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mmu_circPdxdc1_558
Basic information of circular RNA
PanCircBase ID:
mmu_circPdxdc1_558
mm39_Chr. Position ID:
chr16|13693841|13705634|-
Gene name:
Pdxdc1
Transcript:
ENSMUST00000023361.12
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
6,5,4,3,2
Exon/intron offsets:
0,3448,5900,8588,11719
Genomic length:
11793
Exon/intron sizes in nt:
190,147,81,66,74
Flanking exon/introns:
chr16:13690387-13693841|chr16:13705634-13720778
Splice length:
558
Other database IDs:
circAtlas: hsa-SCAF8_0001
Human Ortholog IDs:
Mature spliced Sequence:
ATAGCAGACCCTACATTAGCTGAAATGGGAAAAAACTTGAAAGAGGCGATGCGGATGCTGGAGAAGAGCCCGAGAAGAACAGAGGAGGAAAATGGAAAGAAGCCAGTATCTGAGGATATTCCAGGGCCACTCCAAGGCAGTGGACAAGATATGGTGAGCATCCTCCAGTTAGTTCAAAATCTGATGCATGGAGATGAAGATGAGGAGCCCCAGAGCACCCGAATCCAAAATATTGGAGAGCAAGGTCACATGGCTTTGTTGGGTCATAGCCTCGGTGCCTATATTTCAACTCTGGATAAAGAGAAGCTGAGAAAGCTCACAACCAGGATACTTTCAGACACTACCTTATGGCTACGCCGGATTTTCAGGTACGAAAATGGATGTGCATATTTCCACGAGGAAGAGAGGGAAGGACTTGCTAAGATCTGTAGGCTTGCCATTCATTCTCGCTATGAAGACTTTGTTGTAGATGGATTCAACGTGTTATATAACAAAAAGCCTGTCATATATCTTAGTGCTGCCGCTAGACCTGGCCTGGGCCAATACCTTTGTAATCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TCTTAGTGCTGCCGCTAGAC
59.54
TTTCCTCCTCTGTTCTTCTCGG
59.44
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
ATCTTAGTGCTGCCGCTAGAC
59.93
TTCCTCCTCTGTTCTTCTCGG
58.83
140
PCR template sequence:
CTTTGTTGTAGATGGATTCAACGTGTTATATAACAAAAAGCCTGTCATATATCTTAGTGCTGCCGCTAGACCTGGCCTGGGCCAATACCTTTGTAATCAGATAGCAGACCCTACATTAGCTGAAATGGGAAAAAACTTGAAAGAGGCGATGCGGATGCTGGAGAAGAGCCCGAGAAGAACAGAGGAGGAAAATGGAAAGA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
6
Interacting miRNAs (#binding sites)
mmu-miR-326-3p(1), mmu-miR-410-3p(1), mmu-miR-207(1), mmu-miR-335-3p(1), mmu-miR-3065-5p(1), mmu-miR-338-3p(1)
siRNAs for circular RNA silencing
Junction sequence
CCTTTGTAATCAGATAGCAGACCCTA
siRNA sets
TGCTATCTGATTACAAAGG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCPDXDC1_558_ORF_1
0.9689
0.159663613
0.993729652
1092
ORF sequence:
ATGGGAAAAAACTTGAAAGAGGCGATGCGGATGCTGGAGAAGAGCCCGAGAAGAACAGAGGAGGAAAATGGAAAGAAGCCAGTATCTGAGGATATTCCAGGGCCACTCCAAGGCAGTGGACAAGATATGGTGAGCATCCTCCAGTTAGTTCAAAATCTGATGCATGGAGATGAAGATGAGGAGCCCCAGAGCACCCGAATCCAAAATATTGGAGAGCAAGGTCACATGGCTTTGTTGGGTCATAGCCTCGGTGCCTATATTTCAACTCTGGATAAAGAGAAGCTGAGAAAGCTCACAACCAGGATACTTTCAGACACTACCTTATGGCTACGCCGGATTTTCAGGTACGAAAATGGATGTGCATATTTCCACGAGGAAGAGAGGGAAGGACTTGCTAAGATCTGTAGGCTTGCCATTCATTCTCGCTATGAAGACTTTGTTGTAGATGGATTCAACGTGTTATATAACAAAAAGCCTGTCATATATCTTAGTGCTGCCGCTAGACCTGGCCTGGGCCAATACCTTTGTAATCAGATAGCAGACCCTACATTAGCTGAAATGGGAAAAAACTTGAAAGAGGCGATGCGGATGCTGGAGAAGAGCCCGAGAAGAACAGAGGAGGAAAATGGAAAGAAGCCAGTATCTGAGGATATTCCAGGGCCACTCCAAGGCAGTGGACAAGATATGGTGAGCATCCTCCAGTTAGTTCAAAATCTGATGCATGGAGATGAAGATGAGGAGCCCCAGAGCACCCGAATCCAAAATATTGGAGAGCAAGGTCACATGGCTTTGTTGGGTCATAGCCTCGGTGCCTATATTTCAACTCTGGATAAAGAGAAGCTGAGAAAGCTCACAACCAGGATACTTTCAGACACTACCTTATGGCTACGCCGGATTTTCAGGTACGAAAATGGATGTGCATATTTCCACGAGGAAGAGAGGGAAGGACTTGCTAAGATCTGTAGGCTTGCCATTCATTCTCGCTATGAAGACTTTGTTGTAGATGGATTCAACGTGTTATATAACAAAAAGCCTGTCATATATCTTAGTGCTGCCGCTAGACCTGGCCTGGGCCAATACCTTTGTAATCAG
Peptide sequence:
MGKNLKEAMRMLEKSPRRTEEENGKKPVSEDIPGPLQGSGQDMVSILQLVQNLMHGDEDEEPQSTRIQNIGEQGHMALLGHSLGAYISTLDKEKLRKLTTRILSDTTLWLRRIFRYENGCAYFHEEEREGLAKICRLAIHSRYEDFVVDGFNVLYNKKPVIYLSAAARPGLGQYLCNQIADPTLAEMGKNLKEAMRMLEKSPRRTEEENGKKPVSEDIPGPLQGSGQDMVSILQLVQNLMHGDEDEEPQSTRIQNIGEQGHMALLGHSLGAYISTLDKEKLRKLTTRILSDTTLWLRRIFRYENGCAYFHEEEREGLAKICRLAIHSRYEDFVVDGFNVLYNKKPVIYLSAAARPGLGQYLCNQ
IRESfinder result
IRESfinder score
0.417888397
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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