top of page
mmu_circSrgap2_356
Basic information of circular RNA
PanCircBase ID:
mmu_circSrgap2_356
mm39_Chr. Position ID:
chr1|131339537|131364605|-
Gene name:
Srgap2
Transcript:
ENSMUST00000097588.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
2
Exon/intron indexes:
4,3
Exon/intron offsets:
0,24875
Genomic length:
25068
Exon/intron sizes in nt:
1,63,193
Flanking exon/introns:
chr1:131291802-131339537|chr1:131364605-131452675
Splice length:
356
Other database IDs:
CIRCpedia: MMU_CIRCpedia_7700, circAtlas: mmu-Srgap2_0008
CIRCpedia: HSA_CIRCpedia_344031
Human Ortholog IDs:
Mature spliced Sequence:
AGATTAGGGCTCAGCTCACAGAGCAGATGAAATGCCTAGATCAGCAATGTGAGCTCCGGGTGCAGCTGTTGCAGGACCTGCAGGACTTCTTCCGCAAGAAGGCTGAGATTGAAATGGACTACTCTCGAAACCTGGAGAAGCTAGCCGAGCGCTTTCTAGCCAAGACACGAAGCACCAAGGACCAGCAATTTAAGAAGGACCAGAATGTTCTTTCTCCAGTCAACTGCTGGAACCTCCTCTTAAACCAAGTGAAGCGGGAGAGCAGGGATCATACCACCCTGAGTGACATCTACCTGAATAATATAATTCCTCGATTTGTTCAAGTCAGCGAGGACTCAGGAAGACTCTTTAAAAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GAGCAGGGATCATACCACCC
59.6
CCGGAGCTCACATTGCTGAT
60.46
156
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GAGCAGGGATCATACCACCC
59.6
CGGAGCTCACATTGCTGATC
59.06
155
PCR template sequence:
GGAGAGCAGGGATCATACCACCCTGAGTGACATCTACCTGAATAATATAATTCCTCGATTTGTTCAAGTCAGCGAGGACTCAGGAAGACTCTTTAAAAAGAGATTAGGGCTCAGCTCACAGAGCAGATGAAATGCCTAGATCAGCAATGTGAGCTCCGGGTGCAGCTGTTGCAGGACCTGCAGGACTTCTTCCGCAAGAA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
5
Interacting miRNAs (#binding sites)
mmu-miR-23b-3p(1), mmu-miR-216a-5p(1), mmu-miR-23a-3p(1), mmu-miR-207(1), mmu-miR-1199-5p(1)
siRNAs for circular RNA silencing
Junction sequence
ACTCTTTAAAAAGAGATTAGGGCTCA
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSRGAP2_356_ORF_1
1.0011
0.318560751
0.622988988
360
ORF sequence:
ATGAAATGCCTAGATCAGCAATGTGAGCTCCGGGTGCAGCTGTTGCAGGACCTGCAGGACTTCTTCCGCAAGAAGGCTGAGATTGAAATGGACTACTCTCGAAACCTGGAGAAGCTAGCCGAGCGCTTTCTAGCCAAGACACGAAGCACCAAGGACCAGCAATTTAAGAAGGACCAGAATGTTCTTTCTCCAGTCAACTGCTGGAACCTCCTCTTAAACCAAGTGAAGCGGGAGAGCAGGGATCATACCACCCTGAGTGACATCTACCTGAATAATATAATTCCTCGATTTGTTCAAGTCAGCGAGGACTCAGGAAGACTCTTTAAAAAGAGATTAGGGCTCAGCTCACAGAGCAGATGA
Peptide sequence:
MKCLDQQCELRVQLLQDLQDFFRKKAEIEMDYSRNLEKLAERFLAKTRSTKDQQFKKDQNVLSPVNCWNLLLNQVKRESRDHTTLSDIYLNNIIPRFVQVSEDSGRLFKKRLGLSSQSR
IRESfinder result
IRESfinder score
0.56817104
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
bottom of page