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mmu_circNfatc3_514
Basic information of circular RNA
PanCircBase ID:
mmu_circNfatc3_514
mm39_Chr. Position ID:
chr8|106818663|106825844|+
Gene name:
Nfatc3
Transcript:
ENSMUST00000212742.2
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
4,5,6
Exon/intron offsets:
0,4132,7040
Genomic length:
7181
Exon/intron sizes in nt:
20,01,73,141
Flanking exon/introns:
chr8:106810605-106818663|chr8:106825844-106827565
Splice length:
514
Other database IDs:
circAtlas: mmu-Nfatc3_0014
circBase: hsa_circ_0039932, circAtlas: hsa-NFATC3_0014, CIRCpedia: HSA_CIRCpedia_81892
Human Ortholog IDs:
Mature spliced Sequence:
CTCCTGGGCTATAGTGAAAAGCCAATAAATCTACAGATGTTTATTGGAACAGCCGATGATAGATATTTACGACCTCATGCATTTTACCAGGTGCATCGGATTACTGGAAAGACAGTTGCTACTGCAAGTCAAGAGATAATAATCGCCAGCACAAAAGTTCTGGAAATCCCACTTCTACCTGAAAATAATATGTCAGCGAGTATTGACTGTGCAGGTATTTTAAAGCTCCGCAACTCAGATATAGAACTTCGAAAAGGAGAAACTGATATTGGCAGAAAAAATACTAGAGTCCGACTTGTATTTCGTGTGCACATCCCACAGCCCAGTGGAAAAGTTCTTTCTCTACAGATAGCATCTATTCCTGTTGAGTGCTCTCAGCGATCTGCTCAAGAACTCCCTCATATTGAGAAGTACAGTATCAACAGTTGCTCTGTCAATGGAGGCCACGAAATGATTGTGACTGGATCTAATTTTCTTCCAGAATCCAAAATAATTTTTCTTGAAAAAGGACAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TCAATGGAGGCCACGAAATGA
60
CCGATGCACCTGGTAAAATGC
60.2
180
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TGTCAATGGAGGCCACGAAA
59.89
GCACCTGGTAAAATGCATGAGG
60.16
177
PCR template sequence:
AGTATCAACAGTTGCTCTGTCAATGGAGGCCACGAAATGATTGTGACTGGATCTAATTTTCTTCCAGAATCCAAAATAATTTTTCTTGAAAAAGGACAAGCTCCTGGGCTATAGTGAAAAGCCAATAAATCTACAGATGTTTATTGGAACAGCCGATGATAGATATTTACGACCTCATGCATTTTACCAGGTGCATCGGA
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-501-3p(1), mmu-miR-511-3p(1), mmu-miR-335-3p(1)
siRNAs for circular RNA silencing
Junction sequence
GAAAAAGGACAAGCTCCTGGGCTATA
siRNA sets
ATAGCCCAGGAGCTTGTCC, TATAGCCCAGGAGCTTGTC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCNFATC3_514_ORF_1
0.9941
-0.013854137
0.518822908
492
ORF sequence:
ATGTTTATTGGAACAGCCGATGATAGATATTTACGACCTCATGCATTTTACCAGGTGCATCGGATTACTGGAAAGACAGTTGCTACTGCAAGTCAAGAGATAATAATCGCCAGCACAAAAGTTCTGGAAATCCCACTTCTACCTGAAAATAATATGTCAGCGAGTATTGACTGTGCAGGTATTTTAAAGCTCCGCAACTCAGATATAGAACTTCGAAAAGGAGAAACTGATATTGGCAGAAAAAATACTAGAGTCCGACTTGTATTTCGTGTGCACATCCCACAGCCCAGTGGAAAAGTTCTTTCTCTACAGATAGCATCTATTCCTGTTGAGTGCTCTCAGCGATCTGCTCAAGAACTCCCTCATATTGAGAAGTACAGTATCAACAGTTGCTCTGTCAATGGAGGCCACGAAATGATTGTGACTGGATCTAATTTTCTTCCAGAATCCAAAATAATTTTTCTTGAAAAAGGACAAGCTCCTGGGCTATAG
Peptide sequence:
MFIGTADDRYLRPHAFYQVHRITGKTVATASQEIIIASTKVLEIPLLPENNMSASIDCAGILKLRNSDIELRKGETDIGRKNTRVRLVFRVHIPQPSGKVLSLQIASIPVECSQRSAQELPHIEKYSINSCSVNGGHEMIVTGSNFLPESKIIFLEKGQAPGL
IRESfinder result
IRESfinder score
0.738808255
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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