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mmu_circPhtf2_1183
Basic information of circular RNA
PanCircBase ID:
mmu_circPhtf2_1183
mm39_Chr. Position ID:
chr5|20977172|20999479|-
Gene name:
Phtf2
Transcript:
ENSMUST00000118174.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
7
Exon/intron indexes:
14,13,12,11,10,9,8
Exon/intron offsets:
0,1510,1828,3704,10098,17454,22120
Genomic length:
22307
Exon/intron sizes in nt:
8,71,32,27,31,29,21,91,00,000
Flanking exon/introns:
chr5:20970911-20977172|chr5:20999479-21006899
Splice length:
1183
Other database IDs:
CIRCpedia: MMU_CIRCpedia_214874, circAtlas: mmu-Phtf2_0023
circAtlas: hsa-SCAF8_0001
Human Ortholog IDs:
Mature spliced Sequence:
GTCAAAGAAGGCAAAGAATTCAATTGATAAGTCAACCGAGACTGACAATGGCTATGTGTCCCTCGATGGGAAGAGGACTGTAAAAAGCAGTGAGGATGGAGCACAGTACCATGAGCCTCAGTGTGAAACTGTTGGACCAGAAGACGCAGCCTGGGCCACACGAACGCCAAGGAGTGTTCCTGCCAAAGATACCCAAAGAAAGATAACAAATGTCTCTGATGAAGTATCCAGTGAGGAGGGTCCCGAAACAGGATACCCATTGCGTGGTCATGTGGACAGAACTTCTGAAAGCGGTCTTCGAAATAGAAAGCCACACCATTATAAAAAGCATTATGCAAATGAGGATGCCCCTAAATCGGGTACTAGTTGCAGCTCTCGCTGTTCAAGTTCCAGACAGGATTCTGAGAGCACAAGGCCAGAATCTGAAACCGAAGATGTATTATGGGAAGACTTGTTACACTGTGCGGAATGCCGCTCATCTTGTACCAGTGAGACAGATGTGGGAAACCCTCAGATAAATCCATGTGGGAAGAAAGAATATAGAGACGACCCTTTTCATCAGAGTCATTTGCCCTGGCTTCATAGTTCCCACCCAGGATTAGAAAAAATCAGTGCTATAGTGTGGGAAGGTAACGACTGTAAGAAAGCAGACATGTCTGTACTTGAAATCAGTGGGATGATAATGAACAGAGTGAACAACCATGTCCCAGGCATAGGATACCAGGTATTTGGAAATGCCATCTCTCTAATCCTGGGCTTGACCCCATTTGTTTTCCGACTGTCACAAGCAACAGACTTGGAGCAGCTCACAGCCCATTCTGCGTCAGAACTTTATGTGATTGCGTTTGGCTCTAACGAAGATGTCATGGTTCTTTCTATGGTCCTGATAAGTTTTGTGGTTCGAGTCTCTCTTGTGTGGATCTTCTTTTTTTTGCTGTGTGTAGCAGAAAGAACATATAAGCAACGATTACTCTTTGCAAAACTCTTTGGACACTTGACGTCTGCAAGGAGAGCTCGCAAATCTGAGGTTCCGCATTTCCGGTTGAAGAAAGTACAGAATATAAAAATGTGGCTGTCTCTGCGTTCCTATCTTAAGCGCCGAGGCCCTCAGCGATCTGTGGATGTCATTGTCTCATCGGCCTTCTTACTGACAATCTCAGTTGTGTTTATCTGCTGTGCACAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CTATCTTAAGCGCCGAGGCC
60.67
CCATCGAGGGACACATAGCC
59.97
166
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CCTATCTTAAGCGCCGAGGC
60.67
CCATCGAGGGACACATAGCC
59.97
167
PCR template sequence:
TTCCTATCTTAAGCGCCGAGGCCCTCAGCGATCTGTGGATGTCATTGTCTCATCGGCCTTCTTACTGACAATCTCAGTTGTGTTTATCTGCTGTGCACAGGTCAAAGAAGGCAAAGAATTCAATTGATAAGTCAACCGAGACTGACAATGGCTATGTGTCCCTCGATGGGAAGAGGACTGTAAAAAGCAGTGAGGATGGA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
6
Interacting miRNAs (#binding sites)
mmu-miR-155-5p(1), mmu-miR-135a-5p(1), mmu-miR-128-3p(1), mmu-miR-29b-2-5p(1), mmu-miR-369-3p(1), mmu-miR-188-3p(1)
siRNAs for circular RNA silencing
Junction sequence
CTGCTGTGCACAGGTCAAAGAAGGCA
siRNA sets
TCTTTGACCTGTGCACAGC, TTCTTTGACCTGTGCACAG, TGCCTTCTTTGACCTGTGC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCPHTF2_1183_ORF_1
0.7985
0.048864737
0.601808435
558
ORF sequence:
ATGTCTGTACTTGAAATCAGTGGGATGATAATGAACAGAGTGAACAACCATGTCCCAGGCATAGGATACCAGGTATTTGGAAATGCCATCTCTCTAATCCTGGGCTTGACCCCATTTGTTTTCCGACTGTCACAAGCAACAGACTTGGAGCAGCTCACAGCCCATTCTGCGTCAGAACTTTATGTGATTGCGTTTGGCTCTAACGAAGATGTCATGGTTCTTTCTATGGTCCTGATAAGTTTTGTGGTTCGAGTCTCTCTTGTGTGGATCTTCTTTTTTTTGCTGTGTGTAGCAGAAAGAACATATAAGCAACGATTACTCTTTGCAAAACTCTTTGGACACTTGACGTCTGCAAGGAGAGCTCGCAAATCTGAGGTTCCGCATTTCCGGTTGAAGAAAGTACAGAATATAAAAATGTGGCTGTCTCTGCGTTCCTATCTTAAGCGCCGAGGCCCTCAGCGATCTGTGGATGTCATTGTCTCATCGGCCTTCTTACTGACAATCTCAGTTGTGTTTATCTGCTGTGCACAGGTCAAAGAAGGCAAAGAATTCAATTGA
Peptide sequence:
MSVLEISGMIMNRVNNHVPGIGYQVFGNAISLILGLTPFVFRLSQATDLEQLTAHSASELYVIAFGSNEDVMVLSMVLISFVVRVSLVWIFFFLLCVAERTYKQRLLFAKLFGHLTSARRARKSEVPHFRLKKVQNIKMWLSLRSYLKRRGPQRSVDVIVSSAFLLTISVVFICCAQVKEGKEFN
IRESfinder result
IRESfinder score
0.547371054
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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