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mmu_ciGfm1_586
Basic information of circular RNA
PanCircBase ID:
mmu_ciGfm1_586
mm39_Chr. Position ID:
chr3|67365303|67365889|+
Gene name:
Gfm1
Transcript:
ENSMUST00000077271.9
CircRNA type:
Circular intronic (ci)RNA
Exon/Intron count:
1
Exon/intron indexes:
13
Exon/intron offsets:
0
Genomic length:
586
Exon/intron sizes in nt:
586
Flanking exon/introns:
chr3:67365303-67375139
Splice length:
586
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GTAAGTATACAATGCAATTAGACTCCGTGAGGCTGAAGTGAAGTTTTATTAGGGGATAGACATAGTACCATTACTGTTGGAAAGACATTTTTAGGTAGTACTATTCTTTATTATGGAATCTATGCAGCTCGGTACTGTAGCCAAGACATAAAGAGTGACACTGGTATTCCTTTGGCCCGTTAGGCTAGATGCCAGTGAGGCCAGTCACACACGTGGTTAGCGAGCATGCTGACGGTTGTCTACGGGTTAGCGTCTTGTTCACTCCGCCTGCCCTTCCTTTGGGAGGCGGCTGTTGTGTTTTACTTTTGTGCCGTACTGTGGATGCCACAGGACTTGCATTTGCCAGGGAATAATCTCCTGCAAGTAAAGAAAGCTAATGTCATTGTGAGACTAGAAAATATAATTGGGTTTCTATTGTCTTGATGCTACTATTTAAAATGTCTTCAGCAGAAATAGCATCAGGCAAATCCAGTCGCTACAAGGATGATACACTTCGACTTGGTGCCTGTCTTAACTGTCAGTAACTTTTACTTAGTTTCAAAAGGAGTAAAGGGACTGTGTGGCTACAAAGCAATTCTTGATTTTC
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
ACTTCGACTTGGTGCCTGTC
60.25
ACTTCACTTCAGCCTCACGG
59.97
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CACTTCGACTTGGTGCCTGT
60.53
ACTTCACTTCAGCCTCACGG
59.97
141
PCR template sequence:
ATACACTTCGACTTGGTGCCTGTCTTAACTGTCAGTAACTTTTACTTAGTTTCAAAAGGAGTAAAGGGACTGTGTGGCTACAAAGCAATTCTTGATTTTCGTAAGTATACAATGCAATTAGACTCCGTGAGGCTGAAGTGAAGTTTTATTAGGGGATAGACATAGTACCATTACTGTTGGAAAGACATTTTTAGGTAGTA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
11
Interacting miRNAs (#binding sites)
mmu-miR-199a-5p(1), mmu-miR-101a-3p(1), mmu-miR-211-5p(1), mmu-miR-204-5p(1), mmu-miR-33-5p(1), mmu-miR-101b-3p(1), mmu-miR-139-5p(1), mmu-miR-153-3p(1), mmu-miR-362-5p(1), mmu-miR-680(1), mmu-miR-99a-5p(1)
siRNAs for circular RNA silencing
Junction sequence
ATTCTTGATTTTCGTAAGTATACAAT
siRNA sets
TATACTTACGAAAATCAAG, ATACTTACGAAAATCAAGA, TACTTACGAAAATCAAGAA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIGFM1_586_ORF_5
0.7428
-0.067514012
0.042045002
144
ORF sequence:
ATGATACACTTCGACTTGGTGCCTGTCTTAACTGTCAGTAACTTTTACTTAGTTTCAAAAGGAGTAAAGGGACTGTGTGGCTACAAAGCAATTCTTGATTTTCGTAAGTATACAATGCAATTAGACTCCGTGAGGCTGAAGTGA
Peptide sequence:
MIHFDLVPVLTVSNFYLVSKGVKGLCGYKAILDFRKYTMQLDSVRLK
IRESfinder result
IRESfinder score
0.633336259
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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