top of page
mmu_circMatr3_1308
Basic information of circular RNA
PanCircBase ID:
mmu_circMatr3_1308
mm39_Chr. Position ID:
chr18|35714222|35721506|+
Gene name:
Matr3
Transcript:
ENSMUST00000166793.10
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
8
Exon/intron indexes:
7,8,9,10,11,12,13,14
Exon/intron offsets:
0,427,749,1546,2708,3345,6461,7162
Genomic length:
7284
Exon/intron sizes in nt:
12,61,26,16,81,32,44,30,00,00,000
Flanking exon/introns:
chr18:35712371-35714222|chr18:35721506-35723432
Splice length:
1308
Other database IDs:
circAtlas: mmu-Matr3_0017
Human Ortholog IDs:
Mature spliced Sequence:
GAAACCAGCCGAGTTGTTCACATTATGGATTTTCAGCGAGGAAAAAACTTGAGATACCAGCTGTTACAACTGGTAGAACCATTTGGAGTCATTTCAAATCATCTGATTTTAAATAAAATTAATGAGGCATTTATTGAAATGGCCACCACAGAAGATGCTCAGGCTGCTGTGGATTATTATACAACTACACCAGCATTAGTGTTTGGCAAGCCAGTGAGAGTTCATTTATCCCAGAAGTATAAGAGAATAAAGAAACCTGAAGGAAAACCAGATCAGAAGTTTGATCAAAAGCAAGAACTTGGTCGTGTGATACATCTCAGCAATTTACCTCATTCTGGCTATTCTGACAGTGCCGTCCTCAAGCTTGCTGAGCCTTATGGGAAAATAAAGAATTATATCTTAATGAGGATGAAAAGTCAGGCTTTTATTGAGATGGAAACCAGAGAAGATGCAATGGCAATGGTTGACCACTGTTTAAAGAAGGCACTTTGGTTTCAGGGGAGATGTGTTAAAGTTGATCTGTCTGAGAAATACAAAAAACTGGTGCTGCGGATTCCTAACAGAGGCATTGACTTACTGAAAAAAGATAAATCCCGGAAAAGATCCTATTCTCCAGATGGAAAAGAATCTCCAAGTGATAAGAAGTCCAAAACTGATGCTCAGAAGACTGAGAGTCCAGCTGAGGGTAAAGAACAAGAAGAGAAGTCGGGTGAGGATGGTGAGAAGGACACCAAGGATGACCAGACAGAACAGGAGCCCAGCATGCTTCTTGAATCTGAAGATGAACTGCTTGTTGATGAGGAAGAAGCTGCAGCACTACTAGAAAGTGGTAGTTCAGTGGGCGATGAGACCGATCTTGCTAATTTAGGGGATGTATCTTCTGATGGGAAAAAGGAGCCTTCAGATAAAGCTGTGAAAAAAGATCCAAGTGCTTCAGCAACATCCAAGAAAAAACTTAAAAAAGTGGACAAGATTGAGGAACTTGATCAAGAAAATGAAGCTGCATTGGAAAATGGGATTAAAAATGAGGAAAATACAGAACCGGGTGCCGAATCTGCTGAGAATGCTGATGATCCAAACAAAGACACAAGTGAAAATGCAGATGGCCAAAATGATGAGAATAAGGAGGATTATACAATTCCCGATGAGTATAGAATCGGACCATATCAGCCTAATGTTCCTGTTGGTATAGACTATGTGATACCTAAAACAGGGTTTTACTGTAAGCTGTGTTCACTCTTTTATACAAATGAAGAAGTTGCAAAGAATACTCATTGCAGCAGCCTTCCTCATTATCAGAAATTAAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
ACTGTAAGCTGTGTTCACTCT
56.89
TGGTTCTACCAGTTGTAACAGCT
59.61
170
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CAGGGTTTTACTGTAAGCTGTGT
58.87
TGGTTCTACCAGTTGTAACAGCT
