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mmu_circSema3c_1027
Basic information of circular RNA
PanCircBase ID:
mmu_circSema3c_1027
mm39_Chr. Position ID:
chr5|17867917|17899863|+
Gene name:
Sema3c
Transcript:
ENSMUST00000030568.14
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
8
Exon/intron indexes:
5,6,7,8,9,10,11,12
Exon/intron offsets:
0,7530,9509,12122,13391,15392,19019,31723
Genomic length:
31946
Exon/intron sizes in nt:
1,20,91,12,01,43,11,57,00,00,000
Flanking exon/introns:
chr5:17860063-17867917|chr5:17899863-17916383
Splice length:
1027
Other database IDs:
circBase: mmu_circ_0012388, CIRCpedia: MMU_CIRCpedia_12025, circAtlas: mmu-Sema3c_0015
circBase: hsa_circ_0080899, circAtlas: hsa-SEMA3C_0030, CIRCpedia: HSA_CIRCpedia_59077
Human Ortholog IDs:
Mature spliced Sequence:
CATGGCTGTGGAAATTTCGTCCGGGTGATTCAGACATTCAACCGTACTCACCTGTATGTCTGTGGGAGTGGAGCGTTCAGCCCAGTGTGCACCTACCTGAACCGGGGAAGGAGGTCAGAGGACCAGGTATTCATGATCGACTCTAAGTGTGAATCTGGCAAAGGACGATGCTCTTTCAACCCGAATGTGAACACTGTGTCTGTTATGATCAATGAGGAACTCTTCTCAGGAATGTATATAGACTTCATGGGAACAGATGCTGCTATTTTCCGAAGTTTAACTAAGAGGAATGCAGTTCGAACTGATCAACATAATTCAAAATGGCTGAGTGAACCCATGTTTGTGGACGCACATGTGATCCCAGATGGCACTGATCCAAATGATGCTAAGGTCTATTTCTTCTTCAAAGAAAGACTGACTGACAACAATAGGAGCACAAAACAGATTCATTCCATGATTGCAAGAATATGCCCTAATGACACTGGTGGACAACGTAGTCTTGTCAACAAGTGGACCACATTCTTAAAGGCAAGACTTGTATGCTCAGTCACAGATGAAGATGGCCCAGAGACACATTTTGATGAACTAGAGGATGTCTTTCTGCTGGAAACTGACAATCCAAGGACAACACTCGTGTATGGCATCTTCACCACATCAAGCTCTGTTTTTAAGGGATCGGCAGTGTGTGTGTATCATTTATCTGATATACAGACTGTATTCAATGGGCCCTTTGCCCACAAGGAAGGGCCCAATCACCAGCTGATCTCCTATCAAGGTAGAATCCCATATCCTCGCCCAGGAACTTGCCCAGGAGGGGCCTTTACACCCAATATGAGAACCACCAAGGACTTCCCAGATGACGTTGTCACTTTTATTCGGAACCACCCTCTCATGTACAATTCCATCTACCCCATCCACAGAAGGCCTCTGATAGTCCGCATAGGCACTGACTACAAGTACACAAAGATTGCTGTGGACCGTGTCAACGCTGCTGATGGGAGATACCACGTTCTGTTTCTGGGCACAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AAGATTGCTGTGGACCGTGT
59.89
CAGGTAGGTGCACACTGGG
60
163
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
ATTGCTGTGGACCGTGTCAA
60.18
CAGGTAGGTGCACACTGGG
60
160
PCR template sequence:
CTGATAGTCCGCATAGGCACTGACTACAAGTACACAAAGATTGCTGTGGACCGTGTCAACGCTGCTGATGGGAGATACCACGTTCTGTTTCTGGGCACAGCATGGCTGTGGAAATTTCGTCCGGGTGATTCAGACATTCAACCGTACTCACCTGTATGTCTGTGGGAGTGGAGCGTTCAGCCCAGTGTGCACCTACCTGA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
8
Interacting miRNAs (#binding sites)
mmu-miR-103-3p(1), mmu-miR-322-5p(1), mmu-miR-29b-3p(1), mmu-miR-326-3p(1), mmu-miR-495-3p(1), mmu-miR-503-5p(1), mmu-miR-107-3p(1), mmu-miR-1198-5p(1)
siRNAs for circular RNA silencing
Junction sequence
TTTCTGGGCACAGCATGGCTGTGGAA
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSEMA3C_1027_ORF_1
0.827
0.166720958
0.989753667
1059
ORF sequence:
ATGGGAGATACCACGTTCTGTTTCTGGGCACAGCATGGCTGTGGAAATTTCGTCCGGGTGATTCAGACATTCAACCGTACTCACCTGTATGTCTGTGGGAGTGGAGCGTTCAGCCCAGTGTGCACCTACCTGAACCGGGGAAGGAGGTCAGAGGACCAGGTATTCATGATCGACTCTAAGTGTGAATCTGGCAAAGGACGATGCTCTTTCAACCCGAATGTGAACACTGTGTCTGTTATGATCAATGAGGAACTCTTCTCAGGAATGTATATAGACTTCATGGGAACAGATGCTGCTATTTTCCGAAGTTTAACTAAGAGGAATGCAGTTCGAACTGATCAACATAATTCAAAATGGCTGAGTGAACCCATGTTTGTGGACGCACATGTGATCCCAGATGGCACTGATCCAAATGATGCTAAGGTCTATTTCTTCTTCAAAGAAAGACTGACTGACAACAATAGGAGCACAAAACAGATTCATTCCATGATTGCAAGAATATGCCCTAATGACACTGGTGGACAACGTAGTCTTGTCAACAAGTGGACCACATTCTTAAAGGCAAGACTTGTATGCTCAGTCACAGATGAAGATGGCCCAGAGACACATTTTGATGAACTAGAGGATGTCTTTCTGCTGGAAACTGACAATCCAAGGACAACACTCGTGTATGGCATCTTCACCACATCAAGCTCTGTTTTTAAGGGATCGGCAGTGTGTGTGTATCATTTATCTGATATACAGACTGTATTCAATGGGCCCTTTGCCCACAAGGAAGGGCCCAATCACCAGCTGATCTCCTATCAAGGTAGAATCCCATATCCTCGCCCAGGAACTTGCCCAGGAGGGGCCTTTACACCCAATATGAGAACCACCAAGGACTTCCCAGATGACGTTGTCACTTTTATTCGGAACCACCCTCTCATGTACAATTCCATCTACCCCATCCACAGAAGGCCTCTGATAGTCCGCATAGGCACTGACTACAAGTACACAAAGATTGCTGTGGACCGTGTCAACGCTGCTGATGGGAGATACCACGTTCTGTTTCTGGGCACA
Peptide sequence:
MGDTTFCFWAQHGCGNFVRVIQTFNRTHLYVCGSGAFSPVCTYLNRGRRSEDQVFMIDSKCESGKGRCSFNPNVNTVSVMINEELFSGMYIDFMGTDAAIFRSLTKRNAVRTDQHNSKWLSEPMFVDAHVIPDGTDPNDAKVYFFFKERLTDNNRSTKQIHSMIARICPNDTGGQRSLVNKWTTFLKARLVCSVTDEDGPETHFDELEDVFLLETDNPRTTLVYGIFTTSSSVFKGSAVCVYHLSDIQTVFNGPFAHKEGPNHQLISYQGRIPYPRPGTCPGGAFTPNMRTTKDFPDDVVTFIRNHPLMYNSIYPIHRRPLIVRIGTDYKYTKIAVDRVNAADGRYHVLFLGT
IRESfinder result
IRESfinder score
0.540491579
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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