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mmu_circNcor2_513
Basic information of circular RNA
PanCircBase ID:
mmu_circNcor2_513
mm39_Chr. Position ID:
chr5|125161944|125168784|-
Gene name:
Ncor2
Transcript:
ENSMUST00000111402.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
12,11,10,9
Exon/intron offsets:
0,1960,2913,6773
Genomic length:
6840
Exon/intron sizes in nt:
179,94,173,67
Flanking exon/introns:
chr5:125158248-125161944|chr5:125168784-125175010
Splice length:
513
Other database IDs:
circAtlas: mmu-Ncor2_0007
circBase: hsa_circ_0029311, circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_7565
Human Ortholog IDs:
Mature spliced Sequence:
AAACCAGGCGATGCGGAAGAAGCTGATCTTGTACTTTAAGCGGAGGAACCACGCGCGCAAGCAGTGGGAACAGCGCTTCTGCCAGCGCTATGACCAGCTCATGGAGGCGTGGGAGAAGAAGGTAGAGCGCATAGAGAACAATCCGCGAAGGAGGGCCAAGGAGAGCAAGGTGAGGGAGTACTACGAGAAACAGTTCCCGGAGATCCGCAAGCAGCGGGAGCTGCAGGAGCGCATGCAGAGCAGGGTGGGCCAGCGTGGCAGTGGGCTCTCCATGTCGGCTGCCCGCAGTGAGCATGAGGTTTCTGAGATCATTGATGGCTTGTCTGAGCAGGAGAATCTGGAGAAGCAGATGCGCCAGCTGGCCGTGATCCCGCCCATGTTGTACGACGCGGACCAGCAGAGGATCAAGTTCATCAACATGAATGGACTCATGGATGACCCCATGAAGGTCTACAAGGACCGTCAGGTTACCAACATGTGGAGCGAGCAGGAGAGGGACACCTTCCGTGAGAA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TGGACTCATGGATGACCCCA
60.25
GCGTGGTTCCTCCGCTTAAA
60.95
144
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TGGACTCATGGATGACCCCA
60.25
CGTGGTTCCTCCGCTTAAAG
58.92
143
PCR template sequence:
TCAACATGAATGGACTCATGGATGACCCCATGAAGGTCTACAAGGACCGTCAGGTTACCAACATGTGGAGCGAGCAGGAGAGGGACACCTTCCGTGAGAAAAACCAGGCGATGCGGAAGAAGCTGATCTTGTACTTTAAGCGGAGGAACCACGCGCGCAAGCAGTGGGAACAGCGCTTCTGCCAGCGCTATGACCAGCTC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
5
Interacting miRNAs (#binding sites)
mmu-miR-205-5p(1), mmu-miR-328-3p(1), mmu-miR-136-5p(1), mmu-miR-666-5p(1), mmu-miR-207(1)
siRNAs for circular RNA silencing
Junction sequence
CCTTCCGTGAGAAAAACCAGGCGATG
siRNA sets
ATCGCCTGGTTTTTCTCAC, TGGTTTTTCTCACGGAAGG, TCGCCTGGTTTTTCTCACG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCNCOR2_513_ORF_1
1.2579
0.663134754
0.999176211
1014
ORF sequence:
ATGCGGAAGAAGCTGATCTTGTACTTTAAGCGGAGGAACCACGCGCGCAAGCAGTGGGAACAGCGCTTCTGCCAGCGCTATGACCAGCTCATGGAGGCGTGGGAGAAGAAGGTAGAGCGCATAGAGAACAATCCGCGAAGGAGGGCCAAGGAGAGCAAGGTGAGGGAGTACTACGAGAAACAGTTCCCGGAGATCCGCAAGCAGCGGGAGCTGCAGGAGCGCATGCAGAGCAGGGTGGGCCAGCGTGGCAGTGGGCTCTCCATGTCGGCTGCCCGCAGTGAGCATGAGGTTTCTGAGATCATTGATGGCTTGTCTGAGCAGGAGAATCTGGAGAAGCAGATGCGCCAGCTGGCCGTGATCCCGCCCATGTTGTACGACGCGGACCAGCAGAGGATCAAGTTCATCAACATGAATGGACTCATGGATGACCCCATGAAGGTCTACAAGGACCGTCAGGTTACCAACATGTGGAGCGAGCAGGAGAGGGACACCTTCCGTGAGAAAAACCAGGCGATGCGGAAGAAGCTGATCTTGTACTTTAAGCGGAGGAACCACGCGCGCAAGCAGTGGGAACAGCGCTTCTGCCAGCGCTATGACCAGCTCATGGAGGCGTGGGAGAAGAAGGTAGAGCGCATAGAGAACAATCCGCGAAGGAGGGCCAAGGAGAGCAAGGTGAGGGAGTACTACGAGAAACAGTTCCCGGAGATCCGCAAGCAGCGGGAGCTGCAGGAGCGCATGCAGAGCAGGGTGGGCCAGCGTGGCAGTGGGCTCTCCATGTCGGCTGCCCGCAGTGAGCATGAGGTTTCTGAGATCATTGATGGCTTGTCTGAGCAGGAGAATCTGGAGAAGCAGATGCGCCAGCTGGCCGTGATCCCGCCCATGTTGTACGACGCGGACCAGCAGAGGATCAAGTTCATCAACATGAATGGACTCATGGATGACCCCATGAAGGTCTACAAGGACCGTCAGGTTACCAACATGTGGAGCGAGCAGGAGAGGGACACCTTCCGTGAG
Peptide sequence:
MRKKLILYFKRRNHARKQWEQRFCQRYDQLMEAWEKKVERIENNPRRRAKESKVREYYEKQFPEIRKQRELQERMQSRVGQRGSGLSMSAARSEHEVSEIIDGLSEQENLEKQMRQLAVIPPMLYDADQQRIKFINMNGLMDDPMKVYKDRQVTNMWSEQERDTFREKNQAMRKKLILYFKRRNHARKQWEQRFCQRYDQLMEAWEKKVERIENNPRRRAKESKVREYYEKQFPEIRKQRELQERMQSRVGQRGSGLSMSAARSEHEVSEIIDGLSEQENLEKQMRQLAVIPPMLYDADQQRIKFINMNGLMDDPMKVYKDRQVTNMWSEQERDTFRE
IRESfinder result
IRESfinder score
0.120434774
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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