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mmu_circArfgef2_1960
Basic information of circular RNA
PanCircBase ID:
mmu_circArfgef2_1960
mm39_Chr. Position ID:
chr2|166701182|166713539|+
Gene name:
Arfgef2
Transcript:
ENSMUST00000099078.10
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
14
Exon/intron indexes:
15,16,17,18,19,20,21,22,23,24,25,26,27,28
Exon/intron offsets:
0,523,1051,1262,2321,4294,5430,6417,7649,7883,8025,9629,10947,12196
Genomic length:
12357
Exon/intron sizes in nt:
1,12,20,68,51,72,15,21,00,00,00,00,00,00,00,00,00,00,00,000
Flanking exon/introns:
chr2:166698510-166701182|chr2:166713539-166715495
Splice length:
1960
Other database IDs:
circAtlas: mmu-Arfgef2_0032
Human Ortholog IDs:
Mature spliced Sequence:
CTTCAATAAGAAGCCCAAGCGAGGTATCCAGTTTCTCCAAGAGCAAGGCATGCTGGGAGCAGCTGTAGAAGATATTGCCCAATTTCTGCACCAGGAGGAGCGGCTGGATTCTACCCAGGTTGGCGAGTTTCTGGGAGACAGCACGAGGTTTAACAAGGAGGTGATGTATGCCTATGTGGACCAACTGGATTTCTGTGAAAAAGAGTTCGTCTCAGCCCTGAGGACATTCCTGGAGGGCTTCCGCCTGCCTGGGGAAGCCCAGAAGATTGACCGGTTAATGGAGAAGTTTGCTGCACGATACATAGAATGTAACCAAGGGCAAACCCTGTTTGCTAGTGCGGACACTGCGTATGTCCTGGCGTACTCCATCATCATGCTGACCACAGACCTGCACAGCCCACAGGTAAAGAATAAGATGACAAAAGAGCAGTATATTAAAATGAACCGGGGCATCAACGACAGCAAAGACCTGCCTGAGGAGTACCTGTCCAGCATCTATGACGAGATAGAGGGCAAGAAGATAGCGATGAAGGAGACAAAGGAGCACACAATTGCGACCAAGTCCACCAAGCAGAGTGTAGCTAGTGAAAAGCAGAGGCGGCTGCTGTACAATGTGGAGATGGAGCAGATGGCTAAAACAGCCAAAGCTCTGATGGAGGCCGTGAGCCATGCCAAAGCCCCGTTTACCAGCGCCACACACTTGGACCATGTCCGGCCAATGTTCAAACTGGTGTGGACGCCGCTGCTGGCAGCCTATAGTATTGGCCTGCAGAACTGTGATGACACGGAGGTGGCCTCCCTGTGTTTGGAAGGCATCAGGTGTGCAGTCCGCATTGCCTGCATCTTTGGAATGCAGCTGGAACGAGATGCCTATGTTCAGGCCCTTGCTCGCTTTTCCCTGCTGACAGCCAGCTCCAGCATCACAGAAATGAAGCAGAAAAACATCGACACCATAAAGACACTCATCACTGTGGCTCACACCGATGGCAACTACCTTGGCAACTCCTGGCATGAGATCTTGAAGTGCATCAGCCAGCTGGAGCTTGCTCAGCTGATAGGAACTGGGGTGAAGACTCGCTACCTCTCTGGCTCTGGGCGGGAACGAGAAGGGAGCCTGAAGGGCCACAGTCTGGCAGGAGAAGAATTCATGGGTCTTGGCCTCGGTAACTTGGTGAGTGGTGGTGTAGACAAAAGACAGATGGCCAGCTTCCAGGAGTCGGTTGGTGAAACAAGCTCACAGAGTGTGGTTGTCGCAGTTGACAGAATTTTTACTGGCTCTACCAGACTGGATGGAAATGCAATAGTTGACTTTGTCCGTTGGCTGTGTGCTGTGTCCATGGATGAGCTGGCTTCTCCCCACCATCCTCGAATGTTCAGCCTGCAGAAGATTGTGGAAATATCATACTACAACATGAACAGGATCCGGCTGCAGTGGTCTCGGATATGGCATGTCATTGGAGATCACTTCAATAAGGTCGGCTGTAACCCCAATGAAGATGTGGCCATCTTCGCAGTTGACTCTCTGCGGCAGCTCTCCATGAAGTTCCTGGAGAAGGGAGAATTAGCCAACTTCCGATTTCAGAAGGATTTTCTGAGGCCATTTGAACATATTATGAAGAAAAACAGGTCCCCGACCATCCGGGACATGGTGATCCGATGCATCGCTCAGATGGTGAGCTCCCAGGCAGCCAACATCCGCTCAGGCTGGAAGAACATCTTTGCTGTGTTCCACCAGGCTGCCTCTGACCACGATGGGAACATTGTGGAGCTGGCCTTCCAAACCACAGGCCACATCGTCTCAACCATCTTCCAGCACCACTTCCCTGCAGCCATCGACTCCTTCCAGGATGCTGTGAAGTGCTTGTCTGAGTTCGCCTGCAATGCAGCTTTCCCTGACACCAGCATGGAGGCCATCCGGCTCATCCGCTTCTGTGGGAAATACGTCTCAGAGAGGCCTCGG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GCAATGCAGCTTTCCCTGAC
60.11
CTGGTGCAGAAATTGGGCAA
59.32
177
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GCAATGCAGCTTTCCCTGAC
60.11
TCCTGGTGCAGAAATTGGGC
60.9
179
PCR template sequence:
CTTGTCTGAGTTCGCCTGCAATGCAGCTTTCCCTGACACCAGCATGGAGGCCATCCGGCTCATCCGCTTCTGTGGGAAATACGTCTCAGAGAGGCCTCGGCTTCAATAAGAAGCCCAAGCGAGGTATCCAGTTTCTCCAAGAGCAAGGCATGCTGGGAGCAGCTGTAGAAGATATTGCCCAATTTCTGCACCAGGAGGAG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
26
Interacting miRNAs (#binding sites)
mmu-miR-207(2), mmu-miR-532-5p(2), mmu-let-7a-5p(1), mmu-let-7e-5p(1), mmu-let-7b-5p(1), mmu-miR-221-3p(1), mmu-let-7c-5p(1), mmu-miR-33-5p(1), mmu-miR-18a-5p(1), mmu-miR-328-3p(1), mmu-miR-196a-5p(1), mmu-miR-320-3p(1), mmu-miR-138-5p(1), mmu-miR-214-3p(1), mmu-miR-128-3p(1), mmu-let-7d-5p(1), mmu-miR-503-5p(1), mmu-miR-433-5p(1), mmu-miR-22-3p(1), mmu-miR-98-5p(1), mmu-miR-325-3p(1), mmu-miR-484(1), mmu-miR-540-3p(1), mmu-miR-490-3p(1), mmu-miR-544-5p(1), mmu-miR-338-3p(1)
siRNAs for circular RNA silencing
Junction sequence
AGAGAGGCCTCGGCTTCAATAAGAAG
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCARFGEF2_1960_ORF_1
1.2063
0.413904423
0.999998362
2040
ORF sequence:
ATGCAGCTTTCCCTGACACCAGCATGGAGGCCATCCGGCTCATCCGCTTCTGTGGGAAATACGTCTCAGAGAGGCCTCGGCTTCAATAAGAAGCCCAAGCGAGGTATCCAGTTTCTCCAAGAGCAAGGCATGCTGGGAGCAGCTGTAGAAGATATTGCCCAATTTCTGCACCAGGAGGAGCGGCTGGATTCTACCCAGGTTGGCGAGTTTCTGGGAGACAGCACGAGGTTTAACAAGGAGGTGATGTATGCCTATGTGGACCAACTGGATTTCTGTGAAAAAGAGTTCGTCTCAGCCCTGAGGACATTCCTGGAGGGCTTCCGCCTGCCTGGGGAAGCCCAGAAGATTGACCGGTTAATGGAGAAGTTTGCTGCACGATACATAGAATGTAACCAAGGGCAAACCCTGTTTGCTAGTGCGGACACTGCGTATGTCCTGGCGTACTCCATCATCATGCTGACCACAGACCTGCACAGCCCACAGGTAAAGAATAAGATGACAAAAGAGCAGTATATTAAAATGAACCGGGGCATCAACGACAGCAAAGACCTGCCTGAGGAGTACCTGTCCAGCATCTATGACGAGATAGAGGGCAAGAAGATAGCGATGAAGGAGACAAAGGAGCACACAATTGCGACCAAGTCCACCAAGCAGAGTGTAGCTAGTGAAAAGCAGAGGCGGCTGCTGTACAATGTGGAGATGGAGCAGATGGCTAAAACAGCCAAAGCTCTGATGGAGGCCGTGAGCCATGCCAAAGCCCCGTTTACCAGCGCCACACACTTGGACCATGTCCGGCCAATGTTCAAACTGGTGTGGACGCCGCTGCTGGCAGCCTATAGTATTGGCCTGCAGAACTGTGATGACACGGAGGTGGCCTCCCTGTGTTTGGAAGGCATCAGGTGTGCAGTCCGCATTGCCTGCATCTTTGGAATGCAGCTGGAACGAGATGCCTATGTTCAGGCCCTTGCTCGCTTTTCCCTGCTGACAGCCAGCTCCAGCATCACAGAAATGAAGCAGAAAAACATCGACACCATAAAGACACTCATCACTGTGGCTCACACCGATGGCAACTACCTTGGCAACTCCTGGCATGAGATCTTGAAGTGCATCAGCCAGCTGGAGCTTGCTCAGCTGATAGGAACTGGGGTGAAGACTCGCTACCTCTCTGGCTCTGGGCGGGAACGAGAAGGGAGCCTGAAGGGCCACAGTCTGGCAGGAGAAGAATTCATGGGTCTTGGCCTCGGTAACTTGGTGAGTGGTGGTGTAGACAAAAGACAGATGGCCAGCTTCCAGGAGTCGGTTGGTGAAACAAGCTCACAGAGTGTGGTTGTCGCAGTTGACAGAATTTTTACTGGCTCTACCAGACTGGATGGAAATGCAATAGTTGACTTTGTCCGTTGGCTGTGTGCTGTGTCCATGGATGAGCTGGCTTCTCCCCACCATCCTCGAATGTTCAGCCTGCAGAAGATTGTGGAAATATCATACTACAACATGAACAGGATCCGGCTGCAGTGGTCTCGGATATGGCATGTCATTGGAGATCACTTCAATAAGGTCGGCTGTAACCCCAATGAAGATGTGGCCATCTTCGCAGTTGACTCTCTGCGGCAGCTCTCCATGAAGTTCCTGGAGAAGGGAGAATTAGCCAACTTCCGATTTCAGAAGGATTTTCTGAGGCCATTTGAACATATTATGAAGAAAAACAGGTCCCCGACCATCCGGGACATGGTGATCCGATGCATCGCTCAGATGGTGAGCTCCCAGGCAGCCAACATCCGCTCAGGCTGGAAGAACATCTTTGCTGTGTTCCACCAGGCTGCCTCTGACCACGATGGGAACATTGTGGAGCTGGCCTTCCAAACCACAGGCCACATCGTCTCAACCATCTTCCAGCACCACTTCCCTGCAGCCATCGACTCCTTCCAGGATGCTGTGAAGTGCTTGTCTGAGTTCGCCTGCAATGCAGCTTTCCCTGACACCAGCATGGAGGCCATCCGGCTCATCCGCTTCTGTGGGAAATACGTCTCAGAGAGGCCTCGG
Peptide sequence:
MQLSLTPAWRPSGSSASVGNTSQRGLGFNKKPKRGIQFLQEQGMLGAAVEDIAQFLHQEERLDSTQVGEFLGDSTRFNKEVMYAYVDQLDFCEKEFVSALRTFLEGFRLPGEAQKIDRLMEKFAARYIECNQGQTLFASADTAYVLAYSIIMLTTDLHSPQVKNKMTKEQYIKMNRGINDSKDLPEEYLSSIYDEIEGKKIAMKETKEHTIATKSTKQSVASEKQRRLLYNVEMEQMAKTAKALMEAVSHAKAPFTSATHLDHVRPMFKLVWTPLLAAYSIGLQNCDDTEVASLCLEGIRCAVRIACIFGMQLERDAYVQALARFSLLTASSSITEMKQKNIDTIKTLITVAHTDGNYLGNSWHEILKCISQLELAQLIGTGVKTRYLSGSGREREGSLKGHSLAGEEFMGLGLGNLVSGGVDKRQMASFQESVGETSSQSVVVAVDRIFTGSTRLDGNAIVDFVRWLCAVSMDELASPHHPRMFSLQKIVEISYYNMNRIRLQWSRIWHVIGDHFNKVGCNPNEDVAIFAVDSLRQLSMKFLEKGELANFRFQKDFLRPFEHIMKKNRSPTIRDMVIRCIAQMVSSQAANIRSGWKNIFAVFHQAASDHDGNIVELAFQTTGHIVSTIFQHHFPAAIDSFQDAVKCLSEFACNAAFPDTSMEAIRLIRFCGKYVSERPR
IRESfinder result
IRESfinder score
0.349430657
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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