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mmu_circHerpud2_562
Basic information of circular RNA
PanCircBase ID:
mmu_circHerpud2_562
mm39_Chr. Position ID:
chr9|25020735|25025239|-
Gene name:
Herpud2
Transcript:
ENSMUST00000008573.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
7,6,5
Exon/intron offsets:
0,971,4381
Genomic length:
4504
Exon/intron sizes in nt:
11,53,24,123
Flanking exon/introns:
chr9:25020301-25020735|chr9:25025239-25036167
Splice length:
562
Other database IDs:
CIRCpedia: HSA_CIRCpedia_351989
Human Ortholog IDs:
Mature spliced Sequence:
AAATGTGGATCACCAGTTTCCTGGGCAAGGTGTGCCCCCTGCGTTCCCAGTGTACCCTGCGCTCAGCCCACTGCAGATGCTGTGGTGGCAGCAGATGTACGCTCATCAGTATTATATGCAATATCAAGCTGCAGTTTCAGCTCAGGCCACATCAAGTGCCGGCTCAGCCCAGCGTGCTGCATCATCACCTCTAAATTTGGCACATGTTCCTGGAGAAGAGCCTCCACCAGCTCCCAACCTAGTGGCCCAAGAAAATGGGCCCATGAATGAGAATGTTCAAATGAATGCACAGGGCGGCCCAGTGCTGAATGAAGAAGACTTGAACCGCGACTGGCTGGACTGGGTGTACACGTTCTCCCGAGCTGCCGTCCTCCTCAGCATCGTATACTTCTATTCTTCTTTCAGTCGGTTTATCATGGTAATGGGAGCCATGCTGCTGGTTTATTTACACCAAGCTGGATGGTTTCCGTTCAGGCAAGAAGGCGGTCAGCAACAAGCTCCCAACAATGTGGACGCTAACAATGACGGGCATAATGCAAACAATCTAGAACTTGAAGAAATG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TGGACGCTAACAATGACGGG
60.39
TACATCTGCTGCCACCACAG
60.04
152
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
ACGCTAACAATGACGGGCAT
60.39
TACATCTGCTGCCACCACAG
60.04
149
PCR template sequence:
GTTTCCGTTCAGGCAAGAAGGCGGTCAGCAACAAGCTCCCAACAATGTGGACGCTAACAATGACGGGCATAATGCAAACAATCTAGAACTTGAAGAAATGAAATGTGGATCACCAGTTTCCTGGGCAAGGTGTGCCCCCTGCGTTCCCAGTGTACCCTGCGCTCAGCCCACTGCAGATGCTGTGGTGGCAGCAGATGTAC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
7
Interacting miRNAs (#binding sites)
mmu-miR-103-3p(1), mmu-miR-135a-5p(1), mmu-miR-191-5p(1), mmu-miR-107-3p(1), mmu-miR-5101(1), mmu-miR-369-3p(1), mmu-miR-3061-5p(1)
siRNAs for circular RNA silencing
Junction sequence
ACTTGAAGAAATGAAATGTGGATCAC
siRNA sets
ACATTTCATTTCTTCAAGT, TGATCCACATTTCATTTCT, ATCCACATTTCATTTCTTC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCHERPUD2_562_ORF_1
0.6953
0.11067629
0.873432056
756
ORF sequence:
ATGCTGTGGTGGCAGCAGATGTACGCTCATCAGTATTATATGCAATATCAAGCTGCAGTTTCAGCTCAGGCCACATCAAGTGCCGGCTCAGCCCAGCGTGCTGCATCATCACCTCTAAATTTGGCACATGTTCCTGGAGAAGAGCCTCCACCAGCTCCCAACCTAGTGGCCCAAGAAAATGGGCCCATGAATGAGAATGTTCAAATGAATGCACAGGGCGGCCCAGTGCTGAATGAAGAAGACTTGAACCGCGACTGGCTGGACTGGGTGTACACGTTCTCCCGAGCTGCCGTCCTCCTCAGCATCGTATACTTCTATTCTTCTTTCAGTCGGTTTATCATGGTAATGGGAGCCATGCTGCTGGTTTATTTACACCAAGCTGGATGGTTTCCGTTCAGGCAAGAAGGCGGTCAGCAACAAGCTCCCAACAATGTGGACGCTAACAATGACGGGCATAATGCAAACAATCTAGAACTTGAAGAAATGAAATGTGGATCACCAGTTTCCTGGGCAAGGTGTGCCCCCTGCGTTCCCAGTGTACCCTGCGCTCAGCCCACTGCAGATGCTGTGGTGGCAGCAGATGTACGCTCATCAGTATTATATGCAATATCAAGCTGCAGTTTCAGCTCAGGCCACATCAAGTGCCGGCTCAGCCCAGCGTGCTGCATCATCACCTCTAAATTTGGCACATGTTCCTGGAGAAGAGCCTCCACCAGCTCCCAACCTAGTGGCCCAAGAAAATGGGCCCATGAATGA
Peptide sequence:
MLWWQQMYAHQYYMQYQAAVSAQATSSAGSAQRAASSPLNLAHVPGEEPPPAPNLVAQENGPMNENVQMNAQGGPVLNEEDLNRDWLDWVYTFSRAAVLLSIVYFYSSFSRFIMVMGAMLLVYLHQAGWFPFRQEGGQQQAPNNVDANNDGHNANNLELEEMKCGSPVSWARCAPCVPSVPCAQPTADAVVAADVRSSVLYAISSCSFSSGHIKCRLSPACCIITSKFGTCSWRRASTSSQPSGPRKWAHE
IRESfinder result
IRESfinder score
0.482835981
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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