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mmu_circDennd1a_417
Basic information of circular RNA
PanCircBase ID:
mmu_circDennd1a_417
mm39_Chr. Position ID:
chr2|37893385|37938806|-
Gene name:
Dennd1a
Transcript:
ENSMUST00000102787.10
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
10,9,8,7,6
Exon/intron offsets:
0,17982,35778,39965,45351
Genomic length:
45421
Exon/intron sizes in nt:
101,111,54,81,70
Flanking exon/introns:
chr2:37873117-37893385|chr2:37938806-38016540
Splice length:
417
Other database IDs:
CIRCpedia: MMU_CIRCpedia_18740, circAtlas: mmu-Dennd1a_0016
circBase: hsa_circ_0088462, circAtlas: hsa-DENND1A_0019, CIRCpedia: HSA_CIRCpedia_62694
Human Ortholog IDs:
Mature spliced Sequence:
CTACCTCCCCTGGTTCGAGGTATTCTATAAGCTCCTTAACATCTTGGCAGATTACACGACGAAACGACAGGAAAGTCAGTGGAATGAACTTCTTGAAACTCTGCACAGACTTCCCATCCCTGATCCTGGAGTGTCTGTTCACCTCAGTGTGCATTCTTACTTCACTGTGCCTGATAGCAGAGAGCTTCCCAGCATACCTGAGAATAGAAATCTGACAGAATATTTTGTGGCTGTGGATGTGAACAACATGTTGCATCTGTACGCCAGCATGCTGTATGAACGCCGGATCCTCATCATCTGCAGCAAGCTCAGTACATTGACGGCCTGCATCCACGGCTCAGCTGCCATGCTCTACCCTATGTACTGGCAGCATGTGTACATCCCTGTGCTGCCCCCACATCTGCTGGACTACTGCTG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AGCTGCCATGCTCTACCCTA
60.4
TTCCTGTCGTTTCGTCGTGT
59.9
151
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CTCAGCTGCCATGCTCTACC
60.53
TTCCTGTCGTTTCGTCGTGT
59.9
154
PCR template sequence:
TGACGGCCTGCATCCACGGCTCAGCTGCCATGCTCTACCCTATGTACTGGCAGCATGTGTACATCCCTGTGCTGCCCCCACATCTGCTGGACTACTGCTGCTACCTCCCCTGGTTCGAGGTATTCTATAAGCTCCTTAACATCTTGGCAGATTACACGACGAAACGACAGGAAAGTCAGTGGAATGAACTTCTTGAAACT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
3
Interacting miRNAs (#binding sites)
mmu-miR-128-3p(1), mmu-miR-199b-3p(1), mmu-miR-199a-3p(1)
siRNAs for circular RNA silencing
Junction sequence
TGGACTACTGCTGCTACCTCCCCTGG
siRNA sets
GAGGTAGCAGCAGTAGTCC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCDENND1A_417_ORF_1
1.0666
0.331665948
0.908750381
585
ORF sequence:
ATGTTGCATCTGTACGCCAGCATGCTGTATGAACGCCGGATCCTCATCATCTGCAGCAAGCTCAGTACATTGACGGCCTGCATCCACGGCTCAGCTGCCATGCTCTACCCTATGTACTGGCAGCATGTGTACATCCCTGTGCTGCCCCCACATCTGCTGGACTACTGCTGCTACCTCCCCTGGTTCGAGGTATTCTATAAGCTCCTTAACATCTTGGCAGATTACACGACGAAACGACAGGAAAGTCAGTGGAATGAACTTCTTGAAACTCTGCACAGACTTCCCATCCCTGATCCTGGAGTGTCTGTTCACCTCAGTGTGCATTCTTACTTCACTGTGCCTGATAGCAGAGAGCTTCCCAGCATACCTGAGAATAGAAATCTGACAGAATATTTTGTGGCTGTGGATGTGAACAACATGTTGCATCTGTACGCCAGCATGCTGTATGAACGCCGGATCCTCATCATCTGCAGCAAGCTCAGTACATTGACGGCCTGCATCCACGGCTCAGCTGCCATGCTCTACCCTATGTACTGGCAGCATGTGTACATCCCTGTGCTGCCCCCACATCTGCTGGACTACTGC
Peptide sequence:
MLHLYASMLYERRILIICSKLSTLTACIHGSAAMLYPMYWQHVYIPVLPPHLLDYCCYLPWFEVFYKLLNILADYTTKRQESQWNELLETLHRLPIPDPGVSVHLSVHSYFTVPDSRELPSIPENRNLTEYFVAVDVNNMLHLYASMLYERRILIICSKLSTLTACIHGSAAMLYPMYWQHVYIPVLPPHLLDYC
IRESfinder result
IRESfinder score
0.676134947
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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