top of page
mmu_circPatl1_282
Basic information of circular RNA
PanCircBase ID:
mmu_circPatl1_282
mm39_Chr. Position ID:
chr19|11908896|11911103|+
Gene name:
Patl1
Transcript:
ENSMUST00000061618.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
11,12,13
Exon/intron offsets:
0,605,2147
Genomic length:
2207
Exon/intron sizes in nt:
124,98,60
Flanking exon/introns:
chr19:11907419-11908896|chr19:11911103-11913042
Splice length:
282
Other database IDs:
circAtlas: mmu-Patl1_0007
Human Ortholog IDs:
Mature spliced Sequence:
AATTACTTTGAAAAACTGGAGAAATTGTCAGCTGCTGAGGAAATACAAGGTGATGGCCCTAAGAAGGAGCGTACCAAGCTCATCACCCCTCAGGTGGCCAAACTGGAGCATGCTTATCAGCCTGTGCAGTTTGAGGGCTCGTTGGGGAAGCTTACTGTCTCTAGTGTGAATAATCCTCGGAAGATGATAGATGCTGTTGTGACATCTCGAAGTGAGGATGATGAAACAAAAGAAAAACAAGTTCGGGATAAGAGAAGAAAAACCCTTGTTATAATTGAGAAA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GCTGTTGTGACATCTCGAAGTG
59.84
GTACGCTCCTTCTTAGGGCC
59.9
164
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GCTGTTGTGACATCTCGAAGTG
59.84
GGTACGCTCCTTCTTAGGGC
59.9
165
PCR template sequence:
GATGATAGATGCTGTTGTGACATCTCGAAGTGAGGATGATGAAACAAAAGAAAAACAAGTTCGGGATAAGAGAAGAAAAACCCTTGTTATAATTGAGAAAAATTACTTTGAAAAACTGGAGAAATTGTCAGCTGCTGAGGAAATACAAGGTGATGGCCCTAAGAAGGAGCGTACCAAGCTCATCACCCCTCAGGTGGCCA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
NA
Interacting miRNAs (#binding sites)
NA
siRNAs for circular RNA silencing
Junction sequence
TATAATTGAGAAAAATTACTTTGAAA
siRNA sets
TTTCAAAGTAATTTTTCTC, TTCAAAGTAATTTTTCTCA, AAAGTAATTTTTCTCAATT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCPATL1_282_ORF_1
1.1985
0.267313793
0.693140567
381
ORF sequence:
ATGATAGATGCTGTTGTGACATCTCGAAGTGAGGATGATGAAACAAAAGAAAAACAAGTTCGGGATAAGAGAAGAAAAACCCTTGTTATAATTGAGAAAAATTACTTTGAAAAACTGGAGAAATTGTCAGCTGCTGAGGAAATACAAGGTGATGGCCCTAAGAAGGAGCGTACCAAGCTCATCACCCCTCAGGTGGCCAAACTGGAGCATGCTTATCAGCCTGTGCAGTTTGAGGGCTCGTTGGGGAAGCTTACTGTCTCTAGTGTGAATAATCCTCGGAAGATGATAGATGCTGTTGTGACATCTCGAAGTGAGGATGATGAAACAAAAGAAAAACAAGTTCGGGATAAGAGAAGAAAAACCCTTGTTATAATTGAGAAA
Peptide sequence:
MIDAVVTSRSEDDETKEKQVRDKRRKTLVIIEKNYFEKLEKLSAAEEIQGDGPKKERTKLITPQVAKLEHAYQPVQFEGSLGKLTVSSVNNPRKMIDAVVTSRSEDDETKEKQVRDKRRKTLVIIEK
IRESfinder result
IRESfinder score
0.459403224
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
bottom of page