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mmu_circPtp4a2_925
Basic information of circular RNA
PanCircBase ID:
mmu_circPtp4a2_925
mm39_Chr. Position ID:
chr4|129732770|129738985|+
Gene name:
Ptp4a2
Transcript:
ENSMUST00000030578.14
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
2,3,4
Exon/intron offsets:
0,3692,6084
Genomic length:
6215
Exon/intron sizes in nt:
701,93,131
Flanking exon/introns:
chr4:129714394-129732770|chr4:129738985-129740257
Splice length:
925
Other database IDs:
CIRCpedia: MMU_CIRCpedia_7418, circAtlas: mmu-Ptp4a2_0006
circBase: hsa_circ_0004893, circAtlas: hsa-PTP4A2_0007, CIRCpedia: HSA_CIRCpedia_31374
Human Ortholog IDs:
Mature spliced Sequence:
GTTTTTCGTTGGAATATACGTTGCACATTTATGGCGATTCTGAGCGTGAGGGCAGACTTCTGCCAGGCTCAGCACAGCCTTTCCGCTGACAAGTGAGCTTGGGGTTATACGTGCCATAATTAACATTGCCTTGACGACTCTGGACACCGAGACTGGCCTCAGAAGTAGTAGGCTTTTTTTTTTTTTAAATTGCAAGCGTATTCTTTTAATGACTCCAGTAAAATTAAGCATCAAGTAAACAAAAGTGGAGAAGAACCTACACTTTTAACTTGTCTCACTAGTGCCTAAATGTAGTAAAAAGGCTGCTTAAATTTTGTATGTAGTTGGATTTATTTTGGAAGCTGAAGGTATCCATCTGCAGACATTGAGGCTCAAGTTGAATTTGGATTCAAGTGGATTCTTAATACTTCTGCCTGTGCTGAAGAGAGAAGCTTCCTAAGGAACAAGCAAGTTGAATAGAGAAAATAGTGATCAATAATAGGCATTTTAGTGGTCTTTTTAATGTTTTCTGCTGCGGAACATTTCAAGATTTATTGATTTCCTCCTCCCCCCATTTTTTTCCCACCACACTCACACACGCACGCTCACACTTTTTATTTGCCATAATGAACCGTCCAGCCCCTGTGGAGATCTCTTATGAGAACATGCGTTTTCTGATAACTCACAACCCCACCAATGCGACTCTCAACAAGTTCACAGAGGAACTTAAGAAGTACGGAGTGACAACTTTGGTTCGAGTTTGTGATGCTACATATGATAAAGCTCCAGTTGAAAAAGAAGGAATCCACGTTCTAGATTGGCCGTTTGATGATGGAGCTCCACCCCCTAATCAGATAGTAGATGATTGGCTAAACCTGTTAAAAACCAAATTTCGTGAAGAGCCAGGCTGTTGTGTTGCAGTGCATTGTGTTGCAGGATTGGGAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AAGAGCCAGGCTGTTGTGTT
60.11
AGCTCACTTGTCAGCGGAAA
59.89
148
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AAGAGCCAGGCTGTTGTGTT
60.11
AAGCTCACTTGTCAGCGGAA
59.89
149
PCR template sequence:
CTAATCAGATAGTAGATGATTGGCTAAACCTGTTAAAAACCAAATTTCGTGAAGAGCCAGGCTGTTGTGTTGCAGTGCATTGTGTTGCAGGATTGGGAAGGTTTTTCGTTGGAATATACGTTGCACATTTATGGCGATTCTGAGCGTGAGGGCAGACTTCTGCCAGGCTCAGCACAGCCTTTCCGCTGACAAGTGAGCTT
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-222-3p(1), mmu-miR-203-3p(1), mmu-miR-183-5p(1), mmu-miR-325-3p(1), mmu-miR-574-5p(1)
siRNAs for circular RNA silencing
Junction sequence
CAGGATTGGGAAGGTTTTTCGTTGGA
siRNA sets
AAAAACCTTCCCAATCCTG, TCCAACGAAAAACCTTCCC, CGAAAAACCTTCCCAATCC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCPTP4A2_925_ORF_1
0.9246
0.056057252
0.327788753
363
ORF sequence:
ATGAACCGTCCAGCCCCTGTGGAGATCTCTTATGAGAACATGCGTTTTCTGATAACTCACAACCCCACCAATGCGACTCTCAACAAGTTCACAGAGGAACTTAAGAAGTACGGAGTGACAACTTTGGTTCGAGTTTGTGATGCTACATATGATAAAGCTCCAGTTGAAAAAGAAGGAATCCACGTTCTAGATTGGCCGTTTGATGATGGAGCTCCACCCCCTAATCAGATAGTAGATGATTGGCTAAACCTGTTAAAAACCAAATTTCGTGAAGAGCCAGGCTGTTGTGTTGCAGTGCATTGTGTTGCAGGATTGGGAAGGTTTTTCGTTGGAATATACGTTGCACATTTATGGCGATTCTGA
Peptide sequence:
MNRPAPVEISYENMRFLITHNPTNATLNKFTEELKKYGVTTLVRVCDATYDKAPVEKEGIHVLDWPFDDGAPPPNQIVDDWLNLLKTKFREEPGCCVAVHCVAGLGRFFVGIYVAHLWRF
IRESfinder result
IRESfinder score
0.768909125
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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