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mmu_circCd2ap_376
Basic information of circular RNA
PanCircBase ID:
mmu_circCd2ap_376
mm39_Chr. Position ID:
chr17|43145055|43156370|-
Gene name:
Cd2ap
Transcript:
ENSMUST00000024709.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
5,4,3
Exon/intron offsets:
0,4537,11161
Genomic length:
11315
Exon/intron sizes in nt:
121,101,154
Flanking exon/introns:
chr17:43140996-43145055|chr17:43156370-43163258
Splice length:
376
Other database IDs:
circAtlas: mmu-Cd2ap_0025
circBase: hsa_circ_0142336, circAtlas: hsa-CD2AP_0007, CIRCpedia: HSA_CIRCpedia_55212
Human Ortholog IDs:
Mature spliced Sequence:
GAAATTAAGCGAGAGACAGAACCCAAGGATGACAATTTGCCCATCAAACGGGAAAGGCAAGGAAATGTAGCAAGTCTTGTACAGCGAATCAGCACTTATGGACTTCCAGCTGGAGGAATTCAGCCACATCCACAAACCAAAGCTATTAAGAAGAAGACAAAAAAGCGTCAGTGTAAAGTTCTTTTTGACTACTCTCCACAAAATGAGGACGAACTGGAATTGATCGTGGGGGATGTCATTGACGTCATTGAAGAGGTAGAAGAAGGCTGGTGGAGTGGAACCCTGAACAATAAGTTGGGACTGTTTCCCTCAAACTTTGTGAAAGAATTAGAGTCCACAGAGGATGGTGAAACTCACAACGCTCAGGAGGAATCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
ACCCTGAACAATAAGTTGGGACT
59.6
TCCTTGCCTTTCCCGTTTGA
59.82
160
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GGAACCCTGAACAATAAGTTGGG
59.49
TCCTTGCCTTTCCCGTTTGA
59.82
163
PCR template sequence:
GGAACCCTGAACAATAAGTTGGGACTGTTTCCCTCAAACTTTGTGAAAGAATTAGAGTCCACAGAGGATGGTGAAACTCACAACGCTCAGGAGGAATCAGGAAATTAAGCGAGAGACAGAACCCAAGGATGACAATTTGCCCATCAAACGGGAAAGGCAAGGAAATGTAGCAAGTCTTGTACAGCGAATCAGCACTTATG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
4
Interacting miRNAs (#binding sites)
mmu-miR-9-5p(1), mmu-miR-221-3p(1), mmu-miR-132-3p(1), mmu-miR-212-3p(1)
siRNAs for circular RNA silencing
Junction sequence
CAGGAGGAATCAGGAAATTAAGCGAG
siRNA sets
TTAATTTCCTGATTCCTCC, CTTAATTTCCTGATTCCTC, AATTTCCTGATTCCTCCTG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCCD2AP_376_ORF_1
1.0177
0.2669602
0.660966885
408
ORF sequence:
ATGGTGAAACTCACAACGCTCAGGAGGAATCAGGAAATTAAGCGAGAGACAGAACCCAAGGATGACAATTTGCCCATCAAACGGGAAAGGCAAGGAAATGTAGCAAGTCTTGTACAGCGAATCAGCACTTATGGACTTCCAGCTGGAGGAATTCAGCCACATCCACAAACCAAAGCTATTAAGAAGAAGACAAAAAAGCGTCAGTGTAAAGTTCTTTTTGACTACTCTCCACAAAATGAGGACGAACTGGAATTGATCGTGGGGGATGTCATTGACGTCATTGAAGAGGTAGAAGAAGGCTGGTGGAGTGGAACCCTGAACAATAAGTTGGGACTGTTTCCCTCAAACTTTGTGAAAGAATTAGAGTCCACAGAGGATGGTGAAACTCACAACGCTCAGGAGGAATCA
Peptide sequence:
MVKLTTLRRNQEIKRETEPKDDNLPIKRERQGNVASLVQRISTYGLPAGGIQPHPQTKAIKKKTKKRQCKVLFDYSPQNEDELELIVGDVIDVIEEVEEGWWSGTLNNKLGLFPSNFVKELESTEDGETHNAQEES
IRESfinder result
IRESfinder score
0.455825006
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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