top of page
mmu_circPtpn4_415_2
Basic information of circular RNA
PanCircBase ID:
mmu_circPtpn4_415_2
mm39_Chr. Position ID:
chr1|119653762|119693211|-
Gene name:
Ptpn4
Transcript:
ENSMUST00000064091.12
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
11,10,9,8,7
Exon/intron offsets:
0,15322,17319,38998,39396
Genomic length:
39449
Exon/intron sizes in nt:
64,89,88,121,53
Flanking exon/introns:
chr1:119649766-119653762|chr1:119693211-119693607
Splice length:
415
Other database IDs:
circAtlas: mmu-Ptpn4_0111
circBase: hsa_circ_0056240, circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_168891
Human Ortholog IDs:
Mature spliced Sequence:
ATTATCCTGTCCTTGTAACACTGCTGCCCTTTTAGCATCATTTGCTGTTCAGTCTGAACTTGGAGACTACAATCAGTCAGAAAACTTGGCAGGCTACCTCTCAGATTATTCTTTCATTCCTAATCAACCTCAAGATTTTGAGAAAGAAATTGCAAAGTTACATCAGCAGCACGTTGGCCTATCTCCTGCAGAAGCAGAATTTAATTACCTAAACGCGGCACGTACCTTAGAACTCTATGGAGTTGAATTTCACTATGCAAGGGATCAAAGTAACAATGAAATCCTGATTGGAGTGATGTCAGGAGGAATTCTGATTTATAAGAACAGGGTACGGATGAATACTTTTCTGTGGTTGAAGATTGTAAAAATTTCTTTTAAATGCAAACAGTTTTTTATTCAACTTAGAAAAGAGTTG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
ACGGATGAATACTTTTCTGTGGT
58.09
GCCTGCCAAGTTTTCTGACTG
60
179
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
ACGGATGAATACTTTTCTGTGGT
58.09
AGCCTGCCAAGTTTTCTGACT
60.13
180
PCR template sequence:
TTATAAGAACAGGGTACGGATGAATACTTTTCTGTGGTTGAAGATTGTAAAAATTTCTTTTAAATGCAAACAGTTTTTTATTCAACTTAGAAAAGAGTTGATTATCCTGTCCTTGTAACACTGCTGCCCTTTTAGCATCATTTGCTGTTCAGTCTGAACTTGGAGACTACAATCAGTCAGAAAACTTGGCAGGCTACCTC
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-let-7b-5p(1), mmu-miR-10a-5p(1), mmu-miR-1904(1)
siRNAs for circular RNA silencing
Junction sequence
TAGAAAAGAGTTGATTATCCTGTCCT
siRNA sets
AGGACAGGATAATCAACTC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCPTPN4_415_2_ORF_1
0.8628
-0.315838975
0.018826598
138
ORF sequence:
ATGTCAGGAGGAATTCTGATTTATAAGAACAGGGTACGGATGAATACTTTTCTGTGGTTGAAGATTGTAAAAATTTCTTTTAAATGCAAACAGTTTTTTATTCAACTTAGAAAAGAGTTGATTATCCTGTCCTTGTAA
Peptide sequence:
MSGGILIYKNRVRMNTFLWLKIVKISFKCKQFFIQLRKELIILSL
IRESfinder result
IRESfinder score
0.82097229
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
bottom of page