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mmu_circTm9sf3_1223
Basic information of circular RNA
PanCircBase ID:
mmu_circTm9sf3_1223
mm39_Chr. Position ID:
chr19|41211522|41244779|-
Gene name:
Tm9sf3
Transcript:
ENSMUST00000025989.10
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
9
Exon/intron indexes:
10,9,8,7,6,5,4,3,2
Exon/intron offsets:
0,9259,11597,15594,17493,22360,23559,24822,33061
Genomic length:
33257
Exon/intron sizes in nt:
14,01,31,95,16,71,32,70,00,00,00,000
Flanking exon/introns:
chr19:41209744-41211522|chr19:41244779-41252197
Splice length:
1223
Other database IDs:
CIRCpedia: MMU_CIRCpedia_220233, circAtlas: mmu-Tm9sf3_0006
circAtlas: hsa-SCAF8_0001
Human Ortholog IDs:
Mature spliced Sequence:
TATCAAGATAAAGAAGAAGTTGTTTTATGGATGAATACTGTTGGGCCCTACCACAATCGCCAAGAAACATATAAATACTTTTCACTTCCATTCTGTGTGGGGTCAAAAAAAAGTATCAGTCATTACCATGAAACTTTGGGAGAAGCACTTCAAGGAGTTGAATTAGAATTTAGTGGCCTGGACATTAAATTTAAAGATGATGTGATGCCAGGCACTTACTGTGAAATTGACTTAGATAAAGAGAAGAGAGATGCGTTTGTGTATGCTATCAAGAATCACTATTGGTATCAGATGTACATAGATGACTTACCAATATGGGGTATTGTTGGTGAAGCAGATGAAAATGGGGAAGATTACTATCTTTGGACCTACAAAAAACTTGAAATAGGCTTTAATGGAAATCGAATTGTTGATGTTAATCTAACTAGTGAAGGAAAGGTCAAGCTGGTTCCAAATACTAAAATACAGATGTCATATTCGGTAAAATGGAAAAAATCGGATGTAAAATTTGAAGATCGATTCGATAAATATCTTGATCCATCCTTTTTTCAGCATAGGATTCACTGGTTTTCAATTTTTAATTCCTTCATGATGGTGATCTTCTTAGTGGGATTAGTTTCAATGATTTTAATGAGAACTTTAAGGAAAGATTATGCCCGATACAGTAAAGAAGAAGAAATGGATGACATGGACAGAGACCTAGGAGACGAGTATGGCTGGAAGCAGGTGCATGGAGATGTGTTCAGACCGTCAAGTCACCCTCTGATCTTCTCCTCCCTCATTGGCTCTGGATGTCAGATATTTGCTGTGTCTCTCATTGTTATTATTGTTGCCATGATAGAGGACTTATATACAGAGAGGGGGTCAATGCTCAGCACAGCCATATTTGTCTATGCTGCTACATCGCCAGTGAACGGGTACTTTGGAGGAAGTCTGTATGCTAGACAAGGAGGAAGGAGATGGATAAAGCAGATGTTTATCGGGGCATTCCTTATCCCAGCTATGGTGTGTGGCACTGCATTCTTCATCAACTTTATAGCCATTTATTACCATGCCTCTAGAGCCATTCCTTTTGGAACAATGGTGGCCGTTTGTTGCATCTGTTTCTTTGTTATCCTTCCTCTAAATCTCGTTGGTACAATACTGGGTCGAAATCTGTCGGGTCAGCCCAACTTCCCTTGTCGTGTCAATGCCGTGCCTCGTCCCATCCCGGAGAAAAAATG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TCGAAATCTGTCGGGTCAGC
60.11
TCTTGGCGATTGTGGTAGGG
59.75
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GGTCGAAATCTGTCGGGTCA
59.75
TCTTGGCGATTGTGGTAGGG
59.75
142
PCR template sequence:
TAAATCTCGTTGGTACAATACTGGGTCGAAATCTGTCGGGTCAGCCCAACTTCCCTTGTCGTGTCAATGCCGTGCCTCGTCCCATCCCGGAGAAAAAATGTATCAAGATAAAGAAGAAGTTGTTTTATGGATGAATACTGTTGGGCCCTACCACAATCGCCAAGAAACATATAAATACTTTTCACTTCCATTCTGTGTGG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
