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mmu_circPdap1_474
Basic information of circular RNA
PanCircBase ID:
mmu_circPdap1_474
mm39_Chr. Position ID:
chr5|145068174|145073803|-
Gene name:
Pdap1
Transcript:
ENSMUST00000031627.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
5,4,3,2
Exon/intron offsets:
0,1494,3700,5537
Genomic length:
5629
Exon/intron sizes in nt:
152,122,108,92
Flanking exon/introns:
chr5:145067185-145068174|chr5:145073803-145076776
Splice length:
474
Other database IDs:
circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_360432
Human Ortholog IDs:
Mature spliced Sequence:
GTAGAAAGGGAGGCCACAAAGGCCGAGTGAGGCAGTATACGAGCCCGGAGGAGATCGATGCCCAGCTACAGGCTGAGAAGCAGAAGGCCAACGAAGAAGATGAACAAGAAGAAGGTGGAGATGGGGCTTCAGGTGACCCAAAAAAGGAAAAGAAATCTCTAGACTCAGATGAAAGTGAAGATGAAGATGATGACTACCAGCAAAAGCGAAAAGGCGTGGAGGGGCTCATTGACATTGAGAACCCCAACCGCGTGGCACAGACAACTAAGAAGGTCACGCAACTGGATCTGGACGGGCCAAAGGAGCTTTCAAGGAGAGAAAGAGAAGAAATAGAGAAGCAAAAAGCAAAAGAACGCTACATGAAGATGCATTTGGCTGGGAAGACAGAGCAGGCCAAGGCTGATCTCGCCCGGCTGGCAATCATCCGGAAACAGCGGGAGGAGGCAGCAAGAAAGAAAGAGGAAGAAAGGAAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GGCAATCATCCGGAAACAGC
59.9
TTCGTTGGCCTTCTGCTTCT
59.89
154
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GGCAATCATCCGGAAACAGC
59.9
TCTTCGTTGGCCTTCTGCTT
59.89
156
PCR template sequence:
GCTGGGAAGACAGAGCAGGCCAAGGCTGATCTCGCCCGGCTGGCAATCATCCGGAAACAGCGGGAGGAGGCAGCAAGAAAGAAAGAGGAAGAAAGGAAAGGTAGAAAGGGAGGCCACAAAGGCCGAGTGAGGCAGTATACGAGCCCGGAGGAGATCGATGCCCAGCTACAGGCTGAGAAGCAGAAGGCCAACGAAGAAGA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
1
Interacting miRNAs (#binding sites)
mmu-miR-1904(1)
siRNAs for circular RNA silencing
Junction sequence
GAAGAAAGGAAAGGTAGAAAGGGAGG
siRNA sets
TTTCTACCTTTCCTTTCTT, CCTCCCTTTCTACCTTTCC, CTCCCTTTCTACCTTTCCT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCPDAP1_474_ORF_1
1.1363
0.533606728
0.963480902
588
ORF sequence:
ATGAAGATGCATTTGGCTGGGAAGACAGAGCAGGCCAAGGCTGATCTCGCCCGGCTGGCAATCATCCGGAAACAGCGGGAGGAGGCAGCAAGAAAGAAAGAGGAAGAAAGGAAAGGTAGAAAGGGAGGCCACAAAGGCCGAGTGAGGCAGTATACGAGCCCGGAGGAGATCGATGCCCAGCTACAGGCTGAGAAGCAGAAGGCCAACGAAGAAGATGAACAAGAAGAAGGTGGAGATGGGGCTTCAGGTGACCCAAAAAAGGAAAAGAAATCTCTAGACTCAGATGAAAGTGAAGATGAAGATGATGACTACCAGCAAAAGCGAAAAGGCGTGGAGGGGCTCATTGACATTGAGAACCCCAACCGCGTGGCACAGACAACTAAGAAGGTCACGCAACTGGATCTGGACGGGCCAAAGGAGCTTTCAAGGAGAGAAAGAGAAGAAATAGAGAAGCAAAAAGCAAAAGAACGCTACATGAAGATGCATTTGGCTGGGAAGACAGAGCAGGCCAAGGCTGATCTCGCCCGGCTGGCAATCATCCGGAAACAGCGGGAGGAGGCAGCAAGAAAGAAAGAGGAAGAAAGGAAA
Peptide sequence:
MKMHLAGKTEQAKADLARLAIIRKQREEAARKKEEERKGRKGGHKGRVRQYTSPEEIDAQLQAEKQKANEEDEQEEGGDGASGDPKKEKKSLDSDESEDEDDDYQQKRKGVEGLIDIENPNRVAQTTKKVTQLDLDGPKELSRREREEIEKQKAKERYMKMHLAGKTEQAKADLARLAIIRKQREEAARKKEEERK
IRESfinder result
IRESfinder score
0.113098292
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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