top of page
mmu_circPicalm_356
Basic information of circular RNA
PanCircBase ID:
mmu_circPicalm_356
mm39_Chr. Position ID:
chr7|89838357|89840961|+
Gene name:
Picalm
Transcript:
ENSMUST00000207225.2
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
13,14,15,16
Exon/intron offsets:
0,2006,2209,2504
Genomic length:
2604
Exon/intron sizes in nt:
10,81,17,31,100
Flanking exon/introns:
chr7:89826811-89838357|chr7:89840961-89844862
Splice length:
356
Other database IDs:
circAtlas: mmu-Picalm_0017
circBase: hsa_circ_0003695, circAtlas: hsa-PICALM_0016, CIRCpedia: HSA_CIRCpedia_5869
Human Ortholog IDs:
Mature spliced Sequence:
GATTCAGTCCTTCTCCAGTTGCACAGCCACATTCTTCAGCTGGCCTTAATGTTGACTTTGAATCTGTGTTTGGAAATAAATCTACGAATGTTGCTGTAGATTCTGGTGGTGGACTTCTCAAACCAACAGTGGCCTCCCAGAACCAGAGTCTTCCTGTTGCCAAACTTCCGCCTAACAAATTAGTGTCTGACGACTTGGATTCATCTTTAGCCAACCTTGTGGGCAATCTTGGCATTGGAAATGGAACCACTAAGAATGATGTAAGTTGGAGTCAACCAGGTGAAAAGAAGTTAACTGGAGGATCTAACTGGCAACCAAAGGTTGCACCAACAACTGCCTGGAGCGCTGCAACAATG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GTTGGAGTCAACCAGGTGAA
57.66
AGTCAACATTAAGGCCAGCTGA
59.96
149
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TGGAGTCAACCAGGTGAAAAGA
59.49
AGTCAACATTAAGGCCAGCTGA
59.96
147
PCR template sequence:
TGATGTAAGTTGGAGTCAACCAGGTGAAAAGAAGTTAACTGGAGGATCTAACTGGCAACCAAAGGTTGCACCAACAACTGCCTGGAGCGCTGCAACAATGGATTCAGTCCTTCTCCAGTTGCACAGCCACATTCTTCAGCTGGCCTTAATGTTGACTTTGAATCTGTGTTTGGAAATAAATCTACGAATGTTGCTGTAGA
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-9-5p(1), mmu-miR-140-5p(1), mmu-miR-7b-5p(1), mmu-miR-7a-5p(1), mmu-miR-182-5p(1), mmu-miR-574-5p(1), mmu-miR-376a-3p(1)
siRNAs for circular RNA silencing
Junction sequence
CGCTGCAACAATGGATTCAGTCCTTC
siRNA sets
GAAGGACTGAATCCATTGT, ACTGAATCCATTGTTGCAG, TGAATCCATTGTTGCAGCG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCPICALM_356_ORF_1
1.0389
-0.153940524
0.038379847
102
ORF sequence:
ATGGATTCAGTCCTTCTCCAGTTGCACAGCCACATTCTTCAGCTGGCCTTAATGTTGACTTTGAATCTGTGTTTGGAAATAAATCTACGAATGTTGCTGTAG
Peptide sequence:
MDSVLLQLHSHILQLALMLTLNLCLEINLRMLL
IRESfinder result
IRESfinder score
0.682074969
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
bottom of page