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mmu_circDscam_1554
Basic information of circular RNA
PanCircBase ID:
mmu_circDscam_1554
mm39_Chr. Position ID:
chr16|96602378|96634693|-
Gene name:
Dscam
Transcript:
ENSMUST00000056102.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
6
Exon/intron indexes:
9,8,7,6,5,4
Exon/intron offsets:
0,18545,19564,24319,28701,32168
Genomic length:
32315
Exon/intron sizes in nt:
2,79,27,62,97,27,62,79,000
Flanking exon/introns:
chr16:96592211-96602378|chr16:96634693-96840097
Splice length:
1554
Other database IDs:
circAtlas: mmu-Dscam_0036
circBase: hsa_circ_0116087, circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_157545
Human Ortholog IDs:
Mature spliced Sequence:
GATCTAGATTTCTCATCACATCCACGGGAGCCTTGTATATTAAAGATGTACAGAACGAAGATGGGCTGTACAACTACCGCTGCATCACGCGGCACAGATACACAGGGGAGACGAGACAAAGCAACAGCGCGAGACTGTTCGTGTCAGACCCAGCAAACTCAGCCCCATCCATCCTGGACGGGTTTGACCACCGCAAAGCCATGGCAGGGCAGCGCGTGGAGCTGCCTTGCAAAGCACTTGGGCACCCCGAGCCAGACTACCGCTGGCTGAAGGACAACATGCCCCTGGAACTTTCTGGAAGGTTCCAAAAGACAGTGACTGGGTTGCTCATTGAGAACAGCCGCCCCTCAGACTCAGGCAGCTATGTGTGTGAAGTATCCAACCGATATGGCACTGCCAAGGTGATAGGCCGCCTGTACGTGAAACAGCCACTGAAAGCCACCATCAGTCCCAGAAAGGTTAAAAGCAGCGTGGGCAGCCAGGTCTCCTTATCCTGCAGTGTGACAGGAAATGAAGACCAGGAACTCTCCTGGTACCGAAATGGCGAAATCCTCAACCCTGGAAAAAACGTGAGGATCACAGGACTCAACCACGCAAACCTTATAATGGATCACATGGTCAAGAGTGATGGGGGTGCCTACCAGTGCTTTGTGCGCAAGGACAAGCTATCTGCTCAAGACTATGTCCAGGTGGTCCTTGAAGACGGAACTCCCAAAATCATTTCTGCCTTTAGCGAGAAAGTGGTGAGCCCGGCAGAGCCAGTGTCCCTCGTGTGCAATGTGAAGGGTACACCCTTGCCCACGGTCACCTGGACCCTGGACGATGACCCCATCCTCAAGGGCAGCGGTCACCGCATCAGCCAAATGATCACGTCCGAGGGGAACGTGGTCAGCTACCTGAATATCTCCAGCTCCCAGGTCCGGGATGGGGGTGTCTACCGCTGCACTGCCAACAACTCGGCTGGAGTCGTCCTGTACCAGGCTCGAATAAACGTAAGAGGGCCTGCAAGCATCAGACCAATGAAAAACATCACTGCGATAGCGGGGCGTGACACGTACATCCACTGCCGCGTAATTGGCTATCCGTATTACTCCATCAAGTGGTACAAGAACGCTAACCTGCTTCCTTTCAACCACCGCCAGGTGGCGTTTGAGAACAATGGGACTCTGAAACTCTCTGATGTGCAGAAAGAAGTTGACGAGGGAGAGTACACGTGTAATGTGCTGGTACAGCCACAGCTCTCCACCAGCCAGAGTGTCCACGTGACAGTGAAAGTTCCACCTTTCATCCAACCTTTTGAGTTCCCAAGATTCTCCATCGGGCAGCGGGTTTTCATCCCATGTGTGGTGGTCTCAGGGGACTTACCCATCACCATCACCTGGCAGAAGGATGGCCGGCCAATTCCAGCAAGCCTCGGAGTAACCATTGACAACATTGACTTCACCAGCTCCCTGAGGATCTCCAACCTCTCCCTAATGCACAATGGGAATTACACCTGCATTGCGAGAAACGAGGCAGCAGCCGTGGAACACCAGAGTCAGCTGATTGTGAGAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CCTGCATTGCGAGAAACGAG
59.9
GCGGTAGTTGTACAGCCCAT
60.11
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CACCTGCATTGCGAGAAACG
60.45
