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mmu_circHerc1_1048
Basic information of circular RNA
PanCircBase ID:
mmu_circHerc1_1048
mm39_Chr. Position ID:
chr9|66305119|66315487|+
Gene name:
Herc1
Transcript:
ENSMUST00000042824.13
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
6
Exon/intron indexes:
13,14,15,16,17,18
Exon/intron offsets:
0,1420,1930,2209,4686,10146
Genomic length:
10368
Exon/intron sizes in nt:
1,26,22,21,53,13,31,92,000
Flanking exon/introns:
chr9:66304700-66305119|chr9:66315487-66318297
Splice length:
1048
Other database IDs:
circAtlas: mmu-Herc1_0130
circAtlas: hsa-HERC1_0342
Human Ortholog IDs:
Mature spliced Sequence:
GTGGTAATTGAAACACTCTCAGTTGGAGCAACCATGCTGTTACCTCCATTAAGAGAACGGATGGAATTACTTCATTCTCTTTTACCCCAAGGACCTGATAGATGGGAAAGCTTATCCAAAGGACAGAGAATGCAACTGGATATAATTCTGACAAGTTTACAAGATCATACCCATGTAGCCTCCCTTCTTGGCTATAGCTCACCTTCCGATGCTGCTGACCTTTCGACTGTGTGCATGGGATATGGAAACCTGTCAGACCAACCATATGGTTCTCAGATCTGCCATCCAGACACTCATCTGGCCGAAATTTTAATGAAGACTCTCTTAAGAAATTTAGGGTTTTATACGGATCAAGCATTTGGAGAGCTGGAAAAGAATAGTGATAAATATCTTCTTGGAACATCATCTTCAGAGAACAGTCAGCCTGCTCATCTTCATGAACTACTGTGTTCATTACAGAAACAACTGCTTGCTTTTTGCCACATTAATAATGTTACTGAGAACTCAAGCAGTGTGGCATTGCTTCATAAACATCTTCAGCTTTTGCTGCCTCATGCCACAGATATTTATTCACGTTCCGCAAATTTGCTTAAAGAAAGTCCTTGGAATGGCAGTGTTGGAGAAAAATTGAGAGATGTGATCTATGTGTCAGCTGCAGGCAGTATGCTCTGCCAGATTGTTAACTCCCTACTGTTACTCCCGGTGTCAGTGGCTCGTCCTTTATTGAGTTACCTCCTCGACCTCTTGCCACCTCTTGATTGCCTTAATAGACTCCTGCCAGCTGCTGCTCTTTTAGAAGACCAAGAATTACAGTGGCCTCTTCATGGGGGGCCAGAAGTAATTGACCCAGCTGGTGTGCCATTACCTCAACCAGCTCAATCTTGGGTATGGCTTGTGGATCTGGAAAGAACAATTGCTCTCCTCATTGGCCGATGTCTTGGTGGCATGCTTCAAGGCTCCCCCGTGTCTCCAGAGGAACAGGATACTGCATATTGGATGAAAACACCACTTTTCAGTGATGGTGTGGAAATGGACACCCCTCAGTTGG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CGTGTCTCCAGAGGAACAGG
59.76
CCATCCGTTCTCTTAATGGAGGT
59.87
150
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CCGTGTCTCCAGAGGAACAG
59.76
CCATCCGTTCTCTTAATGGAGGT
59.87
151
PCR template sequence:
CTTCAAGGCTCCCCCGTGTCTCCAGAGGAACAGGATACTGCATATTGGATGAAAACACCACTTTTCAGTGATGGTGTGGAAATGGACACCCCTCAGTTGGGTGGTAATTGAAACACTCTCAGTTGGAGCAACCATGCTGTTACCTCCATTAAGAGAACGGATGGAATTACTTCATTCTCTTTTACCCCAAGGACCTGATA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
