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mmu_circMatr3_888
Basic information of circular RNA
PanCircBase ID:
mmu_circMatr3_888
mm39_Chr. Position ID:
chr18|35715768|35721506|+
Gene name:
Matr3
Transcript:
ENSMUST00000166793.10
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
10,11,12,13,14
Exon/intron offsets:
0,1162,1799,4915,5616
Genomic length:
5738
Exon/intron sizes in nt:
1,32,44,36,72,23,122
Flanking exon/introns:
chr18:35715139-35715768|chr18:35721506-35723432
Splice length:
888
Other database IDs:
circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_123699
Human Ortholog IDs:
Mature spliced Sequence:
GCTTTTATTGAGATGGAAACCAGAGAAGATGCAATGGCAATGGTTGACCACTGTTTAAAGAAGGCACTTTGGTTTCAGGGGAGATGTGTTAAAGTTGATCTGTCTGAGAAATACAAAAAACTGGTGCTGCGGATTCCTAACAGAGGCATTGACTTACTGAAAAAAGATAAATCCCGGAAAAGATCCTATTCTCCAGATGGAAAAGAATCTCCAAGTGATAAGAAGTCCAAAACTGATGCTCAGAAGACTGAGAGTCCAGCTGAGGGTAAAGAACAAGAAGAGAAGTCGGGTGAGGATGGTGAGAAGGACACCAAGGATGACCAGACAGAACAGGAGCCCAGCATGCTTCTTGAATCTGAAGATGAACTGCTTGTTGATGAGGAAGAAGCTGCAGCACTACTAGAAAGTGGTAGTTCAGTGGGCGATGAGACCGATCTTGCTAATTTAGGGGATGTATCTTCTGATGGGAAAAAGGAGCCTTCAGATAAAGCTGTGAAAAAAGATCCAAGTGCTTCAGCAACATCCAAGAAAAAACTTAAAAAAGTGGACAAGATTGAGGAACTTGATCAAGAAAATGAAGCTGCATTGGAAAATGGGATTAAAAATGAGGAAAATACAGAACCGGGTGCCGAATCTGCTGAGAATGCTGATGATCCAAACAAAGACACAAGTGAAAATGCAGATGGCCAAAATGATGAGAATAAGGAGGATTATACAATTCCCGATGAGTATAGAATCGGACCATATCAGCCTAATGTTCCTGTTGGTATAGACTATGTGATACCTAAAACAGGGTTTTACTGTAAGCTGTGTTCACTCTTTTATACAAATGAAGAAGTTGCAAAGAATACTCATTGCAGCAGCCTTCCTCATTATCAGAAATTAAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CAGGGTTTTACTGTAAGCTGTGT
58.87
GGTCAACCATTGCCATTGCA
59.68
147
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CAGGGTTTTACTGTAAGCTGTGT
58.87
TGGTCAACCATTGCCATTGC
59.68
148
PCR template sequence:
AACAGGGTTTTACTGTAAGCTGTGTTCACTCTTTTATACAAATGAAGAAGTTGCAAAGAATACTCATTGCAGCAGCCTTCCTCATTATCAGAAATTAAAGGCTTTTATTGAGATGGAAACCAGAGAAGATGCAATGGCAATGGTTGACCACTGTTTAAAGAAGGCACTTTGGTTTCAGGGGAGATGTGTTAAAGTTGATC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
3
Interacting miRNAs (#binding sites)
mmu-miR-20b-5p(1), mmu-miR-93-5p(1), mmu-miR-17-5p(1)
siRNAs for circular RNA silencing
Junction sequence
TCAGAAATTAAAGGCTTTTATTGAGA
siRNA sets
TAAAAGCCTTTAATTTCTG, AAAAGCCTTTAATTTCTGA, ATAAAAGCCTTTAATTTCT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCMATR3_888_ORF_1
1.1594
0.212334423
0.999971603
1764
ORF sequence:
