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mmu_circHsf2_588
Basic information of circular RNA
PanCircBase ID:
mmu_circHsf2_588
mm39_Chr. Position ID:
chr10|57371993|57378806|+
Gene name:
Hsf2
Transcript:
ENSMUST00000220353.2
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
6
Exon/intron indexes:
2,3,4,5,6,7
Exon/intron offsets:
0,257,1599,3518,5472,6725
Genomic length:
6813
Exon/intron sizes in nt:
109,128,125,76,62,88
Flanking exon/introns:
chr10:57362697-57371993|chr10:57378806-57380645
Splice length:
588
Other database IDs:
circBase: mmu_circ_0002292, CIRCpedia: MMU_CIRCpedia_23838, circAtlas: mmu-Hsf2_0005
Human Ortholog IDs:
Mature spliced Sequence:
AATGGACAAAGTTTTCTGGTCTTGGATGAGCAAAGATTTGCAAAGGAAATTCTTCCTAAGTACTTCAAACACAATAACATGGCGAGCTTTGTGAGACAACTAAATATGTATGGCTTCCGAAAAGTAGTGCATATCGAATCTGGAATTATCAAACAGGAAAGAGATGGCCCTGTTGAATTTCAGCATCCTTATTTCAAGCAAGGCCAGGATGACCTGTTGGAGAACATTAAAAGGAAGGTTTCATCTTCAAAACCAGAGGAAAATAAAATTCGTCAGGAAGATTTAACAAAAATTATTAGTAGTGCTCAGAAGGTTCAAATAAAACAAGAAACTATTGAGTCCAGGCTTTCAGAATTAAAAAGTGAGAATGAATCCCTTTGGAAGGAGGTGTCAGAACTAAGAGCAAAGCATGCCCAGCAGCAACAAGTTATTCGGAAGATTGTCCAGTTTATTGTTACATTGGTTCAGAATAATCAACTTGTGAGTTTAAAACGTAAAAGGCCTCTACTTCTAAACACAAATGGAGCCCCAAAGAAGAATCTATATCAGCACATAGTCAAAGAACCAACTGATAATCACCATCATAAA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TGGAGCCCCAAAGAAGAATCT
59
TCTCACAAAGCTCGCCATGT
59.96
163
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TGGAGCCCCAAAGAAGAATCT
59
TGTCTCACAAAGCTCGCCAT
59.96
165
PCR template sequence:
AAAACGTAAAAGGCCTCTACTTCTAAACACAAATGGAGCCCCAAAGAAGAATCTATATCAGCACATAGTCAAAGAACCAACTGATAATCACCATCATAAAAATGGACAAAGTTTTCTGGTCTTGGATGAGCAAAGATTTGCAAAGGAAATTCTTCCTAAGTACTTCAAACACAATAACATGGCGAGCTTTGTGAGACAAC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
2
Interacting miRNAs (#binding sites)
mmu-miR-136-5p(1), mmu-miR-350-3p(1)
siRNAs for circular RNA silencing
Junction sequence
TCACCATCATAAAAATGGACAAAGTT
siRNA sets
ACTTTGTCCATTTTTATGA, AACTTTGTCCATTTTTATG, TTTGTCCATTTTTATGATG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCHSF2_588_ORF_1
1.1102
0.043820412
0.992584087
1098
ORF sequence:
ATGGCGAGCTTTGTGAGACAACTAAATATGTATGGCTTCCGAAAAGTAGTGCATATCGAATCTGGAATTATCAAACAGGAAAGAGATGGCCCTGTTGAATTTCAGCATCCTTATTTCAAGCAAGGCCAGGATGACCTGTTGGAGAACATTAAAAGGAAGGTTTCATCTTCAAAACCAGAGGAAAATAAAATTCGTCAGGAAGATTTAACAAAAATTATTAGTAGTGCTCAGAAGGTTCAAATAAAACAAGAAACTATTGAGTCCAGGCTTTCAGAATTAAAAAGTGAGAATGAATCCCTTTGGAAGGAGGTGTCAGAACTAAGAGCAAAGCATGCCCAGCAGCAACAAGTTATTCGGAAGATTGTCCAGTTTATTGTTACATTGGTTCAGAATAATCAACTTGTGAGTTTAAAACGTAAAAGGCCTCTACTTCTAAACACAAATGGAGCCCCAAAGAAGAATCTATATCAGCACATAGTCAAAGAACCAACTGATAATCACCATCATAAAAATGGACAAAGTTTTCTGGTCTTGGATGAGCAAAGATTTGCAAAGGAAATTCTTCCTAAGTACTTCAAACACAATAACATGGCGAGCTTTGTGAGACAACTAAATATGTATGGCTTCCGAAAAGTAGTGCATATCGAATCTGGAATTATCAAACAGGAAAGAGATGGCCCTGTTGAATTTCAGCATCCTTATTTCAAGCAAGGCCAGGATGACCTGTTGGAGAACATTAAAAGGAAGGTTTCATCTTCAAAACCAGAGGAAAATAAAATTCGTCAGGAAGATTTAACAAAAATTATTAGTAGTGCTCAGAAGGTTCAAATAAAACAAGAAACTATTGAGTCCAGGCTTTCAGAATTAAAAAGTGAGAATGAATCCCTTTGGAAGGAGGTGTCAGAACTAAGAGCAAAGCATGCCCAGCAGCAACAAGTTATTCGGAAGATTGTCCAGTTTATTGTTACATTGGTTCAGAATAATCAACTTGTGAGTTTAAAACGTAAAAGGCCTCTACTTCTAAACACAAATGGAGCCCCAAAGAAGAATCTATATCAGCACATAGTCAAAGAACCAACTGATAATCACCATCATAAA
Peptide sequence:
MASFVRQLNMYGFRKVVHIESGIIKQERDGPVEFQHPYFKQGQDDLLENIKRKVSSSKPEENKIRQEDLTKIISSAQKVQIKQETIESRLSELKSENESLWKEVSELRAKHAQQQQVIRKIVQFIVTLVQNNQLVSLKRKRPLLLNTNGAPKKNLYQHIVKEPTDNHHHKNGQSFLVLDEQRFAKEILPKYFKHNNMASFVRQLNMYGFRKVVHIESGIIKQERDGPVEFQHPYFKQGQDDLLENIKRKVSSSKPEENKIRQEDLTKIISSAQKVQIKQETIESRLSELKSENESLWKEVSELRAKHAQQQQVIRKIVQFIVTLVQNNQLVSLKRKRPLLLNTNGAPKKNLYQHIVKEPTDNHHHK
IRESfinder result
IRESfinder score
0.606925316
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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