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mmu_ciScn3a_5475
Basic information of circular RNA
PanCircBase ID:
mmu_ciScn3a_5475
mm39_Chr. Position ID:
chr2|65361281|65366756|-
Gene name:
Scn3a
Transcript:
ENSMUST00000066432.12
CircRNA type:
Circular intronic (ci)RNA
Exon/Intron count:
1
Exon/intron indexes:
2
Exon/intron offsets:
0
Genomic length:
5475
Exon/intron sizes in nt:
5475
Flanking exon/introns:
chr2:65361266-65366756
Splice length:
5475
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GTGAGTGCTTACTTTATATGGCCAACCCATTCTCAATTAGATGTGCAAACCAGGGGCTTCTGTGCATTAGAACATTGCCATTGTCATATGTGAAATAGTTCACGGCACTCTTTACTGCTACACGTCTTGAAGAACAGAAACATTGATAAGAAATGAAATCTCTGCTACAGAAGAATAAGCATAAACCATTTCTACCATTTCATAGTATTGAGATAAGTGGGAAAACTTAAATTCGACAGCAAAGATAAGCATCTGCTATTGCTAATCCATTTGGCTGCTTGATAAACAGCCAATTTGTAATTATAAGGTGAATGCTATACTTATTTTTTAGTTCATACTTGGCTTGATATTTCTTACAGTCATATTTTCTTATCTATTCCTATAGACAGGTAATTCATGGAGAAACATGTTTATCCAGACATACATTTTTAGTCTTTTCCCTCTAACTTGGCATATGATTAGGAACTTCTATAGGCTTCATTGAGATCATGATAGGAGAACTGCTAGACTATCTACAAATAGTTAAAGCATTACCACAATGAAAGAAATATCACTGTTAGAAGAGAAAACATAGTAATGATAATAATAACAAGAATTTCCATGTAATTTAAAGGAACAACTATGACTATATTTCTCTGATGTTTAAAATAACTACACAGTTATGCCAGAATTAGTTTCACTACTTAAACCTGCTTTGTTAGACCCATAGGAAATCTAAATAAAGAATATTATTTTAATACCTACATGAATATTTTAGTACCCTTTAGTCACGATGTATAGCTTACCTTCACAATGAGAAAACAGTTTATTGTAAAGACAAATTAACATCATTCCAAGTTGATGATTTCTGGATTAACAACTAAACAGACCACCTTTACTTGTCAAAGTAGAACTTTAGAAAAGCAATGGTTGAAGACACTGCATTCTTTAAGTAGTTAGTGTATGATATGACCTTTTAAGTCCTGGGGATGGGAGACGGCTCGGTGGTTCAGAGCATTTGCTGCTCCTACAGAGGACTGGGGTTTGGTTCACAGCACCCATGTCAGGTGGCTCAGGACTGTCTGCAATGACAACGACAGCAGATCTGACCCTCTCTGTGTGAATACTCTCACACATATGTACATACATAGACAAAGGCATACAGATAGATAAAGATTTTTAAAAGGCTTTACAAACATTGTAAGTCCTTCTTACTAAGTTTAACAAAGGAAGGCACTAAATATACATTCATATGCTTCTAAAAGAAACTGTGATTTACTACAGAGATGATCAAGAATGAATTGAAATTTAGAAACTCTGATGGCTTCTAAAGGATGGTTAACAATAAGATGTTTCTCCCAGAGACTAGAAAAACAGGCCTCATTTGAGAAAAAAAAATAAATGTCTTAACATACACATTTGCAACCTTGTGTGTTGTCTCATACTTGTAAGTCCAACATTTGGGAGACAGCCAGAAGAGTCAGGAGCTCAAGGTCAACCGAAGCTACAGAAAAGAGCTTGAGCTACAAACCCCACAGTATGTTTTAAAAATTATTTTCAAGACACAGAAATTTGTTTTACTTTGATATGAAATTGTTATTACTCCTTTAAAAACAAACAAACAAACAAACAAACAAACAAACAAAATGAAGGAGCCATCAGTTTGATAGGCTTACCAGGGTAGAAAGGAAGAAAATGGAGATATTACTCAATGGGAAGAGAGCTATATTTTCTTGCATTAAAAGCATTTCCTTTCCAATGACAACACCATCTCTTTATGAAAGGGATACCCTTGGCTAATCCCACCCTTTGATTAAGTAAGCTGTTTGGACCCCATGTTCAACAAGGACTCTCCTGTCCAATTTGTTTTTCCCACAGATTTCCTGAGGGAAAGGTACCACTATAATTCTTTTTCTACATGAGAATATAACATACACATTTTAATGTCAATTGATTGTCATCTGACTTGATAGGTCAGGCTCTCAAGGTTGGTTAGTTTTCTAGTTTGCTACTAGAGAACAGAATTGTCCTCTGTGCACGGGAAAGGACAGGCATTGCTCACCCCAAACTGGAAACCATAACACTTGGATCATAATTTACTCTAGTGAATGTAAGTGACTCTAAACTCTCAAAGGAGGAGCCCTGCCTTCATTAATGAAATATCTCTAAGGATGAGAATTCAGGTGCTACTTACAGAAATGTGATTTGTGACTCTTAAAGTTAAAGGGAGAAAATAGTGTATAATTCATAGAATTTCACCATAGTACAAAGCCATGTTACTGCATGATCATTTGTGTAAAAGACCACATAGAGCTTGAGAGCTTCATGTAATGACTAGCTGTCACTGATTAGTGATGTATCTTAGTGCCGAATATAACTAGATGAGTAAGACCACAATATATTTTAATAGCATTTAAGTTGGCCAGGTTAACGGCTTAAAAATAGTGGCATGATAATAATAGCTAACATTTGTTGGGCTCACCCTATGTCAGGAGCCACTCGAATACTCCAGTTCATTTCATACCAATGAGCCAGTTCATGAAGCAGTTGCTCTCGCTAGTCTCAGTTTCCAGATGGGAACGTAAAGTCAAGGCCAATTCCTTCACTTACCAAAGTCATTCTCCATCAATGATAGATCAAGGCTTGGAGCACTTGACCGCTGGTCAAACTCTCTGCAGTAACAATAAATGTAAAAATAAGATGGTCAAAAGTTGGTTGCACCACACTTTTAAACACTTTTTATTGATTCTTTGTGAATTTCATATCTTGTACCTCAATCCAACTCGTCTCCCTGTCCCTTCGTATATAACCTCTGCCCTTGGCAACACCACCCCTACCATGAACAAAAACAAAACAAACCAAACAAACAAAAAATATCTAGCCATGGAAGTTGCAGTGTGTCCTGGTGATCACACAGTATATCTTTTGCCCAAACAGACTGACTTGCAAACGTTCATTGCAGTGAGTCATTGGTCTGGTTCGGGGCCTCTGGCCTCTGCTATGTCATCAATACAGGATCCTCACAGGGACTCCACTCAGATATGTTGTTGTTGCCCTGGGCTGTACCATCTTTTAAAATTCTGTGCCTGATATATTTCATTAAGGTATAAATCTGCTGCTTCTCTCACAAAACTAAGAACTTCAGTGAAGTTATTAGTATTTATTCAGGGAAAAAAGTAATTAGCACTCCTGATAATAACCTTTGTGAAAAACTTCAGCCACAGTGTTTATAACAATACTGGCGATAAGCACCGAATCTTTTCACAGTGCCTCACCACCTATTGTTTCTTGGAAACCCGACTTTACAGTTGGTGTAACTTCTCTGAGTTCCAGCCATCTCTTACATTCTTGTGTAGCTTTTGGTGTAGGTACATCATTCGATGACGTCAGAACCCCAGACTTCAAACATCACCCTGTAATTCTTTCACTACGTAGATCATTAGAATTTTACTCCTTGTTTCTCAACTCTCAGGGTATGCACAGTTATACCTTCAGAGTAGATGCACTATGTTCACCAGTATGGGAGCCACTAGCACCCACAGCCTAACCTTGCAGGAGAAGCAGAGGATTTCATATTTAAAGGACAATTCATTCTTGCGTAGTCTATTTTGGGAGATATTTCAAAATACACACCCCCTTTTTAATGTTGCAAGCAGAAATTGCTTTTTCAGGGAAATTGTTTAAAAGAGCATGAGTTAATGCACTTTAAATCACTGGGGACTTTTACACACAATTGCAGCCGCTGATGCCTAAATGGATCTTGATCGCTGTACTGTACTCTGAATTCATGACAGCCCACTTACGCTACTACAGTTCAAGGGCAGGCTTAGCGAGGCTCATTGTCACTTGCAGGTAATCTTGATGCTAGTAAGGGATAGTTTACTTGCCCTCTTCCTAGAATTTATAGAGCTCAGCTCATTGAAAATGGTTAGTTAAGTAACAGTTGGCTCAATGGTCTTAAACACAGAAGGGCGGTAAAAGGGTTGCTTGTTGTCCCTGCTCACAGTATAAACATTCCTGCCTGCCTCTTCAAACAGAGCCTGTTGCGGGTTGCTGTGAATGTATGTGATGTAGCCTTAGTAAAAGGGTGCAAACATATTATTAAGTAAATCAGTACATACAACAGATGTCATGAAGGTGAACAGTGCCTTAAAGGTAAACCCATATTTAATTAGAACAGCGTTTATTGGCAAAGCACGCTATTAAAAACTGTGGGGGGAAATGCAGCCATAAACTGCAGGCTCTTTGTGCTCAGTCATTTATAAAAGCACCTAACCAGGTTCTCCTACAAATGAACCCCGTGTGGAAATTGCTACCTGATGATGATTACCAGCAACGTATGAGAGAGTACAAAGTAATACACTAAGGGTTAGTGGCAGGAGAACCAGCTAAGGAATGATCAGAAGGCAGCGTGATTTATTTGGGAAAATGTAAAGGAGGGAGTGATTTGGGTACTGAGAGTGGAAAAAAGAGATTGGATAATAAGACCGCCTGCATATTAGAATTACTCAAGGAGAATGTTGAAAACACCTAAATATCTGCCATACTCCTAAACTTAAATATTGACAATTCTGAAGAACCAGGACATCCTAGCATGAGGGTCATGACAGGTAGGATAACCTTGCATAGTTAGTTAGACCTTGCTACAGGTATTGCTCTCTTCACTGAGTCTATCACCATGTGAATCACAGCTGGAGGGACAGATTGATAGGTTCTGAGTGGGACTGACAAGTGGATTAAATGGCTGGAACAGAGATGACTCTAGTGGTAAAAAATAAAGGATGATCCATCCTGGGTTTCTTGAGAGGTAGTCATGGGTCTGCATAGCTTAAATGCTAAGATGATGTTGTATGTTTCAGATTATGACCTTTAACTGTGGCTTGGTCTTTGAAGTCATATATTTAAAATTAATTTTCAACGCAGCTGTCTTTTCTCAGTACAAGCTATGAAGTGGATCATTCTTAAAACACAAAATCTGGTTCGATAACTTATTTCAATGTCTTAGATCAATTCAGCTGCTACAAAAATGATGGGAGGCTACCACAAGCTAGGGTTAGAAGGTTTGAAGTTATTAATTTCAATAAATTCTGTAATTAAATAATGATACTGATAAAAGATTATTTTAACACTTATATATACTGAATGATCTGAAAAGTTACCAAAGCTGGAGACAGATGGTAAGCCTCAAATAGAAATGAACCTTGTAAAGTTCTTTAATTTGAGTTTTGAAAATGTGTAAGACTATCAGTTTGTATGTATCAACACGTTTGGGGGCTAAGAGATAGATAAGGTAGCAGCCCAGTGGGCCTTTGTGTGTCTGTATGTGTAGGGGAGAAACGCTTAGTCTGTGTCTAGTAAACAAGATATTGGTTATGTTCCAACTGGCCTAAATGAACACATTTGTACAAAAAAAGTCAGGTAAAAGTTCTCGATGTGTGTTATAAATGCTTCAAATAAGCCTGCATGTCTAATTTGGTAATCTCTCTCTCTCTCTCA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CAGGTAAAAGTTCTCGATGTGTGT
