes:
21,20,19,18,17,16,15,14,13,12,11,10
Exon/intron offsets:
0,316,1130,3574,3969,4261,7056,8939,11320,13666,16355,18445
Genomic length:
18527
Exon/intron sizes in nt:
216,118,157,159,193,141,85,192,24,157,153,82
Flanking exon/introns:
chr16:90754560-90757131|chr16:90775658-90776638
Splice length:
1677
Other database IDs:
circAtlas: mmu-Synj1_0024
Human Ortholog IDs:
Mature spliced Sequence:
GTGCCAGAGTGGTACAGTTCGAACAAACTGCTTGGATTGTCTGGATAGAACAAATAGTGTGCAGGCATTCCTTGGCTTAGAGATGCTCGCTAAGCAGCTGGAAGCTCTGGGCTTGGCTGAGAAGCCTCAGCTGGTGACCCGCTTCCAAGAAGTTTTCCGGTCCATGTGGTCTGTGAATGGCGACTCAATCAGTAAAATATATGCAGGCACCGGGGCCCTGGAAGGGAAGGCCAAGTTAAAAGATGGTGCGCGATCTGTCACCAGAACCATCCAGAATAACTTCTTCGACAGCTCCAAGCAGGAAGCCATTGATGTCCTGCTCCTGGGAAATACTCTCAACAGCGATTTAGCTGACAAAGCCCGAGCGCTTCTAACTACTGGAAGTTTGCGTGTTTCTGAACAGACATTACAGTCAGCATCTTCCAAAGTCTTAAAGAACATGTGTGAGAACTTCTACAAATACTCAAAGCCCAAGAAGATCCGAGTGTGTGTTGGCACCTGGAATGTGAACGGCGGGAAGCAGTTCCGCAGCATAGCGTTCAAGAACCAGACGCTCACAGACTGGCTTCTGGACGCTCCCAAGTTAGCCGGCATCCAGGAGTTTCAAGATAAGAGAAGTAAGCCAACTGATATATTTGCAATTGGCTTTGAAGAAATGGTGGAGCTGAATGCTGGGAACATTGTGAATGCAAGCACAACCAACCAGAAGCTGTGGGCAGTGGAGCTGCAGAAGACCATCTCCAGGGACAACAAGTATGTCCTGCTGGCCTCGGAGCAGCTGGTGGGTGTCTGCCTGTTTGTCTTTATCAGACCACAGCACGCTCCTTTTATCAGGGATGTTGCAGTTGATACTGTGAAAACTGGCATGGGAGGTGCAACTGGAAACAAGGGCGCCGTTGCAATTCGGATGCTCTTCCACACCACCAGCCTTTGCTTCGTCTGCAGCCACTTTGCTGCAGGGCAGTCCCAAGTCAAAGAGAGAAATGAAGATTTTGTAGAAATAGCACGAAAACTGAGTTTCCCCATGGGACGAATGCTCTTCTCCCATGACTATGTATTTTGGTGTGGTGATTTCAACTATCGAATTGACCTTCCGAATGAAGAGGTTAAAGAGCTCATAAGACAACAAAACTGGGATTCTCTGATCGCTGGGGATCAGCTCATCAACCAGAAAAATGCAGGACAGATCTTTAGAGGATTCTTAGAGGGAAAAGTAACGTTTGCTCCAACCTATAAATATGACTTGTTTTCTGAAGACTATGACACCAGTGAGAAGTGTCGCACCCCTGCTTGGACAGACCGTGTCCTCTGGAGAAGGAGGAAGTGGCCTTTTGACAGATCAGCTGAAGATTTAGATCTCCTGAATGCTAGTTTCCAAGATGAAAGTAAAATTCTTTATACATGGACCCCTGGCACCTTGCTGCACTATGGAAGAGCCGAGCTGAAGACTTCTGACCATAGGCCCGTCGTTGCCTTGATTGACATAGATATATTTGAAGTTGAAGCTGAAGAGAGACAAAAAATTTATAAAGAAGTTATTGCCGTCCAGGGCCCACCAGATGGCACAGTGCTGGTCTCAATCAAAAGTTCTGCACAAGAAAGTACTTTTTTTGATGATGCTTTGATTGATGAGCTTCTGCGGCAGTTTGCACACTTTGGTGAAGTTATACTCATAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GATTGATGAGCTTCTGCGGC
