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mmu_circPtp4a1_826
Basic information of circular RNA
PanCircBase ID:
mmu_circPtp4a1_826
mm39_Chr. Position ID:
chr1|30983616|30985720|-
Gene name:
Ptp4a1
Transcript:
ENSMUST00000232841.2
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
4,3,2
Exon/intron offsets:
0,402,1502
Genomic length:
2104
Exon/intron sizes in nt:
1,31,93,602
Flanking exon/introns:
chr1:30983087-30983616|chr1:30985720-30988077
Splice length:
826
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
CAGTTCTGTGGTGTTCTCGGTCACACATTTATGGAGTTTCTGAAGGGCAGTGGAGATTACTGCCAGGCACAGCACGACCTCTATGCAGACAAGTGAACTGTAGAAATTCATTACTACTCCACCAAGAAACCCCCATAAGAGTGGATAACCTGGACACAGGCGTGTTGAATTGAAATCTGCAGAGCATTTGACAAGAGCTCAGACCTGGATGGGGTAAACCTCAGTGCACTTCCTTTGTATTGCCTCAGTATTACTGGATTGAAGACTCACTGCTTCTTGTTAGGAGGTTCATTTCATTGCCCGTTTCTCCCAATTCATACTCAAGCACTGAGAATTTCAAGTGGAGTATATTGAATATTGAAGTAGACTTCAGGTTGTTTTTTGGTTTTGTTTTGGTTTTTTTTTTTTTTTTTTCTGTTTTGGTTTTAAATCATTTCTGTATTCAATTTTTTAATTCTTTCATAACCCTATTGGGTGTTTTTTTAAACTAAATTAACATGGCTCGAATGAACCGCCCTGCTCCTGTGGAAGTCACATACAAGAACATGCGATTTCTTATTACACACAATCCAACCAATGCGACCTTAAACAAATTTATAGAGGAACTTAAGAAGTATGGAGTTACCACAATAGTAAGAGTATGTGAAGCAACTTACGACACTACTCTTGTGGAGAAAGAAGGCATTCATGTTCTTGACTGGCCTTTTGATGATGGTGCACCACCATCCAACCAGATTGTCGATGACTGGCTAAGTCTTGTGAAGATTAAGTTTCGTGAAGAACCTGGTTGCTGTATTGCTGTCCATTGTGTCGCAGGCCTTGGCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TCGTGAAGAACCTGGTTGCT
59.53
TGCATAGAGGTCGTGCTGTG
60.11
141
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TCGTGAAGAACCTGGTTGCT
59.53
TGTCTGCATAGAGGTCGTGC
59.83
145
PCR template sequence:
CCAACCAGATTGTCGATGACTGGCTAAGTCTTGTGAAGATTAAGTTTCGTGAAGAACCTGGTTGCTGTATTGCTGTCCATTGTGTCGCAGGCCTTGGCAGCAGTTCTGTGGTGTTCTCGGTCACACATTTATGGAGTTTCTGAAGGGCAGTGGAGATTACTGCCAGGCACAGCACGACCTCTATGCAGACAAGTGAACTG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
7
Interacting miRNAs (#binding sites)
mmu-miR-429-3p(1), mmu-miR-200b-3p(1), mmu-miR-200c-3p(1), mmu-miR-203-3p(1), mmu-miR-139-5p(1), mmu-miR-324-3p(1), mmu-miR-297a-5p(1)
siRNAs for circular RNA silencing
Junction sequence
CAGGCCTTGGCAGCAGTTCTGTGGTG
siRNA sets
ACAGAACTGCTGCCAAGGC, GAACTGCTGCCAAGGCCTG, AGAACTGCTGCCAAGGCCT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCPTP4A1_826_ORF_1
0.9661
0.085200666
0.388814526
372
ORF sequence:
ATGGCTCGAATGAACCGCCCTGCTCCTGTGGAAGTCACATACAAGAACATGCGATTTCTTATTACACACAATCCAACCAATGCGACCTTAAACAAATTTATAGAGGAACTTAAGAAGTATGGAGTTACCACAATAGTAAGAGTATGTGAAGCAACTTACGACACTACTCTTGTGGAGAAAGAAGGCATTCATGTTCTTGACTGGCCTTTTGATGATGGTGCACCACCATCCAACCAGATTGTCGATGACTGGCTAAGTCTTGTGAAGATTAAGTTTCGTGAAGAACCTGGTTGCTGTATTGCTGTCCATTGTGTCGCAGGCCTTGGCAGCAGTTCTGTGGTGTTCTCGGTCACACATTTATGGAGTTTCTGA
Peptide sequence:
MARMNRPAPVEVTYKNMRFLITHNPTNATLNKFIEELKKYGVTTIVRVCEATYDTTLVEKEGIHVLDWPFDDGAPPSNQIVDDWLSLVKIKFREEPGCCIAVHCVAGLGSSSVVFSVTHLWSF
IRESfinder result
IRESfinder score
0.878769791
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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