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mmu_circPtbp2_865
Basic information of circular RNA
PanCircBase ID:
mmu_circPtbp2_865
mm39_Chr. Position ID:
chr3|119533963|119555427|-
Gene name:
Ptbp2
Transcript:
ENSMUST00000029780.12
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
6
Exon/intron indexes:
8,7,6,5,4,3
Exon/intron offsets:
0,7277,7475,11549,12629,21388
Genomic length:
21464
Exon/intron sizes in nt:
196,111,165,144,173,76
Flanking exon/introns:
chr3:119519854-119533963|chr3:119555427-119575152
Splice length:
865
Other database IDs:
circBase: mmu_circ_0010399, CIRCpedia: MMU_CIRCpedia_4896, circAtlas: mmu-Ptbp2_0002
circBase: hsa_circ_0013250, circAtlas: hsa-PTBP2_0002, CIRCpedia: HSA_CIRCpedia_33279
Human Ortholog IDs:
Mature spliced Sequence:
AGAGGATCTGACGAGCTACTCTCAGGCAGTGTTCTCAGCAGCCCCAACTCTAATATGAGTGGCATGGTAGTTACAGCCAACGGTAACGATAGTAAGAAATTTAAAGGAGAAGATAAAATGGATGGGGCTCCCTCTCGTGTACTTCACATTCGAAAGTTACCTGGTGAAGTGACTGAAACAGAAGTTATTGCTTTAGGTTTACCTTTTGGTAAGGTGACTAACATCCTTATGCTGAAAGGAAAAAACCAGGCATTTTTGGAACTGGCAACAGAGGAAGCAGCTATTACTATGGTTAATTACTATTCTGCTGTGACACCTCATCTTCGTAACCAACCAATTTACATCCAGTACTCCAATCACAAAGAACTAAAGACAGATAATACATTAAACCAACGTGCGCAAGTAGTTCTTCAAGCTGTGACAGCGGTCCAGACAGCAAATACACCTCTTAGTGGCACCACAGTCAGTGAGAGTGCGGTGACTCCAGCCCAGAGTCCAGTACTTAGAATAATTATTGACAATATGTACTACCCTGTAACACTTGATGTCCTTCACCAAATATTTTCTAAGTTTGGTGCTGTATTGAAGATAATCACATTTACAAAAAACAACCAGTTTCAGGCTTTGCTCCAGTATGGTGATCCGGTAAACGCTCAACAAGCCAAGCTAGCCCTAGATGGTCAAAATATTTATAATGCTTGCTGTACCCTAAGGATTGATTTTTCCAAACTTGTGAATTTGAATGTAAAATACAACAATGATAAAAGTAGGGATTATACTCGACCTGATCTGCCATCTGGAGACGGCCAGCCTGCGTTAGACCCAGCCATTGCTGCAGCATTTGCCAAGGAGACATCCCTACTAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
ACTCGACCTGATCTGCCATC
59.25
TAGAGTTGGGGCTGCTGAGA
60.25
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GATCTGCCATCTGGAGACGG
59.97
TGGCTGTAACTACCATGCCA
59.01
158
PCR template sequence:
AGTAGGGATTATACTCGACCTGATCTGCCATCTGGAGACGGCCAGCCTGCGTTAGACCCAGCCATTGCTGCAGCATTTGCCAAGGAGACATCCCTACTAGAGAGGATCTGACGAGCTACTCTCAGGCAGTGTTCTCAGCAGCCCCAACTCTAATATGAGTGGCATGGTAGTTACAGCCAACGGTAACGATAGTAAGAAAT
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-200a-3p(1), mmu-miR-141-3p(1), mmu-miR-200b-3p(1), mmu-miR-29b-3p(1), mmu-miR-29c-3p(1), mmu-miR-324-3p(1), mmu-miR-539-5p(1)
siRNAs for circular RNA silencing
Junction sequence
ACATCCCTACTAGAGAGGATCTGACG
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCPTBP2_865_ORF_1
0.9827
0.068026418
0.940132264
822
ORF sequence:
ATGAGTGGCATGGTAGTTACAGCCAACGGTAACGATAGTAAGAAATTTAAAGGAGAAGATAAAATGGATGGGGCTCCCTCTCGTGTACTTCACATTCGAAAGTTACCTGGTGAAGTGACTGAAACAGAAGTTATTGCTTTAGGTTTACCTTTTGGTAAGGTGACTAACATCCTTATGCTGAAAGGAAAAAACCAGGCATTTTTGGAACTGGCAACAGAGGAAGCAGCTATTACTATGGTTAATTACTATTCTGCTGTGACACCTCATCTTCGTAACCAACCAATTTACATCCAGTACTCCAATCACAAAGAACTAAAGACAGATAATACATTAAACCAACGTGCGCAAGTAGTTCTTCAAGCTGTGACAGCGGTCCAGACAGCAAATACACCTCTTAGTGGCACCACAGTCAGTGAGAGTGCGGTGACTCCAGCCCAGAGTCCAGTACTTAGAATAATTATTGACAATATGTACTACCCTGTAACACTTGATGTCCTTCACCAAATATTTTCTAAGTTTGGTGCTGTATTGAAGATAATCACATTTACAAAAAACAACCAGTTTCAGGCTTTGCTCCAGTATGGTGATCCGGTAAACGCTCAACAAGCCAAGCTAGCCCTAGATGGTCAAAATATTTATAATGCTTGCTGTACCCTAAGGATTGATTTTTCCAAACTTGTGAATTTGAATGTAAAATACAACAATGATAAAAGTAGGGATTATACTCGACCTGATCTGCCATCTGGAGACGGCCAGCCTGCGTTAGACCCAGCCATTGCTGCAGCATTTGCCAAGGAGACATCCCTACTAGAGAGGATCTGA
Peptide sequence:
MSGMVVTANGNDSKKFKGEDKMDGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKGKNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYIQYSNHKELKTDNTLNQRAQVVLQAVTAVQTANTPLSGTTVSESAVTPAQSPVLRIIIDNMYYPVTLDVLHQIFSKFGAVLKIITFTKNNQFQALLQYGDPVNAQQAKLALDGQNIYNACCTLRIDFSKLVNLNVKYNNDKSRDYTRPDLPSGDGQPALDPAIAAAFAKETSLLERI
IRESfinder result
IRESfinder score
0.676639924
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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