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mmu_circKatnal1_628
Basic information of circular RNA
PanCircBase ID:
mmu_circKatnal1_628
mm39_Chr. Position ID:
chr5|148830958|148858222|-
Gene name:
Katnal1
Transcript:
ENSMUST00000047257.15
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
5,4,3,2
Exon/intron offsets:
0,10418,24447,27088
Genomic length:
27264
Exon/intron sizes in nt:
1,28,16,31,61,176
Flanking exon/introns:
chr5:148830598-148830958|chr5:148858222-148865335
Splice length:
628
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GTGTCTGAAAGAAGATGAATTTGGCGGAGATTTGTGAGAATGCGAAGAAAGGCCGGGAATATGCGCTTCTGGGAAATTATGACTCGTCAATGGTGTATTACCAGGGAGTGATACAGCAGATCCAGAGACACTGCCAGTCACTGAGAGACCCGGCCACCAAAGCCAAGTGGCAGCAGGTACGGCAGGAACTCTTGGAAGAATATGAACAGGTTAAGAGTATCGTCAGCACTTTAGAAAGCTTTAAGATGGACAAGCCCCCTGACTTCCCCGTGTCTTGCCGAGATGAACCGTTTAGAGACCCTGCAGTATGGCCACCCCCTGTCCCTGCGGAACACAGAGCACCCCCTCAAATCAGGCGTCCAAATCGCGAAGTGAGGCCTCTGCGGAAAGACGTGGGGGCAGGAGCCCGGGGACTCGTGGGCCGAGCACACCAGATATCGAAGAGTGACAAACCTGCAAGTCGGGACAAGGACTATAGAGCAAGAGGGAGAGATGACAAGGCAAGGAAAAATGTGCAAGATGGTGCAAGTGACAGCGAGATTCCCAAGTTTGATGGCGCCGGGTATGATAAGGATCTGGTGGAAGCCCTGGAGAGGGACATTGTGTCCAGGAACCCTAGCATTCACTG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
ATGGCGCCGGGTATGATAAG
60.04
TCCCAGAAGCGCATATTCCC
59.89
150
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GATGGCGCCGGGTATGATAA
60.04
TCCCAGAAGCGCATATTCCC
59.89
151
PCR template sequence:
GTGACAGCGAGATTCCCAAGTTTGATGGCGCCGGGTATGATAAGGATCTGGTGGAAGCCCTGGAGAGGGACATTGTGTCCAGGAACCCTAGCATTCACTGGTGTCTGAAAGAAGATGAATTTGGCGGAGATTTGTGAGAATGCGAAGAAAGGCCGGGAATATGCGCTTCTGGGAAATTATGACTCGTCAATGGTGTATTA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
11
Interacting miRNAs (#binding sites)
mmu-miR-20b-5p(1), mmu-miR-106a-5p(1), mmu-miR-93-5p(1), mmu-miR-20a-5p(1), mmu-miR-17-5p(1), mmu-miR-34c-5p(1), mmu-miR-34a-5p(1), mmu-miR-31-5p(1), mmu-miR-106b-5p(1), mmu-miR-34b-5p(1), mmu-miR-342-5p(1)
siRNAs for circular RNA silencing
Junction sequence
CTAGCATTCACTGGTGTCTGAAAGAA
siRNA sets
TCAGACACCAGTGAATGCT, TTCTTTCAGACACCAGTGA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCKATNAL1_628_ORF_1
0.8639
0.288281039
0.901192198
651
ORF sequence:
ATGAATTTGGCGGAGATTTGTGAGAATGCGAAGAAAGGCCGGGAATATGCGCTTCTGGGAAATTATGACTCGTCAATGGTGTATTACCAGGGAGTGATACAGCAGATCCAGAGACACTGCCAGTCACTGAGAGACCCGGCCACCAAAGCCAAGTGGCAGCAGGTACGGCAGGAACTCTTGGAAGAATATGAACAGGTTAAGAGTATCGTCAGCACTTTAGAAAGCTTTAAGATGGACAAGCCCCCTGACTTCCCCGTGTCTTGCCGAGATGAACCGTTTAGAGACCCTGCAGTATGGCCACCCCCTGTCCCTGCGGAACACAGAGCACCCCCTCAAATCAGGCGTCCAAATCGCGAAGTGAGGCCTCTGCGGAAAGACGTGGGGGCAGGAGCCCGGGGACTCGTGGGCCGAGCACACCAGATATCGAAGAGTGACAAACCTGCAAGTCGGGACAAGGACTATAGAGCAAGAGGGAGAGATGACAAGGCAAGGAAAAATGTGCAAGATGGTGCAAGTGACAGCGAGATTCCCAAGTTTGATGGCGCCGGGTATGATAAGGATCTGGTGGAAGCCCTGGAGAGGGACATTGTGTCCAGGAACCCTAGCATTCACTGGTGTCTGAAAGAAGATGAATTTGGCGGAGATTTGTGA
Peptide sequence:
MNLAEICENAKKGREYALLGNYDSSMVYYQGVIQQIQRHCQSLRDPATKAKWQQVRQELLEEYEQVKSIVSTLESFKMDKPPDFPVSCRDEPFRDPAVWPPPVPAEHRAPPQIRRPNREVRPLRKDVGAGARGLVGRAHQISKSDKPASRDKDYRARGRDDKARKNVQDGASDSEIPKFDGAGYDKDLVEALERDIVSRNPSIHWCLKEDEFGGDL
IRESfinder result
IRESfinder score
0.288884154
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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