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mmu_circKdm1a_282
Basic information of circular RNA
PanCircBase ID:
mmu_circKdm1a_282
mm39_Chr. Position ID:
chr4|136297768|136300476|-
Gene name:
Kdm1a
Transcript:
ENSMUST00000116273.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
7,6,5
Exon/intron offsets:
0,1760,2615
Genomic length:
2708
Exon/intron sizes in nt:
82,107,93
Flanking exon/introns:
chr4:136295978-136297768|chr4:136300476-136301335
Splice length:
282
Other database IDs:
circBase: hsa_circ_0010815, circAtlas: hsa-KDM1A_0015, CIRCpedia: HSA_CIRCpedia_30641
Human Ortholog IDs:
Mature spliced Sequence:
GCGATACTGTGCTTGTCCACCGAGTTCACAGTTACTTAGAGCGCCATGGTCTTATCAACTTCGGCATCTACAAGAGGATAAAACCCTTACCAATTAAAAAGACAGGAAAGGTGATTATTATAGGTTCAGGTGTTTCTGGCTTGGCAGCAGCTCGACAGCTACAGAGTTTTGGGATGGATGTCACACTTCTGGAAGCCAGGGATCGAGTAGGTGGACGAGTTGCTACATTTCGAAAAGGAAACTATGTAGCTGATCTTGGCGCCATGGTTGTAACAGGTCTTG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AAGCCAGGGATCGAGTAGGT
60.03
AAGACCATGGCGCTCTAAGT
59.09
143
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TGGAAGCCAGGGATCGAGTA
60.03
AAGACCATGGCGCTCTAAGT
59.09
146
PCR template sequence:
ACACTTCTGGAAGCCAGGGATCGAGTAGGTGGACGAGTTGCTACATTTCGAAAAGGAAACTATGTAGCTGATCTTGGCGCCATGGTTGTAACAGGTCTTGGCGATACTGTGCTTGTCCACCGAGTTCACAGTTACTTAGAGCGCCATGGTCTTATCAACTTCGGCATCTACAAGAGGATAAAACCCTTACCAATTAAAAA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
2
Interacting miRNAs (#binding sites)
mmu-miR-221-3p(1), mmu-miR-362-5p(1)
siRNAs for circular RNA silencing
Junction sequence
GTAACAGGTCTTGGCGATACTGTGCT
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCKDM1A_282_ORF_1
1.0641
0.144289278
0.531671275
390
ORF sequence:
ATGGATGTCACACTTCTGGAAGCCAGGGATCGAGTAGGTGGACGAGTTGCTACATTTCGAAAAGGAAACTATGTAGCTGATCTTGGCGCCATGGTTGTAACAGGTCTTGGCGATACTGTGCTTGTCCACCGAGTTCACAGTTACTTAGAGCGCCATGGTCTTATCAACTTCGGCATCTACAAGAGGATAAAACCCTTACCAATTAAAAAGACAGGAAAGGTGATTATTATAGGTTCAGGTGTTTCTGGCTTGGCAGCAGCTCGACAGCTACAGAGTTTTGGGATGGATGTCACACTTCTGGAAGCCAGGGATCGAGTAGGTGGACGAGTTGCTACATTTCGAAAAGGAAACTATGTAGCTGATCTTGGCGCCATGGTTGTAACAGGTCTT
Peptide sequence:
MDVTLLEARDRVGGRVATFRKGNYVADLGAMVVTGLGDTVLVHRVHSYLERHGLINFGIYKRIKPLPIKKTGKVIIIGSGVSGLAAARQLQSFGMDVTLLEARDRVGGRVATFRKGNYVADLGAMVVTGL
IRESfinder result
IRESfinder score
0.425555769
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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