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mmu_ciPsma1_480
Basic information of circular RNA
PanCircBase ID:
mmu_ciPsma1_480
mm39_Chr. Position ID:
chr7|113869087|113869567|-
Gene name:
Psma1
Transcript:
ENSMUST00000033008.10
CircRNA type:
Circular intronic (ci)RNA
Exon/Intron count:
1
Exon/intron indexes:
6
Exon/intron offsets:
0
Genomic length:
480
Exon/intron sizes in nt:
480
Flanking exon/introns:
chr7:113869085-113869567
Splice length:
480
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GTAAGTTCTTGTATTATCTACTTTACTGCTTCTGTGACAGAGTACCTTACACAAACCACCTGGGGAAGAAGGGTTTATTCTGATGTAGGGTTGAGGAGCCGAGAGCGTGCTGTGATGGGGAACCTGAGGTGGCCGGCCAGTCATGCTGCATTGCAGTTAGAATGCAGGAGAGATGAGCACTGATGTTCAGCTTGTTTGCTCCTGTAGGTAATCCAGGACAGAGCCTATAAGATGGTGCTAGTCAATGTCAGACTGAGTTTTCCCTGTTCATTTAAATGTGTCTGGAGCCGGGCATGGGCTTGCATGCTTTTAATCTCAGTACTAGGGAGTCAGATGCAATTGGATCTCTGACTTCAGATTTATTAAAATAATAACCTTCACACTTATCACAGTTATATCCTAACAATGGTTTAGCCTAGAAATTTTATGATTTCTAGTCAATTGAAAGTAAAGAATTATATAATCTGTTTTTCTGTTTAT
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TCCTAACAATGGTTTAGCCTAGA
56.71
CTTCCCCAGGTGGTTTGTGT
60.11
151
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TCCTAACAATGGTTTAGCCTAGA
56.71
TCTTCCCCAGGTGGTTTGTG
59.82
152
PCR template sequence:
CACTTATCACAGTTATATCCTAACAATGGTTTAGCCTAGAAATTTTATGATTTCTAGTCAATTGAAAGTAAAGAATTATATAATCTGTTTTTCTGTTTATGTAAGTTCTTGTATTATCTACTTTACTGCTTCTGTGACAGAGTACCTTACACAAACCACCTGGGGAAGAAGGGTTTATTCTGATGTAGGGTTGAGGAGCC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
5
Interacting miRNAs (#binding sites)
mmu-miR-29b-3p(1), mmu-miR-29a-3p(1), mmu-miR-29c-3p(1), mmu-miR-300-3p(1), mmu-miR-673-5p(1)
siRNAs for circular RNA silencing
Junction sequence
TTTTTCTGTTTATGTAAGTTCTTGTA
siRNA sets
CAAGAACTTACATAAACAG, ACAAGAACTTACATAAACA, TACAAGAACTTACATAAAC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIPSMA1_480_ORF_1
0.6196
-0.218974163
0.035627712
237
ORF sequence:
ATGATTTCTAGTCAATTGAAAGTAAAGAATTATATAATCTGTTTTTCTGTTTATGTAAGTTCTTGTATTATCTACTTTACTGCTTCTGTGACAGAGTACCTTACACAAACCACCTGGGGAAGAAGGGTTTATTCTGATGTAGGGTTGAGGAGCCGAGAGCGTGCTGTGATGGGGAACCTGAGGTGGCCGGCCAGTCATGCTGCATTGCAGTTAGAATGCAGGAGAGATGAGCACTGA
Peptide sequence:
MISSQLKVKNYIICFSVYVSSCIIYFTASVTEYLTQTTWGRRVYSDVGLRSRERAVMGNLRWPASHAALQLECRRDEH
IRESfinder result
IRESfinder score
0.839764171
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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