59.25
TAATGCACAGAAGCCCCTGG
60.03
150
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AGGTAAAAGTTCTCGATGTGTGT
58.04
TAATGCACAGAAGCCCCTGG
60.03
149
PCR template sequence:
ACATTTGTACAAAAAAAGTCAGGTAAAAGTTCTCGATGTGTGTTATAAATGCTTCAAATAAGCCTGCATGTCTAATTTGGTAATCTCTCTCTCTCTCTCAGTGAGTGCTTACTTTATATGGCCAACCCATTCTCAATTAGATGTGCAAACCAGGGGCTTCTGTGCATTAGAACATTGCCATTGTCATATGTGAAATAGTT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
51
Interacting miRNAs (#binding sites)
mmu-miR-297a-5p(4), mmu-miR-5101(3), mmu-miR-15a-5p(2), mmu-miR-322-5p(2), mmu-miR-181b-5p(2), mmu-miR-182-5p(2), mmu-miR-511-3p(2), mmu-miR-466d-3p(2), mmu-miR-466a-5p(2), mmu-miR-1187(2), mmu-miR-466p-5p(2), mmu-miR-300-3p(2), mmu-miR-539-5p(2), mmu-miR-181d-5p(2), mmu-miR-155-5p(1), mmu-miR-16-5p(1), mmu-miR-141-3p(1), mmu-miR-106a-5p(1), mmu-miR-93-5p(1), mmu-miR-20a-5p(1), mmu-miR-181a-5p(1), mmu-miR-150-5p(1), mmu-miR-221-3p(1), mmu-miR-135a-5p(1), mmu-miR-101a-3p(1), mmu-miR-26a-5p(1), mmu-miR-15b-5p(1), mmu-miR-298-5p(1), mmu-miR-217-5p(1), mmu-miR-101b-3p(1), mmu-miR-709(1), mmu-miR-214-3p(1), mmu-miR-136-5p(1), mmu-miR-434-3p(1), mmu-miR-494-3p(1), mmu-miR-29b-1-5p(1), mmu-miR-382-3p(1), mmu-miR-127-5p(1), mmu-miR-192-5p(1), mmu-miR-215-5p(1), mmu-miR-690(1), mmu-miR-802-5p(1), mmu-miR-377-3p(1), mmu-miR-1198-5p(1), mmu-miR-207(1), mmu-miR-466b-3p(1), mmu-miR-350-3p(1), mmu-miR-670-5p(1), mmu-miR-490-3p(1), mmu-miR-1904(1), mmu-miR-3061-5p(1)
siRNAs for circular RNA silencing
Junction sequence
TCTCTCTCTCTCAGTGAGTGCTTACT
siRNA sets
AGTAAGCACTCACTGAGAG, GTAAGCACTCACTGAGAGA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CISCN3A_5475_ORF_5
0.3541
-0.463603508
0.0029391
126
ORF sequence:
ATGTCTAATTTGGTAATCTCTCTCTCTCTCTCAGTGAGTGCTTACTTTATATGGCCAACCCATTCTCAATTAGATGTGCAAACCAGGGGCTTCTGTGCATTAGAACATTGCCATTGTCATATGTGA
Peptide sequence:
MSNLVISLSLSVSAYFIWPTHSQLDVQTRGFCALEHCHCHM
IRESfinder result
IRESfinder score
0.820809499
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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