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mmu_circMed1_476
Basic information of circular RNA
PanCircBase ID:
mmu_circMed1_476
mm39_Chr. Position ID:
chr11|98057524|98062596|-
Gene name:
Med1
Transcript:
ENSMUST00000092735.12
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
12,11,10,9,8
Exon/intron offsets:
0,820,2664,4249,4997
Genomic length:
5072
Exon/intron sizes in nt:
125,112,90,74,75
Flanking exon/introns:
chr11:98057200-98057524|chr11:98062596-98064046
Splice length:
476
Other database IDs:
CIRCpedia: MMU_CIRCpedia_35742
circBase: hsa_circ_0043431, circAtlas: hsa-SCAF8_0001
Human Ortholog IDs:
Mature spliced Sequence:
CAAACTGAAGACTAAAATGTATCTGGCTCTCCAATCCTTAGAACAGGACCTTTCTAAAATGGCTATTATGTACTGGAAGGCAACCAACGCCGCTCCCTTGGATAAGATTCTTCATGGAAGTGTTGGTTATCTCACCCCGCGGAGTGGGGGTCATTTAATGAATATGAAATACTATGCCTCTCCATCTGACCTGCTGGATGATAAGACTGCCTCTCCTATCATTTTGCATGAAAAGAATGTTCCTCGGTCTTTGGGAATGAATGCCTCAGTGACAATTGAAGGAACCTCTGCTATGTACAAACTCCCAATTGCCCCATTAATTATGGGGTCACACCCAGCTGACAACAAATGGACCCCTTCTTTCTCCGCAGTCACTAGTGCCAACAGTGTTGATCTTCCTGCGTGTTTCTTCTTGAAATTTCCCCAGCCAATTCCAGTATCTAAAGCATTTGTTCAGAAACTGCAAAATTGCACAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TTTCCCCAGCCAATTCCAGT
59.51
CGTTGGTTGCCTTCCAGTAC
59.13
147
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TTTCCCCAGCCAATTCCAGT
59.51
GCGTTGGTTGCCTTCCAGTA
60.89
148
PCR template sequence:
AGTGCCAACAGTGTTGATCTTCCTGCGTGTTTCTTCTTGAAATTTCCCCAGCCAATTCCAGTATCTAAAGCATTTGTTCAGAAACTGCAAAATTGCACAGCAAACTGAAGACTAAAATGTATCTGGCTCTCCAATCCTTAGAACAGGACCTTTCTAAAATGGCTATTATGTACTGGAAGGCAACCAACGCCGCTCCCTTG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
4
Interacting miRNAs (#binding sites)
mmu-miR-200a-3p(1), mmu-miR-141-3p(1), mmu-miR-214-3p(1), mmu-miR-96-5p(1)
siRNAs for circular RNA silencing
Junction sequence
CAAAATTGCACAGCAAACTGAAGACT
siRNA sets
AGTCTTCAGTTTGCTGTGC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCMED1_476_ORF_1
0.9652
0.018682662
0.495798033
468
ORF sequence:
ATGTATCTGGCTCTCCAATCCTTAGAACAGGACCTTTCTAAAATGGCTATTATGTACTGGAAGGCAACCAACGCCGCTCCCTTGGATAAGATTCTTCATGGAAGTGTTGGTTATCTCACCCCGCGGAGTGGGGGTCATTTAATGAATATGAAATACTATGCCTCTCCATCTGACCTGCTGGATGATAAGACTGCCTCTCCTATCATTTTGCATGAAAAGAATGTTCCTCGGTCTTTGGGAATGAATGCCTCAGTGACAATTGAAGGAACCTCTGCTATGTACAAACTCCCAATTGCCCCATTAATTATGGGGTCACACCCAGCTGACAACAAATGGACCCCTTCTTTCTCCGCAGTCACTAGTGCCAACAGTGTTGATCTTCCTGCGTGTTTCTTCTTGAAATTTCCCCAGCCAATTCCAGTATCTAAAGCATTTGTTCAGAAACTGCAAAATTGCACAGCAAACTGA
Peptide sequence:
MYLALQSLEQDLSKMAIMYWKATNAAPLDKILHGSVGYLTPRSGGHLMNMKYYASPSDLLDDKTASPIILHEKNVPRSLGMNASVTIEGTSAMYKLPIAPLIMGSHPADNKWTPSFSAVTSANSVDLPACFFLKFPQPIPVSKAFVQKLQNCTAN
IRESfinder result
IRESfinder score
0.701657537
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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