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mmu_circPsmd1_497
Basic information of circular RNA
PanCircBase ID:
mmu_circPsmd1_497
mm39_Chr. Position ID:
chr1|86055857|86061506|+
Gene name:
Psmd1
Transcript:
ENSMUST00000027432.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
20,21,22,23
Exon/intron offsets:
0,2501,4578,5502
Genomic length:
5649
Exon/intron sizes in nt:
1,70,93,87,147
Flanking exon/introns:
chr1:86054280-86055857|chr1:86061506-86064684
Splice length:
497
Other database IDs:
circAtlas: hsa-SCAF8_0001
Human Ortholog IDs:
Mature spliced Sequence:
GTGGTCATAATGTCACAATCTCCTTACAGTCCAGGACTGGGCACACTCATATGCCGTCTGTGGTTGGCGTCCTTGTCTTCACCCAGTTCTGGTTCTGGTTTCCCCTTTCACACTTCCTGTCATTGGCTTATACTCCTACCTGTGTCATTGGCCTTAACAAGGATTTAAAGATGCCGAAAGTTCAATATAAATCAAATTGTAAACCATCCACATTCGCATATCCTGCCCCTCTGGAAGTACCAAAAGAAAAAGAAAAGGAAAAGGTTTCCACCGCTGTGTTGTCTATTACTGCCAAAGCTAAAAAAAAAGAAAAAGAAAAAGAAAAAAAGGAGGAGGAGAAGATGGAAGTGGATGAAGCAGAGAAGAAGGAAGAGAAAGAGAAGAAAAAAGAACCTGAACCAAACTTCCAGCTGTTGGATAATCCAGCACGAGTTATGCCTGCCCAGCTGAAGGTCTTAAGTATGACAGAGACCTGCAGATACCAGCCTTTTAAACCA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TCCAGCACGAGTTATGCCTG
60.11
ACTGGGTGAAGACAAGGACG
59.61
163
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TCCAGCACGAGTTATGCCTG
60.11
GAAGACAAGGACGCCAACCA
60.53
156
PCR template sequence:
ACCAAACTTCCAGCTGTTGGATAATCCAGCACGAGTTATGCCTGCCCAGCTGAAGGTCTTAAGTATGACAGAGACCTGCAGATACCAGCCTTTTAAACCAGTGGTCATAATGTCACAATCTCCTTACAGTCCAGGACTGGGCACACTCATATGCCGTCTGTGGTTGGCGTCCTTGTCTTCACCCAGTTCTGGTTCTGGTT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
3
Interacting miRNAs (#binding sites)
mmu-miR-183-5p(1), mmu-miR-758-3p(1), mmu-miR-207(1)
siRNAs for circular RNA silencing
Junction sequence
GCCTTTTAAACCAGTGGTCATAATGT
siRNA sets
ATGACCACTGGTTTAAAAG, ATTATGACCACTGGTTTAA, TTATGACCACTGGTTTAAA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCPSMD1_497_ORF_1
0.691
0.049751975
0.659282704
615
ORF sequence:
ATGCCGTCTGTGGTTGGCGTCCTTGTCTTCACCCAGTTCTGGTTCTGGTTTCCCCTTTCACACTTCCTGTCATTGGCTTATACTCCTACCTGTGTCATTGGCCTTAACAAGGATTTAAAGATGCCGAAAGTTCAATATAAATCAAATTGTAAACCATCCACATTCGCATATCCTGCCCCTCTGGAAGTACCAAAAGAAAAAGAAAAGGAAAAGGTTTCCACCGCTGTGTTGTCTATTACTGCCAAAGCTAAAAAAAAAGAAAAAGAAAAAGAAAAAAAGGAGGAGGAGAAGATGGAAGTGGATGAAGCAGAGAAGAAGGAAGAGAAAGAGAAGAAAAAAGAACCTGAACCAAACTTCCAGCTGTTGGATAATCCAGCACGAGTTATGCCTGCCCAGCTGAAGGTCTTAAGTATGACAGAGACCTGCAGATACCAGCCTTTTAAACCAGTGGTCATAATGTCACAATCTCCTTACAGTCCAGGACTGGGCACACTCATATGCCGTCTGTGGTTGGCGTCCTTGTCTTCACCCAGTTCTGGTTCTGGTTTCCCCTTTCACACTTCCTGTCATTGGCTTATACTCCTACCTGTGTCATTGGCCTTAACAAGGATTTAA
Peptide sequence:
MPSVVGVLVFTQFWFWFPLSHFLSLAYTPTCVIGLNKDLKMPKVQYKSNCKPSTFAYPAPLEVPKEKEKEKVSTAVLSITAKAKKKEKEKEKKEEEKMEVDEAEKKEEKEKKKEPEPNFQLLDNPARVMPAQLKVLSMTETCRYQPFKPVVIMSQSPYSPGLGTLICRLWLASLSSPSSGSGFPFHTSCHWLILLPVSLALTRI
IRESfinder result
IRESfinder score
0.568623497
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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