GCGGTAGTTGTACAGCCCAT
60.11
142
PCR template sequence:
AGGATCTCCAACCTCTCCCTAATGCACAATGGGAATTACACCTGCATTGCGAGAAACGAGGCAGCAGCCGTGGAACACCAGAGTCAGCTGATTGTGAGAGGATCTAGATTTCTCATCACATCCACGGGAGCCTTGTATATTAAAGATGTACAGAACGAAGATGGGCTGTACAACTACCGCTGCATCACGCGGCACAGATA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
14
Interacting miRNAs (#binding sites)
mmu-miR-34c-5p(2), mmu-miR-149-5p(2), mmu-miR-34b-5p(2), mmu-miR-23b-3p(1), mmu-miR-34a-5p(1), mmu-miR-125b-5p(1), mmu-miR-23a-3p(1), mmu-miR-138-5p(1), mmu-miR-125a-5p(1), mmu-miR-22-3p(1), mmu-miR-212-3p(1), mmu-miR-425-5p(1), mmu-miR-323-3p(1), mmu-miR-296-3p(1)
siRNAs for circular RNA silencing
Junction sequence
CTGATTGTGAGAGGATCTAGATTTCT
siRNA sets
AATCTAGATCCTCTCACAA, CTAGATCCTCTCACAATCA, GAAATCTAGATCCTCTCAC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCDSCAM_1554_ORF_1
1.1311
0.383359245
0.999999996
2907
ORF sequence:
ATGGCAGGGCAGCGCGTGGAGCTGCCTTGCAAAGCACTTGGGCACCCCGAGCCAGACTACCGCTGGCTGAAGGACAACATGCCCCTGGAACTTTCTGGAAGGTTCCAAAAGACAGTGACTGGGTTGCTCATTGAGAACAGCCGCCCCTCAGACTCAGGCAGCTATGTGTGTGAAGTATCCAACCGATATGGCACTGCCAAGGTGATAGGCCGCCTGTACGTGAAACAGCCACTGAAAGCCACCATCAGTCCCAGAAAGGTTAAAAGCAGCGTGGGCAGCCAGGTCTCCTTATCCTGCAGTGTGACAGGAAATGAAGACCAGGAACTCTCCTGGTACCGAAATGGCGAAATCCTCAACCCTGGAAAAAACGTGAGGATCACAGGACTCAACCACGCAAACCTTATAATGGATCACATGGTCAAGAGTGATGGGGGTGCCTACCAGTGCTTTGTGCGCAAGGACAAGCTATCTGCTCAAGACTATGTCCAGGTGGTCCTTGAAGACGGAACTCCCAAAATCATTTCTGCCTTTAGCGAGAAAGTGGTGAGCCCGGCAGAGCCAGTGTCCCTCGTGTGCAATGTGAAGGGTACACCCTTGCCCACGGTCACCTGGACCCTGGACGATGACCCCATCCTCAAGGGCAGCGGTCACCGCATCAGCCAAATGATCACGTCCGAGGGGAACGTGGTCAGCTACCTGAATATCTCCAGCTCCCAGGTCCGGGATGGGGGTGTCTACCGCTGCACTGCCAACAACTCGGCTGGAGTCGTCCTGTACCAGGCTCGAATAAACGTAAGAGGGCCTGCAAGCATCAGACCAATGAAAAACATCACTGCGATAGCGGGGCGTGACACGTACATCCACTGCCGCGTAATTGGCTATCCGTATTACTCCATCAAGTGGTACAAGAACGCTAACCTGCTTCCTTTCAACCACCGCCAGGTGGCGTTTGAGAACAATGGGACTCTGAAACTCTCTGATGTGCAGAAAGAAGTTGACGAGGGAGAGTACACGTGTAATGTGCTGGTACAGCCACAGCTCTCCACCAGCCAGAGTGTCCACGTGACAGTGAAAGTTCCACCTTTCATCCAACCTTTTGAGTTCCCAAGATTCTCCATCGGGCAGCGGGTTTTCATCCCATGTGTGGTGGTCTCAGGGGACTTACCCATCACCATCACCTGGCAGAAGGATGGCCGGCCAATTCCAGCAAGCCTCGGAGTAACCATTGACAACATTGACTTCACCAGCTCCCTGAGGATCTCCAACCTCTCCCTAATGCACAATGGGAATTACACCTGCATTGCGAGAAACGAGGCAGCAGCCGTGGAACACCAGAGTCAGCTGATTGTGAGAGGATCTAGATTTCTCATCACATCCACGGGAGCCTTGTATATTAAAGATGTACAGAACGAAGATGGGCTGTACAACTACCGCTGCATCACGCGGCACAGATACACAGGGGAGACGAGACAAAGCAACAGCGCGAGACTGTTCGTGTCAGACCCAGCAAACTCAGCCCCATCCATCCTGGACGGGTTTGACCACCGCAAAGCCATGGCAGGGCAGCGCGTGGAGCTGCCTTGCAAAGCACTTGGGCACCCCGAGCCAGACTACCGCTGGCTGAAGGACAACATGCCCCTGGAACTTTCTGGAAGGTTCCAAAAGACAGTGACTGGGTTGCTCATTGAGAACAGCCGCCCCTCAGACTCAGGCAGCTATGTGTGTGAAGTATCCAACCGATATGGCACTGCCAAGGTGATAGGCCGCCTGTACGTGAAACAGCCACTGAAAGCCACCATCAGTCCCAGAAAGGTTAAAAGCAGCGTGGGCAGCCAGGTCTCCTTATCCTGCAGTGTGACAGGAAATGAAGACCAGGAACTCTCCTGGTACCGAAATGGCGAAATCCTCAACCCTGGAAAAAACGTGAGGATCACAGGACTCAACCACGCAAACCTTATAATGGATCACATGGTCAAGAGTGATGGGGGTGCCTACCAGTGCTTTGTGCGCAAGGACAAGCTATCTGCTCAAGACTATGTCCAGGTGGTCCTTGAAGACGGAACTCCCAAAATCATTTCTGCCTTTAGCGAGAAAGTGGTGAGCCCGGCAGAGCCAGTGTCCCTCGTGTGCAATGTGAAGGGTACACCCTTGCCCACGGTCACCTGGACCCTGGACGATGACCCCATCCTCAAGGGCAGCGGTCACCGCATCAGCCAAATGATCACGTCCGAGGGGAACGTGGTCAGCTACCTGAATATCTCCAGCTCCCAGGTCCGGGATGGGGGTGTCTACCGCTGCACTGCCAACAACTCGGCTGGAGTCGTCCTGTACCAGGCTCGAATAAACGTAAGAGGGCCTGCAAGCATCAGACCAATGAAAAACATCACTGCGATAGCGGGGCGTGACACGTACATCCACTGCCGCGTAATTGGCTATCCGTATTACTCCATCAAGTGGTACAAGAACGCTAACCTGCTTCCTTTCAACCACCGCCAGGTGGCGTTTGAGAACAATGGGACTCTGAAACTCTCTGATGTGCAGAAAGAAGTTGACGAGGGAGAGTACACGTGTAATGTGCTGGTACAGCCACAGCTCTCCACCAGCCAGAGTGTCCACGTGACAGTGAAAGTTCCACCTTTCATCCAACCTTTTGAGTTCCCAAGATTCTCCATCGGGCAGCGGGTTTTCATCCCATGTGTGGTGGTCTCAGGGGACTTACCCATCACCATCACCTGGCAGAAGGATGGCCGGCCAATTCCAGCAAGCCTCGGAGTAACCATTGACAACATTGACTTCACCAGCTCCCTGAGGATCTCCAACCTCTCCCTAATGCACAATGGGAATTACACCTGCATTGCGAGAAACGAGGCAGCAGCCGTGGAACACCAGAGTCAGCTGATTGTGAGA
Peptide sequence:
MAGQRVELPCKALGHPEPDYRWLKDNMPLELSGRFQKTVTGLLIENSRPSDSGSYVCEVSNRYGTAKVIGRLYVKQPLKATISPRKVKSSVGSQVSLSCSVTGNEDQELSWYRNGEILNPGKNVRITGLNHANLIMDHMVKSDGGAYQCFVRKDKLSAQDYVQVVLEDGTPKIISAFSEKVVSPAEPVSLVCNVKGTPLPTVTWTLDDDPILKGSGHRISQMITSEGNVVSYLNISSSQVRDGGVYRCTANNSAGVVLYQARINVRGPASIRPMKNITAIAGRDTYIHCRVIGYPYYSIKWYKNANLLPFNHRQVAFENNGTLKLSDVQKEVDEGEYTCNVLVQPQLSTSQSVHVTVKVPPFIQPFEFPRFSIGQRVFIPCVVVSGDLPITITWQKDGRPIPASLGVTIDNIDFTSSLRISNLSLMHNGNYTCIARNEAAAVEHQSQLIVRGSRFLITSTGALYIKDVQNEDGLYNYRCITRHRYTGETRQSNSARLFVSDPANSAPSILDGFDHRKAMAGQRVELPCKALGHPEPDYRWLKDNMPLELSGRFQKTVTGLLIENSRPSDSGSYVCEVSNRYGTAKVIGRLYVKQPLKATISPRKVKSSVGSQVSLSCSVTGNEDQELSWYRNGEILNPGKNVRITGLNHANLIMDHMVKSDGGAYQCFVRKDKLSAQDYVQVVLEDGTPKIISAFSEKVVSPAEPVSLVCNVKGTPLPTVTWTLDDDPILKGSGHRISQMITSEGNVVSYLNISSSQVRDGGVYRCTANNSAGVVLYQARINVRGPASIRPMKNITAIAGRDTYIHCRVIGYPYYSIKWYKNANLLPFNHRQVAFENNGTLKLSDVQKEVDEGEYTCNVLVQPQLSTSQSVHVTVKVPPFIQPFEFPRFSIGQRVFIPCVVVSGDLPITITWQKDGRPIPASLGVTIDNIDFTSSLRISNLSLMHNGNYTCIARNEAAAVEHQSQLIVR
IRESfinder result
IRESfinder score
0.389541111
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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