59.69
AGCGAGCATCTCTAAGCCAA
59.17
145
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
ATTGATGAGCTTCTGCGGCA
60.39
AGCGAGCATCTCTAAGCCAA
59.17
144
PCR template sequence:
CAATCAAAAGTTCTGCACAAGAAAGTACTTTTTTTGATGATGCTTTGATTGATGAGCTTCTGCGGCAGTTTGCACACTTTGGTGAAGTTATACTCATAAGGTGCCAGAGTGGTACAGTTCGAACAAACTGCTTGGATTGTCTGGATAGAACAAATAGTGTGCAGGCATTCCTTGGCTTAGAGATGCTCGCTAAGCAGCTG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
23
Interacting miRNAs (#binding sites)
mmu-miR-23b-3p(1), mmu-miR-15a-5p(1), mmu-miR-93-5p(1), mmu-miR-20a-5p(1), mmu-miR-17-5p(1), mmu-miR-135a-5p(1), mmu-miR-19b-3p(1), mmu-miR-15b-5p(1), mmu-miR-19a-3p(1), mmu-miR-23a-3p(1), mmu-miR-138-5p(1), mmu-miR-214-3p(1), mmu-miR-382-3p(1), mmu-miR-218-5p(1), mmu-miR-382-5p(1), mmu-miR-340-5p(1), mmu-miR-324-3p(1), mmu-miR-383-5p(1), mmu-miR-342-5p(1), mmu-miR-499-5p(1), mmu-miR-540-3p(1), mmu-miR-670-5p(1), mmu-miR-3105-3p(1)
siRNAs for circular RNA silencing
Junction sequence
TTATACTCATAAGGTGCCAGAGTGGT
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSYNJ1_1677_ORF_1
1.0789
0.229624716
0.999999999
3270
ORF sequence:
ATGCTCGCTAAGCAGCTGGAAGCTCTGGGCTTGGCTGAGAAGCCTCAGCTGGTGACCCGCTTCCAAGAAGTTTTCCGGTCCATGTGGTCTGTGAATGGCGACTCAATCAGTAAAATATATGCAGGCACCGGGGCCCTGGAAGGGAAGGCCAAGTTAAAAGATGGTGCGCGATCTGTCACCAGAACCATCCAGAATAACTTCTTCGACAGCTCCAAGCAGGAAGCCATTGATGTCCTGCTCCTGGGAAATACTCTCAACAGCGATTTAGCTGACAAAGCCCGAGCGCTTCTAACTACTGGAAGTTTGCGTGTTTCTGAACAGACATTACAGTCAGCATCTTCCAAAGTCTTAAAGAACATGTGTGAGAACTTCTACAAATACTCAAAGCCCAAGAAGATCCGAGTGTGTGTTGGCACCTGGAATGTGAACGGCGGGAAGCAGTTCCGCAGCATAGCGTTCAAGAACCAGACGCTCACAGACTGGCTTCTGGACGCTCCCAAGTTAGCCGGCATCCAGGAGTTTCAAGATAAGAGAAGTAAGCCAACTGATATATTTGCAATTGGCTTTGAAGAAATGGTGGAGCTGAATGCTGGGAACATTGTGAATGCAAGCACAACCAACCAGAAGCTGTGGGCAGTGGAGCTGCAGAAGACCATCTCCAGGGACAACAAGTATGTCCTGCTGGCCTCGGAGCAGCTGGTGGGTGTCTGCCTGTTTGTCTTTATCAGACCACAGCACGCTCCTTTTATCAGGGATGTTGCAGTTGATACTGTGAAAACTGGCATGGGAGGTGCAACTGGAAACAAGGGCGCCGTTGCAATTCGGATGCTCTTCCACACCACCAGCCTTTGCTTCGTCTGCAGCCACTTTGCTGCAGGGCAGTCCCAAGTCAAAGAGAGAAATGAAGATTTTGTAGAAATAGCACGAAAACTGAGTTTCCCCATGGGACGAATGCTCTTCTCCCATGACTATGTATTTTGGTGTGGTGATTTCAACTATCGAATTGACCTTCCGAATGAAGAGGTTAAAGAGCTCATAAGACAACAAAACTGGGATTCTCTGATCGCTGGGGATCAGCTCATCAACCAGAAAAATGCAGGACAGATCTTTAGAGGATTCTTAGAGGGAAAAGTAACGTTTGCTCCAACCTATAAATATGACTTGTTTTCTGAAGACTATGACACCAGTGAGAAGTGTCGCACCCCTGCTTGGACAGACCGTGTCCTCTGGAGAAGGAGGAAGTGGCCTTTTGACAGATCAGCTGAAGATTTAGATCTCCTGAATGCTAGTTTCCAAGATGAAAGTAAAATTCTTTATACATGGACCCCTGGCACCTTGCTGCACTATGGAAGAGCCGAGCTGAAGACTTCTGACCATAGGCCCGTCGTTGCCTTGATTGACATAGATATATTTGAAGTTGAAGCTGAAGAGAGACAAAAAATTTATAAAGAAGTTATTGCCGTCCAGGGCCCACCAGATGGCACAGTGCTGGTCTCAATCAAAAGTTCTGCACAAGAAAGTACTTTTTTTGATGATGCTTTGATTGATGAGCTTCTGCGGCAGTTTGCACACTTTGGTGAAGTTATACTCATAAGGTGCCAGAGTGGTACAGTTCGAACAAACTGCTTGGATTGTCTGGATAGAACAAATAGTGTGCAGGCATTCCTTGGCTTAGAGATGCTCGCTAAGCAGCTGGAAGCTCTGGGCTTGGCTGAGAAGCCTCAGCTGGTGACCCGCTTCCAAGAAGTTTTCCGGTCCATGTGGTCTGTGAATGGCGACTCAATCAGTAAAATATATGCAGGCACCGGGGCCCTGGAAGGGAAGGCCAAGTTAAAAGATGGTGCGCGATCTGTCACCAGAACCATCCAGAATAACTTCTTCGACAGCTCCAAGCAGGAAGCCATTGATGTCCTGCTCCTGGGAAATACTCTCAACAGCGATTTAGCTGACAAAGCCCGAGCGCTTCTAACTACTGGAAGTTTGCGTGTTTCTGAACAGACATTACAGTCAGCATCTTCCAAAGTCTTAAAGAACATGTGTGAGAACTTCTACAAATACTCAAAGCCCAAGAAGATCCGAGTGTGTGTTGGCACCTGGAATGTGAACGGCGGGAAGCAGTTCCGCAGCATAGCGTTCAAGAACCAGACGCTCACAGACTGGCTTCTGGACGCTCCCAAGTTAGCCGGCATCCAGGAGTTTCAAGATAAGAGAAGTAAGCCAACTGATATATTTGCAATTGGCTTTGAAGAAATGGTGGAGCTGAATGCTGGGAACATTGTGAATGCAAGCACAACCAACCAGAAGCTGTGGGCAGTGGAGCTGCAGAAGACCATCTCCAGGGACAACAAGTATGTCCTGCTGGCCTCGGAGCAGCTGGTGGGTGTCTGCCTGTTTGTCTTTATCAGACCACAGCACGCTCCTTTTATCAGGGATGTTGCAGTTGATACTGTGAAAACTGGCATGGGAGGTGCAACTGGAAACAAGGGCGCCGTTGCAATTCGGATGCTCTTCCACACCACCAGCCTTTGCTTCGTCTGCAGCCACTTTGCTGCAGGGCAGTCCCAAGTCAAAGAGAGAAATGAAGATTTTGTAGAAATAGCACGAAAACTGAGTTTCCCCATGGGACGAATGCTCTTCTCCCATGACTATGTATTTTGGTGTGGTGATTTCAACTATCGAATTGACCTTCCGAATGAAGAGGTTAAAGAGCTCATAAGACAACAAAACTGGGATTCTCTGATCGCTGGGGATCAGCTCATCAACCAGAAAAATGCAGGACAGATCTTTAGAGGATTCTTAGAGGGAAAAGTAACGTTTGCTCCAACCTATAAATATGACTTGTTTTCTGAAGACTATGACACCAGTGAGAAGTGTCGCACCCCTGCTTGGACAGACCGTGTCCTCTGGAGAAGGAGGAAGTGGCCTTTTGACAGATCAGCTGAAGATTTAGATCTCCTGAATGCTAGTTTCCAAGATGAAAGTAAAATTCTTTATACATGGACCCCTGGCACCTTGCTGCACTATGGAAGAGCCGAGCTGAAGACTTCTGACCATAGGCCCGTCGTTGCCTTGATTGACATAGATATATTTGAAGTTGAAGCTGAAGAGAGACAAAAAATTTATAAAGAAGTTATTGCCGTCCAGGGCCCACCAGATGGCACAGTGCTGGTCTCAATCAAAAGTTCTGCACAAGAAAGTACTTTTTTTGATGATGCTTTGATTGATGAGCTTCTGCGGCAGTTTGCACACTTTGGTGAAGTTATACTCATA
Peptide sequence:
MLAKQLEALGLAEKPQLVTRFQEVFRSMWSVNGDSISKIYAGTGALEGKAKLKDGARSVTRTIQNNFFDSSKQEAIDVLLLGNTLNSDLADKARALLTTGSLRVSEQTLQSASSKVLKNMCENFYKYSKPKKIRVCVGTWNVNGGKQFRSIAFKNQTLTDWLLDAPKLAGIQEFQDKRSKPTDIFAIGFEEMVELNAGNIVNASTTNQKLWAVELQKTISRDNKYVLLASEQLVGVCLFVFIRPQHAPFIRDVAVDTVKTGMGGATGNKGAVAIRMLFHTTSLCFVCSHFAAGQSQVKERNEDFVEIARKLSFPMGRMLFSHDYVFWCGDFNYRIDLPNEEVKELIRQQNWDSLIAGDQLINQKNAGQIFRGFLEGKVTFAPTYKYDLFSEDYDTSEKCRTPAWTDRVLWRRRKWPFDRSAEDLDLLNASFQDESKILYTWTPGTLLHYGRAELKTSDHRPVVALIDIDIFEVEAEERQKIYKEVIAVQGPPDGTVLVSIKSSAQESTFFDDALIDELLRQFAHFGEVILIRCQSGTVRTNCLDCLDRTNSVQAFLGLEMLAKQLEALGLAEKPQLVTRFQEVFRSMWSVNGDSISKIYAGTGALEGKAKLKDGARSVTRTIQNNFFDSSKQEAIDVLLLGNTLNSDLADKARALLTTGSLRVSEQTLQSASSKVLKNMCENFYKYSKPKKIRVCVGTWNVNGGKQFRSIAFKNQTLTDWLLDAPKLAGIQEFQDKRSKPTDIFAIGFEEMVELNAGNIVNASTTNQKLWAVELQKTISRDNKYVLLASEQLVGVCLFVFIRPQHAPFIRDVAVDTVKTGMGGATGNKGAVAIRMLFHTTSLCFVCSHFAAGQSQVKERNEDFVEIARKLSFPMGRMLFSHDYVFWCGDFNYRIDLPNEEVKELIRQQNWDSLIAGDQLINQKNAGQIFRGFLEGKVTFAPTYKYDLFSEDYDTSEKCRTPAWTDRVLWRRRKWPFDRSAEDLDLLNASFQDESKILYTWTPGTLLHYGRAELKTSDHRPVVALIDIDIFEVEAEERQKIYKEVIAVQGPPDGTVLVSIKSSAQESTFFDDALIDELLRQFAHFGEVILI
IRESfinder result
IRESfinder score
0.543102892
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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