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mmu_circSec31a_567
Basic information of circular RNA
PanCircBase ID:
mmu_circSec31a_567
mm39_Chr. Position ID:
chr5|100516152|100523912|-
Gene name:
Sec31a
Transcript:
ENSMUST00000182988.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
15,14,13,12
Exon/intron offsets:
0,5131,6914,7667
Genomic length:
7760
Exon/intron sizes in nt:
59,291,124,93
Flanking exon/introns:
chr5:100513853-100516152|chr5:100523912-100526686
Splice length:
567
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GTTAGAATTGCCCCTACTGTCACTACCTGGAGTAACAAAACTCCCACTGCCCTCCCCAGCCATCCACCTGCAGCCTCTCCCTCTGACACACAGGGAGAAAATCCCCCACCTCCAGGTTTCATAATGCAGGGCAATGTCATTCCAAACCCTGCTGCCCCGCTGCCCACGGCTCCAGGCCACATGCCCAGCCAGCTGCCACCTTACCCACAGCCGCAGCCTTACCAGCCAGCCCAGCAGTATTCCTTCGGAACAGGGGGGGCAGCAGCTTATCGACCTCAACAGCCTGTTGCTCCTCCTGCTTCTAACGCTTACCCTAACACCCCGTACATATCTCCTGTGGCTTCCTATTCTGGGCAGCCTCAGATGTACACAGCCCAGCAAGCCTCCTCACCTACCTCCAGCTCTGCTGCTTCTTTCCCCCCTCCCTCCTCTGGAGCATCCTTCCAGCATGGCGGACCAGGAGCTCCACCATCATCTTCAGCTTATGCACTGCCTCCTGGAACAACAGGTCCTCAGAATGGTTGGAATGATCCTCCAGCTCTGAACAGAGTGCCGAAGAAGAAGAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AGCTTATGCACTGCCTCCTG
60.11
GAGGGCAGTGGGAGTTTTGT
60.18
142
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CAGCTTATGCACTGCCTCCT
60.11
GAGGGCAGTGGGAGTTTTGT
60.18
143
PCR template sequence:
ACCATCATCTTCAGCTTATGCACTGCCTCCTGGAACAACAGGTCCTCAGAATGGTTGGAATGATCCTCCAGCTCTGAACAGAGTGCCGAAGAAGAAGAAGGTTAGAATTGCCCCTACTGTCACTACCTGGAGTAACAAAACTCCCACTGCCCTCCCCAGCCATCCACCTGCAGCCTCTCCCTCTGACACACAGGGAGAAA
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-429-3p(1), mmu-miR-200b-3p(1), mmu-miR-34c-5p(1), mmu-miR-34a-5p(1), mmu-miR-200c-3p(1), mmu-miR-15b-5p(1), mmu-miR-152-3p(1), mmu-miR-148b-3p(1), mmu-miR-709(1), mmu-miR-34b-5p(1), mmu-miR-98-5p(1), mmu-miR-190b-5p(1), mmu-miR-3470b(1), mmu-miR-490-3p(1)
siRNAs for circular RNA silencing
Junction sequence
GAAGAAGAAGAAGGTTAGAATTGCCC
siRNA sets
AATTCTAACCTTCTTCTTC, ATTCTAACCTTCTTCTTCT, TTCTAACCTTCTTCTTCTT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSEC31A_567_ORF_1
1.1617
0.17739513
0.992694112
1011
ORF sequence:
ATGCAGGGCAATGTCATTCCAAACCCTGCTGCCCCGCTGCCCACGGCTCCAGGCCACATGCCCAGCCAGCTGCCACCTTACCCACAGCCGCAGCCTTACCAGCCAGCCCAGCAGTATTCCTTCGGAACAGGGGGGGCAGCAGCTTATCGACCTCAACAGCCTGTTGCTCCTCCTGCTTCTAACGCTTACCCTAACACCCCGTACATATCTCCTGTGGCTTCCTATTCTGGGCAGCCTCAGATGTACACAGCCCAGCAAGCCTCCTCACCTACCTCCAGCTCTGCTGCTTCTTTCCCCCCTCCCTCCTCTGGAGCATCCTTCCAGCATGGCGGACCAGGAGCTCCACCATCATCTTCAGCTTATGCACTGCCTCCTGGAACAACAGGTCCTCAGAATGGTTGGAATGATCCTCCAGCTCTGAACAGAGTGCCGAAGAAGAAGAAGGTTAGAATTGCCCCTACTGTCACTACCTGGAGTAACAAAACTCCCACTGCCCTCCCCAGCCATCCACCTGCAGCCTCTCCCTCTGACACACAGGGAGAAAATCCCCCACCTCCAGGTTTCATAATGCAGGGCAATGTCATTCCAAACCCTGCTGCCCCGCTGCCCACGGCTCCAGGCCACATGCCCAGCCAGCTGCCACCTTACCCACAGCCGCAGCCTTACCAGCCAGCCCAGCAGTATTCCTTCGGAACAGGGGGGGCAGCAGCTTATCGACCTCAACAGCCTGTTGCTCCTCCTGCTTCTAACGCTTACCCTAACACCCCGTACATATCTCCTGTGGCTTCCTATTCTGGGCAGCCTCAGATGTACACAGCCCAGCAAGCCTCCTCACCTACCTCCAGCTCTGCTGCTTCTTTCCCCCCTCCCTCCTCTGGAGCATCCTTCCAGCATGGCGGACCAGGAGCTCCACCATCATCTTCAGCTTATGCACTGCCTCCTGGAACAACAGGTCCTCAGAATGGTTGGAATGATCCTCCAGCTCTGAACAGAGTGCCGAAGAAGAAGAAG
Peptide sequence:
MQGNVIPNPAAPLPTAPGHMPSQLPPYPQPQPYQPAQQYSFGTGGAAAYRPQQPVAPPASNAYPNTPYISPVASYSGQPQMYTAQQASSPTSSSAASFPPPSSGASFQHGGPGAPPSSSAYALPPGTTGPQNGWNDPPALNRVPKKKKVRIAPTVTTWSNKTPTALPSHPPAASPSDTQGENPPPPGFIMQGNVIPNPAAPLPTAPGHMPSQLPPYPQPQPYQPAQQYSFGTGGAAAYRPQQPVAPPASNAYPNTPYISPVASYSGQPQMYTAQQASSPTSSSAASFPPPSSGASFQHGGPGAPPSSSAYALPPGTTGPQNGWNDPPALNRVPKKKK
IRESfinder result
IRESfinder score
0.626820267
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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