12
Interacting miRNAs (#binding sites)
mmu-miR-200a-3p(1), mmu-miR-141-3p(1), mmu-miR-1a-3p(1), mmu-miR-103-3p(1), mmu-miR-15b-5p(1), mmu-miR-709(1), mmu-miR-199b-3p(1), mmu-miR-194-5p(1), mmu-miR-199a-3p(1), mmu-miR-324-3p(1), mmu-miR-107-3p(1), mmu-miR-802-5p(1)
siRNAs for circular RNA silencing
Junction sequence
ACCCCTCAGTTGGGTGGTAATTGAAA
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCHERC1_1048_ORF_1
0.9968
-0.053895896
0.983908431
1077
ORF sequence:
ATGGTGTGGAAATGGACACCCCTCAGTTGGGTGGTAATTGAAACACTCTCAGTTGGAGCAACCATGCTGTTACCTCCATTAAGAGAACGGATGGAATTACTTCATTCTCTTTTACCCCAAGGACCTGATAGATGGGAAAGCTTATCCAAAGGACAGAGAATGCAACTGGATATAATTCTGACAAGTTTACAAGATCATACCCATGTAGCCTCCCTTCTTGGCTATAGCTCACCTTCCGATGCTGCTGACCTTTCGACTGTGTGCATGGGATATGGAAACCTGTCAGACCAACCATATGGTTCTCAGATCTGCCATCCAGACACTCATCTGGCCGAAATTTTAATGAAGACTCTCTTAAGAAATTTAGGGTTTTATACGGATCAAGCATTTGGAGAGCTGGAAAAGAATAGTGATAAATATCTTCTTGGAACATCATCTTCAGAGAACAGTCAGCCTGCTCATCTTCATGAACTACTGTGTTCATTACAGAAACAACTGCTTGCTTTTTGCCACATTAATAATGTTACTGAGAACTCAAGCAGTGTGGCATTGCTTCATAAACATCTTCAGCTTTTGCTGCCTCATGCCACAGATATTTATTCACGTTCCGCAAATTTGCTTAAAGAAAGTCCTTGGAATGGCAGTGTTGGAGAAAAATTGAGAGATGTGATCTATGTGTCAGCTGCAGGCAGTATGCTCTGCCAGATTGTTAACTCCCTACTGTTACTCCCGGTGTCAGTGGCTCGTCCTTTATTGAGTTACCTCCTCGACCTCTTGCCACCTCTTGATTGCCTTAATAGACTCCTGCCAGCTGCTGCTCTTTTAGAAGACCAAGAATTACAGTGGCCTCTTCATGGGGGGCCAGAAGTAATTGACCCAGCTGGTGTGCCATTACCTCAACCAGCTCAATCTTGGGTATGGCTTGTGGATCTGGAAAGAACAATTGCTCTCCTCATTGGCCGATGTCTTGGTGGCATGCTTCAAGGCTCCCCCGTGTCTCCAGAGGAACAGGATACTGCATATTGGATGAAAACACCACTTTTCAGTGATGGTGTGGAAATGGACACCCCTCAGTTG
Peptide sequence:
MVWKWTPLSWVVIETLSVGATMLLPPLRERMELLHSLLPQGPDRWESLSKGQRMQLDIILTSLQDHTHVASLLGYSSPSDAADLSTVCMGYGNLSDQPYGSQICHPDTHLAEILMKTLLRNLGFYTDQAFGELEKNSDKYLLGTSSSENSQPAHLHELLCSLQKQLLAFCHINNVTENSSSVALLHKHLQLLLPHATDIYSRSANLLKESPWNGSVGEKLRDVIYVSAAGSMLCQIVNSLLLLPVSVARPLLSYLLDLLPPLDCLNRLLPAAALLEDQELQWPLHGGPEVIDPAGVPLPQPAQSWVWLVDLERTIALLIGRCLGGMLQGSPVSPEEQDTAYWMKTPLFSDGVEMDTPQL
IRESfinder result
IRESfinder score
0.782605315
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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