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mmu_ciHnrnpk_1119
Basic information of circular RNA
PanCircBase ID:
mmu_ciHnrnpk_1119
mm39_Chr. Position ID:
chr13|58545850|58546969|-
Gene name:
Hnrnpk
Transcript:
ENSMUST00000116403.9
CircRNA type:
Circular intronic (ci)RNA
Exon/Intron count:
1
Exon/intron indexes:
6
Exon/intron offsets:
0
Genomic length:
1119
Exon/intron sizes in nt:
1119
Flanking exon/introns:
chr13:58545610-58546969
Splice length:
1119
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GTAAGTATTAAACTACTGAACAAGCAAGCACATTCATTGTATGTTTCTAGAATTTTAAAGGTTCACATCTTAGAAATCACTGACTAGCTACAAACCATTTGTAATAATTAATGGTTATGTAAATGACTTCTTTTTTTTTAAAACCCTGATTAAGGTGGAACATAATTAAATCTTTTCATATTTTAATAAAACCCTTCAAATTAATTCATTTCAAATAAGATTAAAACATCTTAATTAGGAATGGAGACAAAGTGTAAAAACCCTTAATTGTATAATTCCTCTTGTATGTGTAAGAGGGATTTAGTCATTTCTGAAAGCCATTGAATATGGCTGATAAAAACTTTATTTCCTTTTTTTTTCTTTTAAATCATCTGTTCCACAGTTTGCAACATGGAGCTCATGCTGACTGATTTCTAAATATGGGTAATGAATAGATTAATCTTGGCAATCAGAACTGTTTGCCTAGGATTTGAGTCTTCATAATTTATAGTGGGTTGACTCTTGTGATTAGACACATTAAATGTTGGCAGCACCAGAAGTGTGTGTGTATTTCTAGAACTGATTACACCAAAATTTATTTTTTTCCCTCATACTATCTACATTTCTTAATGTTTATCTTGGTAAAATTGAGGCAAATAACTTTGAGTACCTAACAGTATTTCATTTCTCTTGGTAACAGATCTTTGTGTTTCTCTTAATAAACTTTAGATTTCGTTGTAATTTTTATAAATCTGCTTATAAGATGTGTTTTATACCTTATGAAACCAAATCAGTCTTAATATTTGGGGGTTTGGTGTGGGAATTTTTGTTTTGTCTTTGAACCTCTTTCCTCTTAATCCAGATGTTCTGTATAATTATCTGGGTTATTTCCCCATTTTCCTCAATTTCAGTAAACTTTTGAGTCATGACAGGTTTTGTGTCTACCCTCACGAGCCAGCCTGCTACTGAAACATTAAAAAACAAAACAAAACCTAGAACCATCATTTAAGGTCCTTAAATGTTAAGAAGCCACGGTCAGGTATAGAGAAGTCCATTATTGTGTTAGTCTTCAGAACAACTTAAGCTTGTTTCATTGAGAGTATGAGTATAGTTTGTATTAAATTAAAATTTATTGCTTTT
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AGTCTTCAGAACAACTTAAGCTTGT
58.88
TGGTTTGTAGCTAGTCAGTGA
56.33
173
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GTCTTCAGAACAACTTAAGCTTGT
57.64
TGGTTTGTAGCTAGTCAGTGA
56.33
172
PCR template sequence:
TATAGAGAAGTCCATTATTGTGTTAGTCTTCAGAACAACTTAAGCTTGTTTCATTGAGAGTATGAGTATAGTTTGTATTAAATTAAAATTTATTGCTTTTGTAAGTATTAAACTACTGAACAAGCAAGCACATTCATTGTATGTTTCTAGAATTTTAAAGGTTCACATCTTAGAAATCACTGACTAGCTACAAACCATTT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
10
Interacting miRNAs (#binding sites)
mmu-miR-429-3p(1), mmu-miR-200b-3p(1), mmu-miR-200c-3p(1), mmu-miR-143-3p(1), mmu-miR-381-3p(1), mmu-miR-136-5p(1), mmu-miR-494-3p(1), mmu-miR-29b-1-5p(1), mmu-miR-382-5p(1), mmu-miR-29b-2-5p(1)
siRNAs for circular RNA silencing
Junction sequence
ATTTATTGCTTTTGTAAGTATTAAAC
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIHNRNPK_1119_ORF_1
0.7189
-0.450283924
0.007463294
126
ORF sequence:
ATGAGTATAGTTTGTATTAAATTAAAATTTATTGCTTTTGTAAGTATTAAACTACTGAACAAGCAAGCACATTCATTGTATGTTTCTAGAATTTTAAAGGTTCACATCTTAGAAATCACTGACTAG
Peptide sequence:
MSIVCIKLKFIAFVSIKLLNKQAHSLYVSRILKVHILEITD
IRESfinder result
IRESfinder score
0.953360141
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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