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mmu_circPtpn21_360
Basic information of circular RNA
PanCircBase ID:
mmu_circPtpn21_360
mm39_Chr. Position ID:
chr12|98648777|98649874|-
Gene name:
Ptpn21
Transcript:
ENSMUST00000170188.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
2
Exon/intron indexes:
15,14
Exon/intron offsets:
0,959
Genomic length:
1097
Exon/intron sizes in nt:
222,138
Flanking exon/introns:
chr12:98646748-98648777|chr12:98649874-98654448
Splice length:
360
Other database IDs:
CIRCpedia: MMU_CIRCpedia_35853, circAtlas: mmu-Ptpn21_0001
circAtlas: hsa-PTPN21_0001
Human Ortholog IDs:
Mature spliced Sequence:
GGGATGAAAAAAACTCGAGCAGATGCAAAAAAAATTGGTCCCCTCAAGCTGGCAGCCCTCAATGGGCTCTCCCTGTCCCGGCTGCCCCTGCCTGATGAAGGAAAAGAAGTGTCCACCAGAGCGACAAATGACGAGAGGTGCAAGGTTCTGGAGCAGCGGTTAGAGCAAGGCATGGTCTTCACCGAATATGAGAGGATCCTTAAGAAGCGGCTGGTTGATGGTGAGTGCTCGACTGCCCGGCTCCCTGAAAATGCAGAGAGAAATCGATTTCAAGATGTGCTCCCCTACGATGATGCGAGAGTCGAGTTGGTGCCAACCAAGGAGAACAACACTGGCTACATCAACGCGTCACACATTAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GAGAGTCGAGTTGGTGCCAA
59.97
CTTCATCAGGCAGGGGCAG
60.45
164
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
ATGCGAGAGTCGAGTTGGTG
60.11
CTTCATCAGGCAGGGGCAG
60.45
168
PCR template sequence:
AAATCGATTTCAAGATGTGCTCCCCTACGATGATGCGAGAGTCGAGTTGGTGCCAACCAAGGAGAACAACACTGGCTACATCAACGCGTCACACATTAAGGGGATGAAAAAAACTCGAGCAGATGCAAAAAAAATTGGTCCCCTCAAGCTGGCAGCCCTCAATGGGCTCTCCCTGTCCCGGCTGCCCCTGCCTGATGAAG
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-434-5p(1), mmu-miR-96-5p(1), mmu-miR-466a-5p(1), mmu-miR-1187(1), mmu-miR-466p-5p(1), mmu-miR-129-5p(1)
siRNAs for circular RNA silencing
Junction sequence
GTCACACATTAAGGGGATGAAAAAAA
siRNA sets
TTTTTCATCCCCTTAATGT, TTTTCATCCCCTTAATGTG, TTTTTTCATCCCCTTAATG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCPTPN21_360_ORF_1
1.1833
0.397165882
0.976763469
717
ORF sequence:
ATGAAAAAAACTCGAGCAGATGCAAAAAAAATTGGTCCCCTCAAGCTGGCAGCCCTCAATGGGCTCTCCCTGTCCCGGCTGCCCCTGCCTGATGAAGGAAAAGAAGTGTCCACCAGAGCGACAAATGACGAGAGGTGCAAGGTTCTGGAGCAGCGGTTAGAGCAAGGCATGGTCTTCACCGAATATGAGAGGATCCTTAAGAAGCGGCTGGTTGATGGTGAGTGCTCGACTGCCCGGCTCCCTGAAAATGCAGAGAGAAATCGATTTCAAGATGTGCTCCCCTACGATGATGCGAGAGTCGAGTTGGTGCCAACCAAGGAGAACAACACTGGCTACATCAACGCGTCACACATTAAGGGGATGAAAAAAACTCGAGCAGATGCAAAAAAAATTGGTCCCCTCAAGCTGGCAGCCCTCAATGGGCTCTCCCTGTCCCGGCTGCCCCTGCCTGATGAAGGAAAAGAAGTGTCCACCAGAGCGACAAATGACGAGAGGTGCAAGGTTCTGGAGCAGCGGTTAGAGCAAGGCATGGTCTTCACCGAATATGAGAGGATCCTTAAGAAGCGGCTGGTTGATGGTGAGTGCTCGACTGCCCGGCTCCCTGAAAATGCAGAGAGAAATCGATTTCAAGATGTGCTCCCCTACGATGATGCGAGAGTCGAGTTGGTGCCAACCAAGGAGAACAACACTGGCTACATCAACGCGTCACACATTAAG
Peptide sequence:
MKKTRADAKKIGPLKLAALNGLSLSRLPLPDEGKEVSTRATNDERCKVLEQRLEQGMVFTEYERILKKRLVDGECSTARLPENAERNRFQDVLPYDDARVELVPTKENNTGYINASHIKGMKKTRADAKKIGPLKLAALNGLSLSRLPLPDEGKEVSTRATNDERCKVLEQRLEQGMVFTEYERILKKRLVDGECSTARLPENAERNRFQDVLPYDDARVELVPTKENNTGYINASHIK
IRESfinder result
IRESfinder score
0.246082292
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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