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mmu_circSec23b_1093
Basic information of circular RNA
PanCircBase ID:
mmu_circSec23b_1093
mm39_Chr. Position ID:
chr2|144404051|144416667|+
Gene name:
Sec23b
Transcript:
ENSMUST00000028916.15
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
9
Exon/intron indexes:
3,4,5,6,7,8,9,10,11
Exon/intron offsets:
0,2434,4631,4969,5751,6484,6968,10347,12535
Genomic length:
12616
Exon/intron sizes in nt:
58,87,237,86,145,159,116,124,81
Flanking exon/introns:
chr2:144401361-144404051|chr2:144416667-144420251
Splice length:
1093
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
TCAAGTGGATTACCGAGCAAAACTCTGGGCCTGCAATTTCTGTTTTCAAAGAAATCAGTTCCCTCCAGCATATGCAGGCATATCTGAGGTGAATCAACCTGCTGAATTGATGCCCCAGTTCTCCACAATTGAGTACATGATCCAGAGAGGTGCTCGGTCTCCTCTGATCTTTCTCTATGTGGTTGACACGTGTTTGGAGGAAGATGACCTTCAAGCACTCAAAGAGTCCCTGCAGATGTCTCTGAGTCTCCTTCCTCCAGATGCCCTGGTTGGTCTCATCACTTTTGGGAGGATGGTGCAGGTTCATGAGCTAAGCTGTGAAGGAATCTCCAAGAGCTATGTCTTCCGAGGGACCAAGGATTTAACTGCAAAGCAAATACAGGAGATGCTGGGCCTGACCAAGTCAGCCATGCCTGTGCAGCAAGCCAGACCTGCTCAACCTCAGGAGCAGCCTTTTGTTTCCAGCAGATTTCTACAGCCCATTCACAAGATTGACATGAACCTCACAGATCTTCTCGGGGAGCTGCAGAGGGACCCATGGCCAGTAACTCAGGGGAAGAGACCACTGCGGTCCACTGGTGTTGCTTTGTCCATTGCTGTTGGCTTGTTGGAGGGGACTTTCCCAAATACTGGAGCCAGGATCATGCTGTTCACTGGCGGGCCCCCGACCCAAGGACCTGGCATGGTGGTTGGAGATGAGTTGAAGACTCCTATTCGTTCCTGGCACGACATTGAGAAAGATAACGCACGATTCATGAAGAAGGCAACCAAGCATTATGAGATGCTTGCTAATCGAACTGCTACAAATGGCCACTGCATTGATATTTATGCTTGTGCCCTTGACCAAACTGGACTTCTGGAGATGAAGTGCTGTCCAAATCTTACAGGAGGCCACATGGTGATGGGAGATTCTTTCAACACTTCTCTTTTCAAGCAGACATTCCAAAGAATTTTTAGTAAAGACTTCAACGGAGATTTCAGAATGGCGTTTGGTGCTACGTTGGATGTAAAGACCTCTCGGGAACTGAAGATTGCAGGAGCCATTGGTCCATGCGTGTCTCTGAATGTGAAAGGGCCATGCGTGTCAGAAAAT
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AGATTGCAGGAGCCATTGGT
59.67
TGCATATGCTGGAGGGAACTG
60.13
141
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AGATTGCAGGAGCCATTGGT
59.67
GCATATGCTGGAGGGAACTGA
59.86
140
PCR template sequence:
TGCTACGTTGGATGTAAAGACCTCTCGGGAACTGAAGATTGCAGGAGCCATTGGTCCATGCGTGTCTCTGAATGTGAAAGGGCCATGCGTGTCAGAAAATTCAAGTGGATTACCGAGCAAAACTCTGGGCCTGCAATTTCTGTTTTCAAAGAAATCAGTTCCCTCCAGCATATGCAGGCATATCTGAGGTGAATCAACCT