ATGGAAACCAGAGAAGATGCAATGGCAATGGTTGACCACTGTTTAAAGAAGGCACTTTGGTTTCAGGGGAGATGTGTTAAAGTTGATCTGTCTGAGAAATACAAAAAACTGGTGCTGCGGATTCCTAACAGAGGCATTGACTTACTGAAAAAAGATAAATCCCGGAAAAGATCCTATTCTCCAGATGGAAAAGAATCTCCAAGTGATAAGAAGTCCAAAACTGATGCTCAGAAGACTGAGAGTCCAGCTGAGGGTAAAGAACAAGAAGAGAAGTCGGGTGAGGATGGTGAGAAGGACACCAAGGATGACCAGACAGAACAGGAGCCCAGCATGCTTCTTGAATCTGAAGATGAACTGCTTGTTGATGAGGAAGAAGCTGCAGCACTACTAGAAAGTGGTAGTTCAGTGGGCGATGAGACCGATCTTGCTAATTTAGGGGATGTATCTTCTGATGGGAAAAAGGAGCCTTCAGATAAAGCTGTGAAAAAAGATCCAAGTGCTTCAGCAACATCCAAGAAAAAACTTAAAAAAGTGGACAAGATTGAGGAACTTGATCAAGAAAATGAAGCTGCATTGGAAAATGGGATTAAAAATGAGGAAAATACAGAACCGGGTGCCGAATCTGCTGAGAATGCTGATGATCCAAACAAAGACACAAGTGAAAATGCAGATGGCCAAAATGATGAGAATAAGGAGGATTATACAATTCCCGATGAGTATAGAATCGGACCATATCAGCCTAATGTTCCTGTTGGTATAGACTATGTGATACCTAAAACAGGGTTTTACTGTAAGCTGTGTTCACTCTTTTATACAAATGAAGAAGTTGCAAAGAATACTCATTGCAGCAGCCTTCCTCATTATCAGAAATTAAAGGCTTTTATTGAGATGGAAACCAGAGAAGATGCAATGGCAATGGTTGACCACTGTTTAAAGAAGGCACTTTGGTTTCAGGGGAGATGTGTTAAAGTTGATCTGTCTGAGAAATACAAAAAACTGGTGCTGCGGATTCCTAACAGAGGCATTGACTTACTGAAAAAAGATAAATCCCGGAAAAGATCCTATTCTCCAGATGGAAAAGAATCTCCAAGTGATAAGAAGTCCAAAACTGATGCTCAGAAGACTGAGAGTCCAGCTGAGGGTAAAGAACAAGAAGAGAAGTCGGGTGAGGATGGTGAGAAGGACACCAAGGATGACCAGACAGAACAGGAGCCCAGCATGCTTCTTGAATCTGAAGATGAACTGCTTGTTGATGAGGAAGAAGCTGCAGCACTACTAGAAAGTGGTAGTTCAGTGGGCGATGAGACCGATCTTGCTAATTTAGGGGATGTATCTTCTGATGGGAAAAAGGAGCCTTCAGATAAAGCTGTGAAAAAAGATCCAAGTGCTTCAGCAACATCCAAGAAAAAACTTAAAAAAGTGGACAAGATTGAGGAACTTGATCAAGAAAATGAAGCTGCATTGGAAAATGGGATTAAAAATGAGGAAAATACAGAACCGGGTGCCGAATCTGCTGAGAATGCTGATGATCCAAACAAAGACACAAGTGAAAATGCAGATGGCCAAAATGATGAGAATAAGGAGGATTATACAATTCCCGATGAGTATAGAATCGGACCATATCAGCCTAATGTTCCTGTTGGTATAGACTATGTGATACCTAAAACAGGGTTTTACTGTAAGCTGTGTTCACTCTTTTATACAAATGAAGAAGTTGCAAAGAATACTCATTGCAGCAGCCTTCCTCATTATCAGAAATTAAAG
Peptide sequence:
METREDAMAMVDHCLKKALWFQGRCVKVDLSEKYKKLVLRIPNRGIDLLKKDKSRKRSYSPDGKESPSDKKSKTDAQKTESPAEGKEQEEKSGEDGEKDTKDDQTEQEPSMLLESEDELLVDEEEAAALLESGSSVGDETDLANLGDVSSDGKKEPSDKAVKKDPSASATSKKKLKKVDKIEELDQENEAALENGIKNEENTEPGAESAENADDPNKDTSENADGQNDENKEDYTIPDEYRIGPYQPNVPVGIDYVIPKTGFYCKLCSLFYTNEEVAKNTHCSSLPHYQKLKAFIEMETREDAMAMVDHCLKKALWFQGRCVKVDLSEKYKKLVLRIPNRGIDLLKKDKSRKRSYSPDGKESPSDKKSKTDAQKTESPAEGKEQEEKSGEDGEKDTKDDQTEQEPSMLLESEDELLVDEEEAAALLESGSSVGDETDLANLGDVSSDGKKEPSDKAVKKDPSASATSKKKLKKVDKIEELDQENEAALENGIKNEENTEPGAESAENADDPNKDTSENADGQNDENKEDYTIPDEYRIGPYQPNVPVGIDYVIPKTGFYCKLCSLFYTNEEVAKNTHCSSLPHYQKLK
IRESfinder result
IRESfinder score
0.521375379
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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