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mmu_ciSnhg4_1821
Basic information of circular RNA
PanCircBase ID:
mmu_ciSnhg4_1821
mm39_Chr. Position ID:
chr18|35712371|35714192|+
Gene name:
Snhg4
Transcript:
ENSMUST00000237592.2
CircRNA type:
Circular intronic (ci)RNA
Exon/Intron count:
1
Exon/intron indexes:
8
Exon/intron offsets:
0
Genomic length:
1821
Exon/intron sizes in nt:
1821
Flanking exon/introns:
chr18:35712371-35714222
Splice length:
1821
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GTTCGTGATACAGCTATTGCTTCTATCCATAATTGTTGCTGGGAATGTGATTTCATTTAAATGTATATTGATTGAATCTTCTGTGGGGGTTGACGGGATTTCAAGACAGGGTTTCTTTGTGTAGGCTGTGGTAGAATAGGCCTGTCCTCAAAGTCAGAGATCCAACTGCTTTTGCCTTAGAATGCTGGAATTAAAGGCATATACCCACCAATGACCAACTCTCGTGGTTCAATCTGAATCACAGTCATTATAACAGGATGGGCGTTTTAATTTCAAGATGTTTGCTGGGTGTGAGGGCATGCATTTATTCTCAGCATTCAGGAGACAAAGTCAGGCAGATCTCTTTGAGTTTGAGGCCAGTCAGGAGCAATACATGACTTTTTTTTTTTTTTAAATTGTGTGTGTGTGTTTAAGCTTTGACATGCTTTGACATGACTAGTAGTATTTAAAAGACCTTTCATAAACAGAATTAGCTTGGAAAGATGGCTCAGGAGCAACAACTATGTTTGATTTCCAGGACCAACATGGTAGAAGGGAAGAACCATTTCCCACAAATGGTGTTGTTCTCTGACCTAACACCACAGCCTATGAATGTCCACACATATAATTTTAAAGAATGTAGTAAGGGCCAGGTGGCAGATCTCTGTTGGTTCCAGGGTTATATAGACAAACCCTGTCTTGAAAAAGATAAAGAGGAAGAATGATGTAAGGATCACTAGAGAGAATATTTTTGAAACTTGACAATAACCACTATTTGATTTTTTGATTTGTTCTGTTCTGTTCTGCTCTGTTTGGAAAAATTTATTCCAGTTCAGGCATGGTGGCATATAGCACTCAGGAAGCAGAGGCAGGTTGGTCTACCTAGTGAGGTTTAGGACACAGCCAAAGATACATATGAAATCCTGTCTCAAAAAAACAGAAAATATGTGAATTTATTCCCATAACATTTAATATGCTCTGTACTTTACATTCTCTATAATGCTAAAAGTTAAGTAATGTTTTCAGGTTGATTATAGAATAAAGAATTTAATGTATAAGGTGGTTTTTTTGGTCAGCCTTTTTGATGGTGTTGTAAATCAAACCTAAGGTCTTGGCTATGTTAGGCCCTATACTTAACCACGACAGCACAGCCTCCCCCCCTCCCCCTCCTTTGTTTTGAGAGTTGATCTGGTTGGCCTTAAACCTTGTGCACAGGGGAATGGTTATGTCTGCCTCCCAAGTAGCTATATCACTAGGTCAGCTTTTCTTTTTAATACAAAATATGTTGATTACAGGCAAGTGTGTTTTTAATCCCAGTACTGGAAGCAGAGGCTCAAGGGAGCTCAAGGTCAGCCTGATTTACAGAATGAATTTGAAGACAGCCATGGATGAGCAATATATTTTAATTGTATCTTCTCCCTAATAACCCAAAACAAGAAATACACCCCCCCATACACACTTGCCCACCAGCATGCATGCGTATGCCCCCAAAACAAACATTAAGATGATGTGGGGGAGACTCTCTTTAAAAATTATTATTGGGCTCAGCAGTTACTAGTAACATGGTTCTTGGAGCTTGGTGCCAACTCTGATGTTGAGTAGCTCACAGTGTTTTATGATGCCAACTCTAGGGAATCTAACCCTCTTCTGGTCTCTACAGGCACTAGCAGGAATACCCACACACATTTAAAAATGTGAAGTTGTATGTGTGTATGCAAATTAGCGCTAGATATTTAATCTGGGGCTTTATGCTTACTATGTGCTAAGTATTATATACTGCTGTCTGGTAAATACATGCTTTAGTTTCTCAAAATGCTTTTTTAAAAGGACTTTTTTTATTTG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
ACTGCTGTCTGGTAAATACATGC
59.06
CGTCAACCCCCACAGAAGAT
59.68
162
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CTGCTGTCTGGTAAATACATGCT
58.81
CGTCAACCCCCACAGAAGAT
59.68
161
PCR template sequence:
GGCTTTATGCTTACTATGTGCTAAGTATTATATACTGCTGTCTGGTAAATACATGCTTTAGTTTCTCAAAATGCTTTTTTAAAAGGACTTTTTTTATTTGGTTCGTGATACAGCTATTGCTTCTATCCATAATTGTTGCTGGGAATGTGATTTCATTTAAATGTATATTGATTGAATCTTCTGTGGGGGTTGACGGGATT
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-466a-5p(2), mmu-miR-1187(2), mmu-miR-466p-5p(2), mmu-miR-23b-3p(1), mmu-miR-200a-3p(1), mmu-miR-141-3p(1), mmu-miR-1a-3p(1), mmu-miR-429-3p(1), mmu-miR-181a-5p(1), mmu-miR-328-3p(1), mmu-miR-23a-3p(1), mmu-miR-181b-5p(1), mmu-miR-215-5p(1), mmu-miR-297a-5p(1), mmu-miR-1198-5p(1), mmu-miR-344d-3p(1), mmu-miR-369-3p(1), mmu-miR-3470b(1), mmu-miR-540-3p(1), mmu-miR-193b-3p(1), mmu-miR-574-5p(1), mmu-miR-181d-5p(1), mmu-miR-7a-1-3p(1)
siRNAs for circular RNA silencing
Junction sequence
CTTTTTTTATTTGGTTCGTGATACAG
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
NA
NA
NA
NA
NA
ORF sequence:
NA
Peptide sequence:
NA
IRESfinder result
IRESfinder score
0.860605901
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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