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mmu_circSec22a_740
Basic information of circular RNA
PanCircBase ID:
mmu_circSec22a_740
mm39_Chr. Position ID:
chr16|35139173|35182129|-
Gene name:
Sec22a
Transcript:
ENSMUST00000043521.5
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
6,5,4,3,2
Exon/intron offsets:
0,10694,28795,30027,42757
Genomic length:
42956
Exon/intron sizes in nt:
6,61,16,19,51,64,199
Flanking exon/introns:
chr16:35134657-35139173|chr16:35182129-35184193
Splice length:
740
Other database IDs:
CIRCpedia: MMU_CIRCpedia_17694, circAtlas: mmu-Sec22a_0005
circBase: hsa_circ_0121659, circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_43221
Human Ortholog IDs:
Mature spliced Sequence:
GTCTTCTGTGGGTTGAAATGTCTATGATTTTGTCTGCCTCAGTCATTCGTGTGAGGGATGGACTACCGCTGTCTGCATCCACTGATTATGAGCAGAGCACAGGAATGCAGGAGTGCAGAAAGTACTTTAAGATGCTGTCCAGGAAACTTGCTCAATTTCCTGATAGATGTACACTGAAAACGGGGCGCTATAACATTAATTTCATTAGCTCTCTGGGAGTGAGCTACATGATGTTGTGCAGTGAGAATTATCCAAATGTTCTCGCCTTCTCTTTCCTGGATGAGCTTCAGAAGGAGTTCATTACTACTTATAACATGATGAAGACAAATACTGCTGTCAGACCATACTGTTTCATTGAATTTGATAACTTCATTCAGAGGACCAAGCAGCGATATAATAATCCCAGGTCTCTTTCAACAAAAATAAATCTGTCTGACATGCAGATGGAAATCAAGCTGAGGCCCCCTTATCAAATCCCAATGTGTGAACTGGGATCAGCAAATGGAGTCACATCTGCATTTTCTGTTGACTGTAAAGGTGCTGGTAAGATTTCTTCTGCCCATCAGCGACTAGAACCAGCAACTCTGTCAGGGATTGTGGCGTTTATCCTTAGTCTTTTATGTGGAGCTCTGAATTTAATTCGAGGCTTTCATGCCATAGAAAGCCTCCTGCAGAGTGATGGTGAGGATCTTAATTACATTATTGCATTTTTCCTTGGGACAGCAGCCTGCCTTTACCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GCCATAGAAAGCCTCCTGCA
60.11
CAGACAGCGGTAGTCCATCC
59.9
162
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TGCCATAGAAAGCCTCCTGC
60.11
CAGACAGCGGTAGTCCATCC
59.9
163
PCR template sequence:
TCGAGGCTTTCATGCCATAGAAAGCCTCCTGCAGAGTGATGGTGAGGATCTTAATTACATTATTGCATTTTTCCTTGGGACAGCAGCCTGCCTTTACCAGGTCTTCTGTGGGTTGAAATGTCTATGATTTTGTCTGCCTCAGTCATTCGTGTGAGGGATGGACTACCGCTGTCTGCATCCACTGATTATGAGCAGAGCAC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
6
Interacting miRNAs (#binding sites)
mmu-miR-136-5p(1), mmu-miR-127-5p(1), mmu-miR-130b-3p(1), mmu-miR-301a-3p(1), mmu-miR-3470b(1), mmu-miR-670-5p(1)
siRNAs for circular RNA silencing
Junction sequence
CTGCCTTTACCAGGTCTTCTGTGGGT
siRNA sets
ACAGAAGACCTGGTAAAGG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSEC22A_740_ORF_1
0.7533
0.031121084
0.840591746
750
ORF sequence:
ATGTCTATGATTTTGTCTGCCTCAGTCATTCGTGTGAGGGATGGACTACCGCTGTCTGCATCCACTGATTATGAGCAGAGCACAGGAATGCAGGAGTGCAGAAAGTACTTTAAGATGCTGTCCAGGAAACTTGCTCAATTTCCTGATAGATGTACACTGAAAACGGGGCGCTATAACATTAATTTCATTAGCTCTCTGGGAGTGAGCTACATGATGTTGTGCAGTGAGAATTATCCAAATGTTCTCGCCTTCTCTTTCCTGGATGAGCTTCAGAAGGAGTTCATTACTACTTATAACATGATGAAGACAAATACTGCTGTCAGACCATACTGTTTCATTGAATTTGATAACTTCATTCAGAGGACCAAGCAGCGATATAATAATCCCAGGTCTCTTTCAACAAAAATAAATCTGTCTGACATGCAGATGGAAATCAAGCTGAGGCCCCCTTATCAAATCCCAATGTGTGAACTGGGATCAGCAAATGGAGTCACATCTGCATTTTCTGTTGACTGTAAAGGTGCTGGTAAGATTTCTTCTGCCCATCAGCGACTAGAACCAGCAACTCTGTCAGGGATTGTGGCGTTTATCCTTAGTCTTTTATGTGGAGCTCTGAATTTAATTCGAGGCTTTCATGCCATAGAAAGCCTCCTGCAGAGTGATGGTGAGGATCTTAATTACATTATTGCATTTTTCCTTGGGACAGCAGCCTGCCTTTACCAGGTCTTCTGTGGGTTGAAATGTCTATGA
Peptide sequence:
MSMILSASVIRVRDGLPLSASTDYEQSTGMQECRKYFKMLSRKLAQFPDRCTLKTGRYNINFISSLGVSYMMLCSENYPNVLAFSFLDELQKEFITTYNMMKTNTAVRPYCFIEFDNFIQRTKQRYNNPRSLSTKINLSDMQMEIKLRPPYQIPMCELGSANGVTSAFSVDCKGAGKISSAHQRLEPATLSGIVAFILSLLCGALNLIRGFHAIESLLQSDGEDLNYIIAFFLGTAACLYQVFCGLKCL
IRESfinder result
IRESfinder score
0.829300913
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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