59.61
179
PCR template sequence:
AACAGGGTTTTACTGTAAGCTGTGTTCACTCTTTTATACAAATGAAGAAGTTGCAAAGAATACTCATTGCAGCAGCCTTCCTCATTATCAGAAATTAAAGGAAACCAGCCGAGTTGTTCACATTATGGATTTTCAGCGAGGAAAAAACTTGAGATACCAGCTGTTACAACTGGTAGAACCATTTGGAGTCATTTCAAATC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
5
Interacting miRNAs (#binding sites)
mmu-miR-20b-5p(1), mmu-miR-93-5p(1), mmu-miR-17-5p(1), mmu-miR-138-5p(1), mmu-miR-183-5p(1)
siRNAs for circular RNA silencing
Junction sequence
TCAGAAATTAAAGGAAACCAGCCGAG
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCMATR3_1308_ORF_1
1.194
0.160160093
0.999999915
2592
ORF sequence:
ATGGATTTTCAGCGAGGAAAAAACTTGAGATACCAGCTGTTACAACTGGTAGAACCATTTGGAGTCATTTCAAATCATCTGATTTTAAATAAAATTAATGAGGCATTTATTGAAATGGCCACCACAGAAGATGCTCAGGCTGCTGTGGATTATTATACAACTACACCAGCATTAGTGTTTGGCAAGCCAGTGAGAGTTCATTTATCCCAGAAGTATAAGAGAATAAAGAAACCTGAAGGAAAACCAGATCAGAAGTTTGATCAAAAGCAAGAACTTGGTCGTGTGATACATCTCAGCAATTTACCTCATTCTGGCTATTCTGACAGTGCCGTCCTCAAGCTTGCTGAGCCTTATGGGAAAATAAAGAATTATATCTTAATGAGGATGAAAAGTCAGGCTTTTATTGAGATGGAAACCAGAGAAGATGCAATGGCAATGGTTGACCACTGTTTAAAGAAGGCACTTTGGTTTCAGGGGAGATGTGTTAAAGTTGATCTGTCTGAGAAATACAAAAAACTGGTGCTGCGGATTCCTAACAGAGGCATTGACTTACTGAAAAAAGATAAATCCCGGAAAAGATCCTATTCTCCAGATGGAAAAGAATCTCCAAGTGATAAGAAGTCCAAAACTGATGCTCAGAAGACTGAGAGTCCAGCTGAGGGTAAAGAACAAGAAGAGAAGTCGGGTGAGGATGGTGAGAAGGACACCAAGGATGACCAGACAGAACAGGAGCCCAGCATGCTTCTTGAATCTGAAGATGAACTGCTTGTTGATGAGGAAGAAGCTGCAGCACTACTAGAAAGTGGTAGTTCAGTGGGCGATGAGACCGATCTTGCTAATTTAGGGGATGTATCTTCTGATGGGAAAAAGGAGCCTTCAGATAAAGCTGTGAAAAAAGATCCAAGTGCTTCAGCAACATCCAAGAAAAAACTTAAAAAAGTGGACAAGATTGAGGAACTTGATCAAGAAAATGAAGCTGCATTGGAAAATGGGATTAAAAATGAGGAAAATACAGAACCGGGTGCCGAATCTGCTGAGAATGCTGATGATCCAAACAAAGACACAAGTGAAAATGCAGATGGCCAAAATGATGAGAATAAGGAGGATTATACAATTCCCGATGAGTATAGAATCGGACCATATCAGCCTAATGTTCCTGTTGGTATAGACTATGTGATACCTAAAACAGGGTTTTACTGTAAGCTGTGTTCACTCTTTTATACAAATGAAGAAGTTGCAAAGAATACTCATTGCAGCAGCCTTCCTCATTATCAGAAATTAAAGGAAACCAGCCGAGTTGTTCACATTATGGATTTTCAGCGAGGAAAAAACTTGAGATACCAGCTGTTACAACTGGTAGAACCATTTGGAGTCATTTCAAATCATCTGATTTTAAATAAAATTAATGAGGCATTTATTGAAATGGCCACCACAGAAGATGCTCAGGCTGCTGTGGATTATTATACAACTACACCAGCATTAGTGTTTGGCAAGCCAGTGAGAGTTCATTTATCCCAGAAGTATAAGAGAATAAAGAAACCTGAAGGAAAACCAGATCAGAAGTTTGATCAAAAGCAAGAACTTGGTCGTGTGATACATCTCAGCAATTTACCTCATTCTGGCTATTCTGACAGTGCCGTCCTCAAGCTTGCTGAGCCTTATGGGAAAATAAAGAATTATATCTTAATGAGGATGAAAAGTCAGGCTTTTATTGAGATGGAAACCAGAGAAGATGCAATGGCAATGGTTGACCACTGTTTAAAGAAGGCACTTTGGTTTCAGGGGAGATGTGTTAAAGTTGATCTGTCTGAGAAATACAAAAAACTGGTGCTGCGGATTCCTAACAGAGGCATTGACTTACTGAAAAAAGATAAATCCCGGAAAAGATCCTATTCTCCAGATGGAAAAGAATCTCCAAGTGATAAGAAGTCCAAAACTGATGCTCAGAAGACTGAGAGTCCAGCTGAGGGTAAAGAACAAGAAGAGAAGTCGGGTGAGGATGGTGAGAAGGACACCAAGGATGACCAGACAGAACAGGAGCCCAGCATGCTTCTTGAATCTGAAGATGAACTGCTTGTTGATGAGGAAGAAGCTGCAGCACTACTAGAAAGTGGTAGTTCAGTGGGCGATGAGACCGATCTTGCTAATTTAGGGGATGTATCTTCTGATGGGAAAAAGGAGCCTTCAGATAAAGCTGTGAAAAAAGATCCAAGTGCTTCAGCAACATCCAAGAAAAAACTTAAAAAAGTGGACAAGATTGAGGAACTTGATCAAGAAAATGAAGCTGCATTGGAAAATGGGATTAAAAATGAGGAAAATACAGAACCGGGTGCCGAATCTGCTGAGAATGCTGATGATCCAAACAAAGACACAAGTGAAAATGCAGATGGCCAAAATGATGAGAATAAGGAGGATTATACAATTCCCGATGAGTATAGAATCGGACCATATCAGCCTAATGTTCCTGTTGGTATAGACTATGTGATACCTAAAACAGGGTTTTACTGTAAGCTGTGTTCACTCTTTTATACAAATGAAGAAGTTGCAAAGAATACTCATTGCAGCAGCCTTCCTCATTATCAGAAATTAAAG
Peptide sequence:
MDFQRGKNLRYQLLQLVEPFGVISNHLILNKINEAFIEMATTEDAQAAVDYYTTTPALVFGKPVRVHLSQKYKRIKKPEGKPDQKFDQKQELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRMKSQAFIEMETREDAMAMVDHCLKKALWFQGRCVKVDLSEKYKKLVLRIPNRGIDLLKKDKSRKRSYSPDGKESPSDKKSKTDAQKTESPAEGKEQEEKSGEDGEKDTKDDQTEQEPSMLLESEDELLVDEEEAAALLESGSSVGDETDLANLGDVSSDGKKEPSDKAVKKDPSASATSKKKLKKVDKIEELDQENEAALENGIKNEENTEPGAESAENADDPNKDTSENADGQNDENKEDYTIPDEYRIGPYQPNVPVGIDYVIPKTGFYCKLCSLFYTNEEVAKNTHCSSLPHYQKLKETSRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNKINEAFIEMATTEDAQAAVDYYTTTPALVFGKPVRVHLSQKYKRIKKPEGKPDQKFDQKQELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRMKSQAFIEMETREDAMAMVDHCLKKALWFQGRCVKVDLSEKYKKLVLRIPNRGIDLLKKDKSRKRSYSPDGKESPSDKKSKTDAQKTESPAEGKEQEEKSGEDGEKDTKDDQTEQEPSMLLESEDELLVDEEEAAALLESGSSVGDETDLANLGDVSSDGKKEPSDKAVKKDPSASATSKKKLKKVDKIEELDQENEAALENGIKNEENTEPGAESAENADDPNKDTSENADGQNDENKEDYTIPDEYRIGPYQPNVPVGIDYVIPKTGFYCKLCSLFYTNEEVAKNTHCSSLPHYQKLK
IRESfinder result
IRESfinder score
0.594271384
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
bottom of page