top of page
mmu_circSh3pxd2a_503
Basic information of circular RNA
PanCircBase ID:
mmu_circSh3pxd2a_503
mm39_Chr. Position ID:
chr19|47260446|47266869|-
Gene name:
Sh3pxd2a
Transcript:
ENSMUST00000081619.10
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
13,12,11
Exon/intron offsets:
0,1176,6305
Genomic length:
6423
Exon/intron sizes in nt:
5,03,35,118
Flanking exon/introns:
chr19:47258396-47260446|chr19:47266869-47271459
Splice length:
503
Other database IDs:
circBase: hsa_circ_0019868, circAtlas: hsa-SH3PXD2A_0003, CIRCpedia: HSA_CIRCpedia_313
Human Ortholog IDs:
Mature spliced Sequence:
AAGAGAAGTATGTCACTGTGCAGCCCTACACCAGCCAGAGCAAAGACGAGATCGGCTTCGAGAAGGGTGTCACCGTGGAGGTGATTCGAAAGAACCTGGAAGGCTGGTGGTACATCAGGTACCTCGGCAAAGAGGGTTGGGCACCAGCGTCCTACCTGAAGAAGGCCAAGGATGACCTGCCGACCCGGAAGAAGAACCTGGCGGGTCCGGTGGAGATCATAGGGAACATTATGGAGATCAGCAACCTTCTCAACAAGAAGGCATCTGGGGATAAGGAGGCTCCGGCTGAAGGCGAGGGATCCGAGGCCCCCATCACCAAGAAAGAGATCAGCTTACCGATCCTCTGCAACGCCTCCAATGGCAGCGCCTTGGCCATTCCCGAGAGGACCACATCCAAGCTAGCCCAGGGCTCCCCAGCTGTGGCCAGGATCGCCCCTCAGAGGGCCCAGATCAGCTCCCCAAATCTGAGGACAAGACCTCCCCCGCGCAGAGAATCCAGCCTG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CCCAGATCAGCTCCCCAAAT
59.45
TCTTTCGAATCACCTCCACGG
60.07
152
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GCTCCCCAAATCTGAGGACA
59.38
TCTTTCGAATCACCTCCACGG
60.07
143
PCR template sequence:
CCAGGGCTCCCCAGCTGTGGCCAGGATCGCCCCTCAGAGGGCCCAGATCAGCTCCCCAAATCTGAGGACAAGACCTCCCCCGCGCAGAGAATCCAGCCTGAAGAGAAGTATGTCACTGTGCAGCCCTACACCAGCCAGAGCAAAGACGAGATCGGCTTCGAGAAGGGTGTCACCGTGGAGGTGATTCGAAAGAACCTGGA
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-298-5p(1), mmu-miR-138-5p(1), mmu-miR-128-3p(1), mmu-miR-433-5p(1), mmu-miR-362-5p(1)
siRNAs for circular RNA silencing
Junction sequence
AGAATCCAGCCTGAAGAGAAGTATGT
siRNA sets
ATACTTCTCTTCAGGCTGG, TACTTCTCTTCAGGCTGGA, ACATACTTCTCTTCAGGCT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSH3PXD2A_503_ORF_1
0.9447
0.278093642
0.550674694
357
ORF sequence:
ATGGAGATCAGCAACCTTCTCAACAAGAAGGCATCTGGGGATAAGGAGGCTCCGGCTGAAGGCGAGGGATCCGAGGCCCCCATCACCAAGAAAGAGATCAGCTTACCGATCCTCTGCAACGCCTCCAATGGCAGCGCCTTGGCCATTCCCGAGAGGACCACATCCAAGCTAGCCCAGGGCTCCCCAGCTGTGGCCAGGATCGCCCCTCAGAGGGCCCAGATCAGCTCCCCAAATCTGAGGACAAGACCTCCCCCGCGCAGAGAATCCAGCCTGAAGAGAAGTATGTCACTGTGCAGCCCTACACCAGCCAGAGCAAAGACGAGATCGGCTTCGAGAAGGGTGTCACCGTGGAGGTGA
Peptide sequence:
MEISNLLNKKASGDKEAPAEGEGSEAPITKKEISLPILCNASNGSALAIPERTTSKLAQGSPAVARIAPQRAQISSPNLRTRPPPRRESSLKRSMSLCSPTPARAKTRSASRRVSPWR
IRESfinder result
IRESfinder score
0.179400418
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
bottom of page