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mmu_circUbe2d2a_280
Basic information of circular RNA
PanCircBase ID:
mmu_circUbe2d2a_280
mm39_Chr. Position ID:
chr18|35926517|35933268|+
Gene name:
Ube2d2a
Transcript:
ENSMUST00000170693.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
2,3,4,5
Exon/intron offsets:
0,6376,6487,6645
Genomic length:
6751
Exon/intron sizes in nt:
64,32,78,106
Flanking exon/introns:
chr18:35905065-35926517|chr18:35933268-35934326
Splice length:
280
Other database IDs:
CIRCpedia: MMU_CIRCpedia_17879
circBase: hsa_circ_0005728, circAtlas: hsa-UBE2D2_0003, CIRCpedia: HSA_CIRCpedia_50480
Human Ortholog IDs:
Mature spliced Sequence:
GAATTGAATGACCTGGCTCGAGATCCCCCAGCACAGTGTTCAGCAGGTCCTGTTGGAGATGATATGTTTCATTGGCAGGCTACAATAATGGGGCCAAATGACAGCCCCTATCAGGGTGGAGTATTTTTCTTGACAATTCATTTCCCAACAGATTACCCCTTCAAACCGCCTAAGGTTGCATTTACAACAAGAATTTATCACCCAAATATTAACAGTAATGGCAGCATTTGTCTTGATATTCTACGGTCACAGTGGTCTCCAGCACTAACTATTTCAAAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CTACGGTCACAGTGGTCTCC
59.47
CATTTGGCCCCATTATTGTAGCC
60.24
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TTCTACGGTCACAGTGGTCTC
59.12
TTTGGCCCCATTATTGTAGCCT
60.02
140
PCR template sequence:
TTTACAACAAGAATTTATCACCCAAATATTAACAGTAATGGCAGCATTTGTCTTGATATTCTACGGTCACAGTGGTCTCCAGCACTAACTATTTCAAAAGGAATTGAATGACCTGGCTCGAGATCCCCCAGCACAGTGTTCAGCAGGTCCTGTTGGAGATGATATGTTTCATTGGCAGGCTACAATAATGGGGCCAAATG
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-200a-3p(1), mmu-miR-141-3p(1)
siRNAs for circular RNA silencing
Junction sequence
ACTATTTCAAAAGGAATTGAATGACC
siRNA sets
CAATTCCTTTTGAAATAGT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCUBE2D2A_280_ORF_1
0.6813
-0.159644612
0.047577909
228
ORF sequence:
ATGTTTCATTGGCAGGCTACAATAATGGGGCCAAATGACAGCCCCTATCAGGGTGGAGTATTTTTCTTGACAATTCATTTCCCAACAGATTACCCCTTCAAACCGCCTAAGGTTGCATTTACAACAAGAATTTATCACCCAAATATTAACAGTAATGGCAGCATTTGTCTTGATATTCTACGGTCACAGTGGTCTCCAGCACTAACTATTTCAAAAGGAATTGAATGA
Peptide sequence:
MFHWQATIMGPNDSPYQGGVFFLTIHFPTDYPFKPPKVAFTTRIYHPNINSNGSICLDILRSQWSPALTISKGIE
IRESfinder result
IRESfinder score
0.737255345
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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