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mmu_circRhot1_540
Basic information of circular RNA
PanCircBase ID:
mmu_circRhot1_540
mm39_Chr. Position ID:
chr11|80124207|80134316|+
Gene name:
Rhot1
Transcript:
ENSMUST00000077451.14
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
7,8,9,10,11
Exon/intron offsets:
0,547,8639,9191,9988
Genomic length:
10109
Exon/intron sizes in nt:
1,09,10,29,91,09,121
Flanking exon/introns:
chr11:80118158-80124207|chr11:80134316-80136827
Splice length:
540
Other database IDs:
circBase: hsa_circ_0106606, circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_129675
Human Ortholog IDs:
Mature spliced Sequence:
GCTGCCTTTGATATTGGTTGGGAACAAATCTGATCTGGTGGAATATAGTAGTATGGAGACCATCCTTCCAATTATGAACCAGTATACAGAGATAGAGACCTGTGTGGAGTGTTCAGCAAAAAACCTAAAGAATATCTCAGAGCTGTTTTATTATGCACAGAAAGCTGTTCTTCATCCTACAGGGCCTCTATACTGCCCAGAGGAGAAAGAGATGAAACCGGCTTGTATAAAGGCCCTCACTCGTATATTTAAAATATCTGATCAGGATAACGACGGCACTCTGAATGATGCTGAGCTCAACTTCTTCCAGAGAATTTGTTTCAACACTCCTTTAGCTCCGCAAGCGCTGGAAGATGTCAAGAATGTGGTTAGAAAGCACTTAAGTGACGGTGTGGCTGACAGTGGGCTGACGCTCAGAGGTTTTCTCTTTTTACATACACTTTTTATCCAGAGGGGGAGGCATGAGACTACTTGGACTGTGCTTCGACGATTTGGTTATGACGATGACCTGGACCTGACGCCTGAGTATTTATTCCCCCT
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TTTATCCAGAGGGGGAGGCA
59.95
TCCACCAGATCAGATTTGTTCCC
60.31
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TTTATCCAGAGGGGGAGGCA
59.95
TCCACCAGATCAGATTTGTTCC
58.04
140
PCR template sequence:
TTTTTATCCAGAGGGGGAGGCATGAGACTACTTGGACTGTGCTTCGACGATTTGGTTATGACGATGACCTGGACCTGACGCCTGAGTATTTATTCCCCCTGCTGCCTTTGATATTGGTTGGGAACAAATCTGATCTGGTGGAATATAGTAGTATGGAGACCATCCTTCCAATTATGAACCAGTATACAGAGATAGAGACC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
1
Interacting miRNAs (#binding sites)
mmu-miR-196a-5p(1)
siRNAs for circular RNA silencing
Junction sequence
ATTTATTCCCCCTGCTGCCTTTGATA
siRNA sets
ATCAAAGGCAGCAGGGGGA, AAAGGCAGCAGGGGGAATA, TATCAAAGGCAGCAGGGGG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCRHOT1_540_ORF_1
1.1557
0.11657641
0.99151919
1026
ORF sequence:
ATGGAGACCATCCTTCCAATTATGAACCAGTATACAGAGATAGAGACCTGTGTGGAGTGTTCAGCAAAAAACCTAAAGAATATCTCAGAGCTGTTTTATTATGCACAGAAAGCTGTTCTTCATCCTACAGGGCCTCTATACTGCCCAGAGGAGAAAGAGATGAAACCGGCTTGTATAAAGGCCCTCACTCGTATATTTAAAATATCTGATCAGGATAACGACGGCACTCTGAATGATGCTGAGCTCAACTTCTTCCAGAGAATTTGTTTCAACACTCCTTTAGCTCCGCAAGCGCTGGAAGATGTCAAGAATGTGGTTAGAAAGCACTTAAGTGACGGTGTGGCTGACAGTGGGCTGACGCTCAGAGGTTTTCTCTTTTTACATACACTTTTTATCCAGAGGGGGAGGCATGAGACTACTTGGACTGTGCTTCGACGATTTGGTTATGACGATGACCTGGACCTGACGCCTGAGTATTTATTCCCCCTGCTGCCTTTGATATTGGTTGGGAACAAATCTGATCTGGTGGAATATAGTAGTATGGAGACCATCCTTCCAATTATGAACCAGTATACAGAGATAGAGACCTGTGTGGAGTGTTCAGCAAAAAACCTAAAGAATATCTCAGAGCTGTTTTATTATGCACAGAAAGCTGTTCTTCATCCTACAGGGCCTCTATACTGCCCAGAGGAGAAAGAGATGAAACCGGCTTGTATAAAGGCCCTCACTCGTATATTTAAAATATCTGATCAGGATAACGACGGCACTCTGAATGATGCTGAGCTCAACTTCTTCCAGAGAATTTGTTTCAACACTCCTTTAGCTCCGCAAGCGCTGGAAGATGTCAAGAATGTGGTTAGAAAGCACTTAAGTGACGGTGTGGCTGACAGTGGGCTGACGCTCAGAGGTTTTCTCTTTTTACATACACTTTTTATCCAGAGGGGGAGGCATGAGACTACTTGGACTGTGCTTCGACGATTTGGTTATGACGATGACCTGGACCTGACGCCTGAGTATTTATTCCCC
Peptide sequence:
METILPIMNQYTEIETCVECSAKNLKNISELFYYAQKAVLHPTGPLYCPEEKEMKPACIKALTRIFKISDQDNDGTLNDAELNFFQRICFNTPLAPQALEDVKNVVRKHLSDGVADSGLTLRGFLFLHTLFIQRGRHETTWTVLRRFGYDDDLDLTPEYLFPLLPLILVGNKSDLVEYSSMETILPIMNQYTEIETCVECSAKNLKNISELFYYAQKAVLHPTGPLYCPEEKEMKPACIKALTRIFKISDQDNDGTLNDAELNFFQRICFNTPLAPQALEDVKNVVRKHLSDGVADSGLTLRGFLFLHTLFIQRGRHETTWTVLRRFGYDDDLDLTPEYLFP
IRESfinder result
IRESfinder score
0.643662187
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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