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mmu_circDennd1a_691
Basic information of circular RNA
PanCircBase ID:
mmu_circDennd1a_691
mm39_Chr. Position ID:
chr2|37826630|37938806|-
Gene name:
Dennd1a
Transcript:
ENSMUST00000102787.10
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
8
Exon/intron indexes:
13,12,11,10,9,8,7,6
Exon/intron offsets:
0,25022,46441,66755,84737,102533,106720,112106
Genomic length:
112176
Exon/intron sizes in nt:
126,102,46,101,111,54,81,70
Flanking exon/introns:
chr2:37748484-37826630|chr2:37938806-38016540
Splice length:
691
Other database IDs:
circAtlas: mmu-Dennd1a_0027
circBase: hsa_circ_0088447, circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_62677
Human Ortholog IDs:
Mature spliced Sequence:
CTACCTCCCCTGGTTCGAGGTATTCTATAAGCTCCTTAACATCTTGGCAGATTACACGACGAAACGACAGGAAAGTCAGTGGAATGAACTTCTTGAAACTCTGCACAGACTTCCCATCCCTGATCCTGGAGTGTCTGTTCACCTCAGTGTGCATTCTTACTTCACTGTGCCTGATAGCAGAGAGCTTCCCAGCATACCTGAGAATAGAAATCTGACAGAATATTTTGTGGCTGTGGATGTGAACAACATGTTGCATCTGTACGCCAGCATGCTGTATGAACGCCGGATCCTCATCATCTGCAGCAAGCTCAGTACATTGACGGCCTGCATCCACGGCTCAGCTGCCATGCTCTACCCTATGTACTGGCAGCATGTGTACATCCCTGTGCTGCCCCCACATCTGCTGGACTACTGCTGTGCTCCCATGCCCTACCTCATAGGAATCCATTTAAGTTTAATGGAGAAGGTCAGGAACATGGCCCTCGATGATGTTGTGATCTTGAACGTGGACACCAACACCCTGGAAACCCCTTTTGATGACCTCCAGAGCCTCCCAAATGATGTGATCTCCTCCCTGAAGAACAGGCTGAAGAAGGTCTCTACAACCACAGGTGATGGGGTGGCCAGAGCCTTCCTCAAGGCCCAGGCTGCTTTCTTTGGCAGCTACCGGAATGCACTGAAAATTGAGCCA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TCTACAACCACAGGTGATGGG
59.37
TTCCTGTCGTTTCGTCGTGT
59.9
166
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GGTCTCTACAACCACAGGTGA
59.03
TTCCTGTCGTTTCGTCGTGT
59.9
170
PCR template sequence:
GAAGGTCTCTACAACCACAGGTGATGGGGTGGCCAGAGCCTTCCTCAAGGCCCAGGCTGCTTTCTTTGGCAGCTACCGGAATGCACTGAAAATTGAGCCACTACCTCCCCTGGTTCGAGGTATTCTATAAGCTCCTTAACATCTTGGCAGATTACACGACGAAACGACAGGAAAGTCAGTGGAATGAACTTCTTGAAACT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
11
Interacting miRNAs (#binding sites)
mmu-let-7a-5p(1), mmu-let-7e-5p(1), mmu-miR-152-3p(1), mmu-miR-148b-3p(1), mmu-miR-148a-3p(1), mmu-miR-128-3p(1), mmu-let-7d-5p(1), mmu-miR-136-5p(1), mmu-miR-22-3p(1), mmu-miR-199b-3p(1), mmu-miR-199a-3p(1)
siRNAs for circular RNA silencing
Junction sequence
GAAAATTGAGCCACTACCTCCCCTGG
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCDENND1A_691_ORF_1
1.2015
0.372236881
0.870050771
474
ORF sequence:
ATGTTGCATCTGTACGCCAGCATGCTGTATGAACGCCGGATCCTCATCATCTGCAGCAAGCTCAGTACATTGACGGCCTGCATCCACGGCTCAGCTGCCATGCTCTACCCTATGTACTGGCAGCATGTGTACATCCCTGTGCTGCCCCCACATCTGCTGGACTACTGCTGTGCTCCCATGCCCTACCTCATAGGAATCCATTTAAGTTTAATGGAGAAGGTCAGGAACATGGCCCTCGATGATGTTGTGATCTTGAACGTGGACACCAACACCCTGGAAACCCCTTTTGATGACCTCCAGAGCCTCCCAAATGATGTGATCTCCTCCCTGAAGAACAGGCTGAAGAAGGTCTCTACAACCACAGGTGATGGGGTGGCCAGAGCCTTCCTCAAGGCCCAGGCTGCTTTCTTTGGCAGCTACCGGAATGCACTGAAAATTGAGCCACTACCTCCCCTGGTTCGAGGTATTCTATAA
Peptide sequence:
MLHLYASMLYERRILIICSKLSTLTACIHGSAAMLYPMYWQHVYIPVLPPHLLDYCCAPMPYLIGIHLSLMEKVRNMALDDVVILNVDTNTLETPFDDLQSLPNDVISSLKNRLKKVSTTTGDGVARAFLKAQAAFFGSYRNALKIEPLPPLVRGIL
IRESfinder result
IRESfinder score
0.579143503
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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