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mmu_circPatl1_707
Basic information of circular RNA
PanCircBase ID:
mmu_circPatl1_707
mm39_Chr. Position ID:
chr19|11913042|11920338|+
Gene name:
Patl1
Transcript:
ENSMUST00000061618.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
14,15,16,17,18
Exon/intron offsets:
0,1541,4005,6950,7146
Genomic length:
7296
Exon/intron sizes in nt:
1,49,16,01,56,92,150
Flanking exon/introns:
chr19:11911103-11913042|chr19:11920338-11920694
Splice length:
707
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
ACCTATAGTTTACTCCTTGATGTGGAGGATTATGAAAGGCGCTATCTCCTAAGTCTAGAAGAAGAGCGGCCTGCCCTGATGGATGAAAGAAAGCACAAAATATGTAGCATGTATGACAACCTGAGGGGCAAATTGCCTGGACAAGAGAGGCCAAGTGATGACCACTTTGTACAGATCATGTGTATCCGAAAAGGGAAGAGAATGGTTGCCCGCATTCTCCCTTTCCTCTCCACAGAGCAAGCAGCTGACATTCTCATGGCAACTGCCAGGAACCTCCCTTTCCTTATCAAGAAGGATGCCCAAGATGAGGTGCTGCCATGCTTACTGAGTCCCTTCTCTCTCCTCCTCTATCATCTTCCTTCAGTGACTGTCACCAGCCTTCTGCAACAGCTAATGAACCTACCTCAGAGTGCAAGTGCACCAGCGCCCTCCAACTCTCACCTCACTGCTGTGCTCCAGAACAAGTTTGGCTTGTCACTGCTCCTAATCCTACTAAGCCGTGGAGAAGACCTACAGAGTTCAGATCCTGCTATAGAATCAACGCAAAATAACCAGTGGACAGAGGTGATGTTCATGGCAACCCGAGAACTTCTACGGATCCCCCAAGCTGCCCTGGCCAAACCAATCTCTATCCCTACAAATCTAGTGTCCCTTTTTTCTCGCTATGTTGACCGGCAGAAACTGAACTTGCTGGAAACAAAACTGCA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TTCTCGCTATGTTGACCGGC
60.46
TCTTTCATCCATCAGGGCAGG
59.79
141
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TTCTCGCTATGTTGACCGGC
60.46
CTTTCATCCATCAGGGCAGG
58.31
140
PCR template sequence:
CTGCCCTGGCCAAACCAATCTCTATCCCTACAAATCTAGTGTCCCTTTTTTCTCGCTATGTTGACCGGCAGAAACTGAACTTGCTGGAAACAAAACTGCAACCTATAGTTTACTCCTTGATGTGGAGGATTATGAAAGGCGCTATCTCCTAAGTCTAGAAGAAGAGCGGCCTGCCCTGATGGATGAAAGAAAGCACAAAA
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-221-3p(1), mmu-miR-196a-5p(1), mmu-miR-138-5p(1), mmu-miR-185-5p(1), mmu-miR-218-5p(1), mmu-miR-207(1)
siRNAs for circular RNA silencing
Junction sequence
AAACAAAACTGCAACCTATAGTTTAC
siRNA sets
TATAGGTTGCAGTTTTGTT, CTATAGGTTGCAGTTTTGT, TAAACTATAGGTTGCAGTT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCPATL1_707_ORF_1
1.0025
0.142221089
0.889331598
681
ORF sequence:
ATGGATGAAAGAAAGCACAAAATATGTAGCATGTATGACAACCTGAGGGGCAAATTGCCTGGACAAGAGAGGCCAAGTGATGACCACTTTGTACAGATCATGTGTATCCGAAAAGGGAAGAGAATGGTTGCCCGCATTCTCCCTTTCCTCTCCACAGAGCAAGCAGCTGACATTCTCATGGCAACTGCCAGGAACCTCCCTTTCCTTATCAAGAAGGATGCCCAAGATGAGGTGCTGCCATGCTTACTGAGTCCCTTCTCTCTCCTCCTCTATCATCTTCCTTCAGTGACTGTCACCAGCCTTCTGCAACAGCTAATGAACCTACCTCAGAGTGCAAGTGCACCAGCGCCCTCCAACTCTCACCTCACTGCTGTGCTCCAGAACAAGTTTGGCTTGTCACTGCTCCTAATCCTACTAAGCCGTGGAGAAGACCTACAGAGTTCAGATCCTGCTATAGAATCAACGCAAAATAACCAGTGGACAGAGGTGATGTTCATGGCAACCCGAGAACTTCTACGGATCCCCCAAGCTGCCCTGGCCAAACCAATCTCTATCCCTACAAATCTAGTGTCCCTTTTTTCTCGCTATGTTGACCGGCAGAAACTGAACTTGCTGGAAACAAAACTGCAACCTATAGTTTACTCCTTGATGTGGAGGATTATGAAAGGCGCTATCTCCTAA
Peptide sequence:
MDERKHKICSMYDNLRGKLPGQERPSDDHFVQIMCIRKGKRMVARILPFLSTEQAADILMATARNLPFLIKKDAQDEVLPCLLSPFSLLLYHLPSVTVTSLLQQLMNLPQSASAPAPSNSHLTAVLQNKFGLSLLLILLSRGEDLQSSDPAIESTQNNQWTEVMFMATRELLRIPQAALAKPISIPTNLVSLFSRYVDRQKLNLLETKLQPIVYSLMWRIMKGAIS
IRESfinder result
IRESfinder score
0.496042958
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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