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-23b-3p(1), mmu-miR-7b-5p(1), mmu-miR-7a-5p(1), mmu-miR-23a-3p(1), mmu-miR-181b-5p(1), mmu-miR-149-5p(1), mmu-miR-351-5p(1), mmu-miR-362-5p(1), mmu-miR-383-5p(1), mmu-miR-680(1), mmu-miR-673-5p(1), mmu-miR-338-3p(1)
siRNAs for circular RNA silencing
Junction sequence
CGTGTCAGAAAATTCAAGTGGATTAC
siRNA sets
AATCCACTTGAATTTTCTG,TAATCCACTTGAATTTTCT,ATCCACTTGAATTTTCTGA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSEC23B_1093_ORF_1
0.9688
0.173043314
0.992921624
1071
ORF sequence:
ATGCCCCAGTTCTCCACAATTGAGTACATGATCCAGAGAGGTGCTCGGTCTCCTCTGATCTTTCTCTATGTGGTTGACACGTGTTTGGAGGAAGATGACCTTCAAGCACTCAAAGAGTCCCTGCAGATGTCTCTGAGTCTCCTTCCTCCAGATGCCCTGGTTGGTCTCATCACTTTTGGGAGGATGGTGCAGGTTCATGAGCTAAGCTGTGAAGGAATCTCCAAGAGCTATGTCTTCCGAGGGACCAAGGATTTAACTGCAAAGCAAATACAGGAGATGCTGGGCCTGACCAAGTCAGCCATGCCTGTGCAGCAAGCCAGACCTGCTCAACCTCAGGAGCAGCCTTTTGTTTCCAGCAGATTTCTACAGCCCATTCACAAGATTGACATGAACCTCACAGATCTTCTCGGGGAGCTGCAGAGGGACCCATGGCCAGTAACTCAGGGGAAGAGACCACTGCGGTCCACTGGTGTTGCTTTGTCCATTGCTGTTGGCTTGTTGGAGGGGACTTTCCCAAATACTGGAGCCAGGATCATGCTGTTCACTGGCGGGCCCCCGACCCAAGGACCTGGCATGGTGGTTGGAGATGAGTTGAAGACTCCTATTCGTTCCTGGCACGACATTGAGAAAGATAACGCACGATTCATGAAGAAGGCAACCAAGCATTATGAGATGCTTGCTAATCGAACTGCTACAAATGGCCACTGCATTGATATTTATGCTTGTGCCCTTGACCAAACTGGACTTCTGGAGATGAAGTGCTGTCCAAATCTTACAGGAGGCCACATGGTGATGGGAGATTCTTTCAACACTTCTCTTTTCAAGCAGACATTCCAAAGAATTTTTAGTAAAGACTTCAACGGAGATTTCAGAATGGCGTTTGGTGCTACGTTGGATGTAAAGACCTCTCGGGAACTGAAGATTGCAGGAGCCATTGGTCCATGCGTGTCTCTGAATGTGAAAGGGCCATGCGTGTCAGAAAATTCAAGTGGATTACCGAGCAAAACTCTGGGCCTGCAATTTCTGTTTTCAAAGAAATCAGTTCCCTCCAGCATATGCAGGCATATCTGA
Peptide sequence:
MPQFSTIEYMIQRGARSPLIFLYVVDTCLEEDDLQALKESLQMSLSLLPPDALVGLITFGRMVQVHELSCEGISKSYVFRGTKDLTAKQIQEMLGLTKSAMPVQQARPAQPQEQPFVSSRFLQPIHKIDMNLTDLLGELQRDPWPVTQGKRPLRSTGVALSIAVGLLEGTFPNTGARIMLFTGGPPTQGPGMVVGDELKTPIRSWHDIEKDNARFMKKATKHYEMLANRTATNGHCIDIYACALDQTGLLEMKCCPNLTGGHMVMGDSFNTSLFKQTFQRIFSKDFNGDFRMAFGATLDVKTSRELKIAGAIGPCVSLNVKGPCVSENSSGLPSKTLGLQFLFSKKSVPSSICRHI
IRESfinder result
IRESfinder score
0.518850166
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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