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mmu_circNpm1_383
Basic information of circular RNA
PanCircBase ID:
mmu_circNpm1_383
mm39_Chr. Position ID:
chr11|33109933|33111225|-
Gene name:
Npm1
Transcript:
ENSMUST00000075641.10
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
6,5,4,3
Exon/intron offsets:
0,400,894,1172
Genomic length:
1292
Exon/intron sizes in nt:
6,21,07,94,120
Flanking exon/introns:
chr11:33107048-33109933|chr11:33111225-33111547
Splice length:
383
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GTCAGTTTAGGAGCAGGGGCAAAAGATGAGTTACACATCGTAGAGGCAGAAGCAATGAACTATGAAGGCAGTCCAATTAAAGTAACACTGGCAACTTTGAAAATGTCTGTACAACCAACAGTTTCCCTAGGGGGCTTTGAAATTACACCACCTGTGGTCTTACGGTTGAAGTGTGGTTCAGGGCCTGTGCACATTAGTGGACAGCATCTAGTAGCTGTAGAGGAAGATGCAGAGTCTGAAGATGAAGATGAGGAGGACGTAAAACTCTTAGGCATGTCTGGAAAGCGATCTGCTCCTGGAGGTGGTAACAAGGTTCCACAGAAAAAAGTAAAACTTGATGAAGATGATGAGGACGATGATGAGGACGATGAGGATGATGAGGA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TCTGCTCCTGGAGGTGGTAA
59.88
GCTTCTGCCTCTACGATGTGT
60.13
148
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TCTGCTCCTGGAGGTGGTAA
59.88
TGCTTCTGCCTCTACGATGTG
60.13
149
PCR template sequence:
AGCGATCTGCTCCTGGAGGTGGTAACAAGGTTCCACAGAAAAAAGTAAAACTTGATGAAGATGATGAGGACGATGATGAGGACGATGAGGATGATGAGGAGTCAGTTTAGGAGCAGGGGCAAAAGATGAGTTACACATCGTAGAGGCAGAAGCAATGAACTATGAAGGCAGTCCAATTAAAGTAACACTGGCAACTTTGA
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-125a-5p(1)
siRNAs for circular RNA silencing
Junction sequence
AGGATGATGAGGAGTCAGTTTAGGAG
siRNA sets
ACTGACTCCTCATCATCCT, AACTGACTCCTCATCATCC, AAACTGACTCCTCATCATC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCNPM1_383_ORF_1
1.291
0.282550135
0.677292469
339
ORF sequence:
ATGAACTATGAAGGCAGTCCAATTAAAGTAACACTGGCAACTTTGAAAATGTCTGTACAACCAACAGTTTCCCTAGGGGGCTTTGAAATTACACCACCTGTGGTCTTACGGTTGAAGTGTGGTTCAGGGCCTGTGCACATTAGTGGACAGCATCTAGTAGCTGTAGAGGAAGATGCAGAGTCTGAAGATGAAGATGAGGAGGACGTAAAACTCTTAGGCATGTCTGGAAAGCGATCTGCTCCTGGAGGTGGTAACAAGGTTCCACAGAAAAAAGTAAAACTTGATGAAGATGATGAGGACGATGATGAGGACGATGAGGATGATGAGGAGTCAGTTTAG
Peptide sequence:
MNYEGSPIKVTLATLKMSVQPTVSLGGFEITPPVVLRLKCGSGPVHISGQHLVAVEEDAESEDEDEEDVKLLGMSGKRSAPGGGNKVPQKKVKLDEDDEDDDEDDEDDEESV
IRESfinder result
IRESfinder score
0.284839932
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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