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mmu_circSema6d_1762
Basic information of circular RNA
PanCircBase ID:
mmu_circSema6d_1762
mm39_Chr. Position ID:
chr2|124495500|124502264|+
Gene name:
Sema6d
Transcript:
ENSMUST00000103241.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
15
Exon/intron indexes:
6,7,8,9,10,11,12,13,14,15,16,17,18,19,20
Exon/intron offsets:
0,566,1215,1397,1572,1905,2429,3249,4063,4390,4829,5065,5987,6226,6702
Genomic length:
6764
Exon/intron sizes in nt:
163,112,61,63,102,91,120,89,218,132,156,174,141,78,62
Flanking exon/introns:
chr2:124331932-124495500|chr2:124502264-124505940
Splice length:
1762
Other database IDs:
CIRCpedia: MMU_CIRCpedia_6360, circAtlas: mmu-Sema6d_0006
circAtlas: hsa-SCAF8_0001
Human Ortholog IDs:
Mature spliced Sequence:
GTAGCTAAGTGGGACTTCTGAGGAGGGGGAGCTCAGATTTCTTCTTGGCCAACCATGGGGTTCCTTCTGCTTTGGTTCTGCGTGCTGTTCCTTCTGGTCTCCAGGTTACGGGCGGTCAGCTTCCCAGAAGACGATGAGCCCCTCAACACGGTTGACTATCACTATTCAAGGCAATATCCGGTTTTTAGAGGACGCCCTTCAGGCAACGAATCGCAGCACAGGCTGGACTTTCAGCTGATGTTGAAAATTCGAGACACACTTTATATTGCTGGCAGGGATCAAGTCTATACAGTGAACTTAAATGAAATCCCCCAAACAGAGGTGATACCAAGCAAGAAGCTGACGTGGAGGTCCAGACAGCAGGATCGAGAAAATTGTGCTATGAAAGGCAAGCATAAAGATGAATGCCACAACTTCATCAAAGTCTTTGTCCCAAGAAATGATGAGATGGTTTTTGTCTGTGGTACCAATGCTTTCAACCCGATGTGCAGATACTATAGGTTGAGAACGTTAGAGTATGATGGGGAAGAAATTAGTGGCCTGGCACGATGCCCGTTTGATGCCCGACAAACCAATGTCGCCCTCTTTGCTGATGGAAAACTCTATTCTGCCACAGTGGCTGATTTCCTGGCCAGTGATGCTGTCATTTACAGAAGCATGGGAGATGGATCTGCCCTTCGCACAATAAAATACGATTCCAAGTGGATCAAAGAACCACACTTCCTTCATGCCATAGAATATGGAAACTATGTCTATTTCTTCTTCAGAGAAATCGCCGTGGAACATAATAACTTAGGCAAGGCTGTGTATTCCCGCGTGGCTCGCATTTGTAAAAACGACATGGGTGGCTCACAGCGGGTCCTGGAGAAACACTGGACTTCCTTCCTTAAGGCTCGGCTGAACTGCTCCGTTCCTGGAGATTCCTTTTTCTACTTCGACGTCCTGCAGTCTATAACAGACATAATCCAAATCAATGGCATCCCCACTGTGGTTGGGGTCTTCACCACACAGCTCAACAGCATTCCTGGTTCTGCAGTCTGTGCCTTTAGCATGGACGACATTGAGAAAGTGTTCAAAGGGCGGTTCAAAGAGCAGAAAACCCCAGACTCTGTTTGGACAGCAGTTCCCGAAGACAAAGTACCAAAACCAAGGCCTGGCTGTTGTGCCAAACACGGCCTCGCAGAAGCTTACAAGACCTCCATCGACTTTCCAGATGACACCCTGGCTTTCATCAAGTCCCACCCGCTGATGGACTCTGCCGTCCCACCCATTGCCGATGAGCCCTGGTTCACAAAGACACGGGTCAGGTACAGGTTGACAGCCATCGAAGTGGACCGTTCAGCAGGGCCATACCAAAACTACACAGTCATCTTTGTTGGCTCTGAAGCTGGCGTGGTACTTAAAGTTTTGGCAAAGACCAGTCCTTTCTCTCTGAATGACAGTGTATTACTCGAAGAGATTGAAGCTTATAACCCAGCCAAGTGCAGCGCCGAGAGTGAGGAGGACAGAAAGGTGGTCTCATTACAGCTGGACAAGGATCACCATGCTTTATACGTGGCCTTCTCTAGCTGCGTGGTCCGCATCCCCCTCAGCCGCTGTGAGCGCTACGGATCGTGTAAAAAGTCTTGCATTGCATCACGTGACCCGTACTGTGGTTGGTTAAGCCAGGGAGTTTGTGAGAGAGTGACCCTAGGGATGCTCCCTGGAGGATATGAGCAGGACACGGAGTACGGCAACACAGCCCACCTAGGGGACTGCCACG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AGTGACCCTAGGGATGCTCC
60.4
AGACCAGAAGGAACAGCACG
59.97
180
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AGTGACCCTAGGGATGCTCC
60.4
AAGCAGAAGGAACCCCATGG
59.96
152
PCR template sequence:
AGCCAGGGAGTTTGTGAGAGAGTGACCCTAGGGATGCTCCCTGGAGGATATGAGCAGGACACGGAGTACGGCAACACAGCCCACCTAGGGGACTGCCACGGTAGCTAAGTGGGACTTCTGAGGAGGGGGAGCTCAGATTTCTTCTTGGCCAACCATGGGGTTCCTTCTGCTTTGGTTCTGCGTGCTGTTCCTTCTGGTCT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
12
Interacting miRNAs (#binding sites)
mmu-miR-27b-3p(1), mmu-miR-27a-3p(1), mmu-miR-199a-5p(1), mmu-miR-324-5p(1), mmu-miR-185-5p(1), mmu-miR-370-3p(1), mmu-miR-362-5p(1), mmu-miR-340-5p(1), mmu-miR-3065-5p(1), mmu-miR-490-3p(1), mmu-miR-1904(1), mmu-miR-193b-3p(1)
siRNAs for circular RNA silencing
Junction sequence
GGGGACTGCCACGGTAGCTAAGTGGG
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSEMA6D_1762_ORF_1
0.9207
0.23137139
0.999939687
1716
ORF sequence:
ATGGGGTTCCTTCTGCTTTGGTTCTGCGTGCTGTTCCTTCTGGTCTCCAGGTTACGGGCGGTCAGCTTCCCAGAAGACGATGAGCCCCTCAACACGGTTGACTATCACTATTCAAGGCAATATCCGGTTTTTAGAGGACGCCCTTCAGGCAACGAATCGCAGCACAGGCTGGACTTTCAGCTGATGTTGAAAATTCGAGACACACTTTATATTGCTGGCAGGGATCAAGTCTATACAGTGAACTTAAATGAAATCCCCCAAACAGAGGTGATACCAAGCAAGAAGCTGACGTGGAGGTCCAGACAGCAGGATCGAGAAAATTGTGCTATGAAAGGCAAGCATAAAGATGAATGCCACAACTTCATCAAAGTCTTTGTCCCAAGAAATGATGAGATGGTTTTTGTCTGTGGTACCAATGCTTTCAACCCGATGTGCAGATACTATAGGTTGAGAACGTTAGAGTATGATGGGGAAGAAATTAGTGGCCTGGCACGATGCCCGTTTGATGCCCGACAAACCAATGTCGCCCTCTTTGCTGATGGAAAACTCTATTCTGCCACAGTGGCTGATTTCCTGGCCAGTGATGCTGTCATTTACAGAAGCATGGGAGATGGATCTGCCCTTCGCACAATAAAATACGATTCCAAGTGGATCAAAGAACCACACTTCCTTCATGCCATAGAATATGGAAACTATGTCTATTTCTTCTTCAGAGAAATCGCCGTGGAACATAATAACTTAGGCAAGGCTGTGTATTCCCGCGTGGCTCGCATTTGTAAAAACGACATGGGTGGCTCACAGCGGGTCCTGGAGAAACACTGGACTTCCTTCCTTAAGGCTCGGCTGAACTGCTCCGTTCCTGGAGATTCCTTTTTCTACTTCGACGTCCTGCAGTCTATAACAGACATAATCCAAATCAATGGCATCCCCACTGTGGTTGGGGTCTTCACCACACAGCTCAACAGCATTCCTGGTTCTGCAGTCTGTGCCTTTAGCATGGACGACATTGAGAAAGTGTTCAAAGGGCGGTTCAAAGAGCAGAAAACCCCAGACTCTGTTTGGACAGCAGTTCCCGAAGACAAAGTACCAAAACCAAGGCCTGGCTGTTGTGCCAAACACGGCCTCGCAGAAGCTTACAAGACCTCCATCGACTTTCCAGATGACACCCTGGCTTTCATCAAGTCCCACCCGCTGATGGACTCTGCCGTCCCACCCATTGCCGATGAGCCCTGGTTCACAAAGACACGGGTCAGGTACAGGTTGACAGCCATCGAAGTGGACCGTTCAGCAGGGCCATACCAAAACTACACAGTCATCTTTGTTGGCTCTGAAGCTGGCGTGGTACTTAAAGTTTTGGCAAAGACCAGTCCTTTCTCTCTGAATGACAGTGTATTACTCGAAGAGATTGAAGCTTATAACCCAGCCAAGTGCAGCGCCGAGAGTGAGGAGGACAGAAAGGTGGTCTCATTACAGCTGGACAAGGATCACCATGCTTTATACGTGGCCTTCTCTAGCTGCGTGGTCCGCATCCCCCTCAGCCGCTGTGAGCGCTACGGATCGTGTAAAAAGTCTTGCATTGCATCACGTGACCCGTACTGTGGTTGGTTAAGCCAGGGAGTTTGTGAGAGAGTGACCCTAGGGATGCTCCCTGGAGGATATGAGCAGGACACGGAGTACGGCAACACAGCCCACCTAGGGGACTGCCACGGTAGCTAA
Peptide sequence:
MGFLLLWFCVLFLLVSRLRAVSFPEDDEPLNTVDYHYSRQYPVFRGRPSGNESQHRLDFQLMLKIRDTLYIAGRDQVYTVNLNEIPQTEVIPSKKLTWRSRQQDRENCAMKGKHKDECHNFIKVFVPRNDEMVFVCGTNAFNPMCRYYRLRTLEYDGEEISGLARCPFDARQTNVALFADGKLYSATVADFLASDAVIYRSMGDGSALRTIKYDSKWIKEPHFLHAIEYGNYVYFFFREIAVEHNNLGKAVYSRVARICKNDMGGSQRVLEKHWTSFLKARLNCSVPGDSFFYFDVLQSITDIIQINGIPTVVGVFTTQLNSIPGSAVCAFSMDDIEKVFKGRFKEQKTPDSVWTAVPEDKVPKPRPGCCAKHGLAEAYKTSIDFPDDTLAFIKSHPLMDSAVPPIADEPWFTKTRVRYRLTAIEVDRSAGPYQNYTVIFVGSEAGVVLKVLAKTSPFSLNDSVLLEEIEAYNPAKCSAESEEDRKVVSLQLDKDHHALYVAFSSCVVRIPLSRCERYGSCKKSCIASRDPYCGWLSQGVCERVTLGMLPGGYEQDTEYGNTAHLGDCHGS
IRESfinder result
IRESfinder score
0.532030689
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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