9
Interacting miRNAs (#binding sites)
mmu-miR-16-5p(1), mmu-miR-15a-5p(1), mmu-miR-103-3p(1), mmu-miR-467b-5p(1), mmu-miR-340-5p(1), mmu-miR-107-3p(1), mmu-miR-383-5p(1), mmu-miR-335-3p(1), mmu-miR-3065-5p(1)
siRNAs for circular RNA silencing
Junction sequence
CGGAGAAAAAATGTATCAAGATAAAG
siRNA sets
ATCTTGATACATTTTTTCT, TATCTTGATACATTTTTTC, TCTTGATACATTTTTTCTC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCTM9SF3_1223_ORF_1
0.6723
0.019440114
0.992489101
1227
ORF sequence:
ATGAATACTGTTGGGCCCTACCACAATCGCCAAGAAACATATAAATACTTTTCACTTCCATTCTGTGTGGGGTCAAAAAAAAGTATCAGTCATTACCATGAAACTTTGGGAGAAGCACTTCAAGGAGTTGAATTAGAATTTAGTGGCCTGGACATTAAATTTAAAGATGATGTGATGCCAGGCACTTACTGTGAAATTGACTTAGATAAAGAGAAGAGAGATGCGTTTGTGTATGCTATCAAGAATCACTATTGGTATCAGATGTACATAGATGACTTACCAATATGGGGTATTGTTGGTGAAGCAGATGAAAATGGGGAAGATTACTATCTTTGGACCTACAAAAAACTTGAAATAGGCTTTAATGGAAATCGAATTGTTGATGTTAATCTAACTAGTGAAGGAAAGGTCAAGCTGGTTCCAAATACTAAAATACAGATGTCATATTCGGTAAAATGGAAAAAATCGGATGTAAAATTTGAAGATCGATTCGATAAATATCTTGATCCATCCTTTTTTCAGCATAGGATTCACTGGTTTTCAATTTTTAATTCCTTCATGATGGTGATCTTCTTAGTGGGATTAGTTTCAATGATTTTAATGAGAACTTTAAGGAAAGATTATGCCCGATACAGTAAAGAAGAAGAAATGGATGACATGGACAGAGACCTAGGAGACGAGTATGGCTGGAAGCAGGTGCATGGAGATGTGTTCAGACCGTCAAGTCACCCTCTGATCTTCTCCTCCCTCATTGGCTCTGGATGTCAGATATTTGCTGTGTCTCTCATTGTTATTATTGTTGCCATGATAGAGGACTTATATACAGAGAGGGGGTCAATGCTCAGCACAGCCATATTTGTCTATGCTGCTACATCGCCAGTGAACGGGTACTTTGGAGGAAGTCTGTATGCTAGACAAGGAGGAAGGAGATGGATAAAGCAGATGTTTATCGGGGCATTCCTTATCCCAGCTATGGTGTGTGGCACTGCATTCTTCATCAACTTTATAGCCATTTATTACCATGCCTCTAGAGCCATTCCTTTTGGAACAATGGTGGCCGTTTGTTGCATCTGTTTCTTTGTTATCCTTCCTCTAAATCTCGTTGGTACAATACTGGGTCGAAATCTGTCGGGTCAGCCCAACTTCCCTTGTCGTGTCAATGCCGTGCCTCGTCCCATCCCGGAGAAAAAATGTATCAAGATAAAGAAGAAGTTGTTTTATGGATGA
Peptide sequence:
MNTVGPYHNRQETYKYFSLPFCVGSKKSISHYHETLGEALQGVELEFSGLDIKFKDDVMPGTYCEIDLDKEKRDAFVYAIKNHYWYQMYIDDLPIWGIVGEADENGEDYYLWTYKKLEIGFNGNRIVDVNLTSEGKVKLVPNTKIQMSYSVKWKKSDVKFEDRFDKYLDPSFFQHRIHWFSIFNSFMMVIFLVGLVSMILMRTLRKDYARYSKEEEMDDMDRDLGDEYGWKQVHGDVFRPSSHPLIFSSLIGSGCQIFAVSLIVIIVAMIEDLYTERGSMLSTAIFVYAATSPVNGYFGGSLYARQGGRRWIKQMFIGAFLIPAMVCGTAFFINFIAIYYHASRAIPFGTMVAVCCICFFVILPLNLVGTILGRNLSGQPNFPCRVNAVPRPIPEKKCIKIKKKLFYG
IRESfinder result
IRESfinder score
0.669376042
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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