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mmu_circNfatc3_1188
Basic information of circular RNA
PanCircBase ID:
mmu_circNfatc3_1188
mm39_Chr. Position ID:
chr8|106827565|106835761|+
Gene name:
Nfatc3
Transcript:
ENSMUST00000212742.2
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
7,8,9
Exon/intron offsets:
0,3091,7191
Genomic length:
8196
Exon/intron sizes in nt:
56,12,71,005
Flanking exon/introns:
chr8:106825844-106827565|chr8:106835761-106854549
Splice length:
1188
Other database IDs:
circAtlas: mmu-Nfatc3_0023
circBase: hsa_circ_0039935, circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_18272
Human Ortholog IDs:
Mature spliced Sequence:
ATGGAAGACCTCATTGGGAGGCTGAAGGAAAAATAATCAGAGAAAAATGTCAAGGGGCTCACATTGTCCTTGAAGTTCCTCCCTATCATAACCCAGCAGTTACATCTGCCGTGCAGGTGCACTTTTATCTTTGCAATGGCAAGAGGAAAAAAAGCCAGTCTCAACGTTTTACTTACACACCAGTTTTGATGAAGCAAGAACAAAGAGAAGACACAGATTTGCCTTCAGTTCCATCTTTGCCTGTGCCTCATTCTGCCCAGGCCCAGAGGCCCTCCTCAGAGACAGGGCACCCCCATGACCGTGCGATGTCAGCACCGGGAAGCCTGCTTTGTCAAGTGCAGCCAGCATATACATCTATGGTAGCCTCCACCCATTTGCCACAGTTGCAGTGTAGGGATGAAGGTGCTGGTAAAGAGCAGCACATAGCAACATCTTCAGTCATGCACCAGCCTTTCCAAGTTACACCAACATCTCCTATAGGGTCTTCCTATCAGTCTATACAAACTAGTATGTATAACGGTCCAACCTGTCTTCCTGTGAATCCTGCCTCTAGTCAAGAATTTGACCCAGTTTTGTTTCAGCAAGATGCAGCTCTTTCTAGTTTAGTAAATCTTGGCTGTCAACCACTGTCACCAATACCATTTCATTCTTCAAATTCAGATGCGACAGGACATCTCTTAGCACATTCACCTCATTCTGTGCAAACCCCACCTCATCTGCAGTCAATGGGATACCATTGTTCAAATGCAGGACAAACAGCTCTTTCTTCTCCAGTGGCAGACCAGATCACAGGTCAGCCTTCTTCTCATTTACAGCCTATTACATATTGTCCTTCACACCCAGGATCTGCTACAGCAGCTTCCCCAGCAGCCTCTCATCCTCTGGCTAGTTCACCGATTTCTGGGCCATCATCCCCTCAGCTGCAGCCTATGCCTTATCAATCTCCTAGCTCAGGAACTGCCTCATCACCATCTCCAACTACCAGAATGCATTCTGGACAGCACTCAACTCAAGCACAAAGTACAGGCCAAGGAGGCCTTTCTGTTCCTTCATCCTTAGTATGTCACAGTTTGTGTGACCCAGCGTCATTTCCGCCTGGTGGTGCAACTGTGAGCATTAAACCTGAACCTGAAGATCAAGAACCTAACTTTGCAACCATTGGTCTACAGGATATCACCTTAGATGATG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GTGGTGCAACTGTGAGCATT
59.33
GGACAATGTGAGCCCCTTGA
59.96
159
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GTGGTGCAACTGTGAGCATT
59.33
TCAAGGACAATGTGAGCCCC
59.96
163
PCR template sequence:
TTTCCGCCTGGTGGTGCAACTGTGAGCATTAAACCTGAACCTGAAGATCAAGAACCTAACTTTGCAACCATTGGTCTACAGGATATCACCTTAGATGATGATGGAAGACCTCATTGGGAGGCTGAAGGAAAAATAATCAGAGAAAAATGTCAAGGGGCTCACATTGTCCTTGAAGTTCCTCCCTATCATAACCCAGCAGT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
18
Interacting miRNAs (#binding sites)
mmu-miR-7b-5p(2), mmu-miR-7a-5p(2), mmu-miR-20b-5p(1), mmu-miR-155-5p(1), mmu-miR-106a-5p(1), mmu-miR-93-5p(1), mmu-miR-20a-5p(1), mmu-miR-17-5p(1), mmu-miR-135a-5p(1), mmu-miR-205-5p(1), mmu-miR-18a-5p(1), mmu-miR-326-3p(1), mmu-miR-138-5p(1), mmu-miR-339-5p(1), mmu-miR-218-5p(1), mmu-miR-370-3p(1), mmu-miR-342-5p(1), mmu-miR-377-3p(1)
siRNAs for circular RNA silencing
Junction sequence
ACCTTAGATGATGATGGAAGACCTCA
siRNA sets
TTCCATCATCATCTAAGGT, CTTCCATCATCATCTAAGG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCNFATC3_1188_ORF_1
1.2622
-0.084267759
0.999996222
2187
ORF sequence:
ATGAAGCAAGAACAAAGAGAAGACACAGATTTGCCTTCAGTTCCATCTTTGCCTGTGCCTCATTCTGCCCAGGCCCAGAGGCCCTCCTCAGAGACAGGGCACCCCCATGACCGTGCGATGTCAGCACCGGGAAGCCTGCTTTGTCAAGTGCAGCCAGCATATACATCTATGGTAGCCTCCACCCATTTGCCACAGTTGCAGTGTAGGGATGAAGGTGCTGGTAAAGAGCAGCACATAGCAACATCTTCAGTCATGCACCAGCCTTTCCAAGTTACACCAACATCTCCTATAGGGTCTTCCTATCAGTCTATACAAACTAGTATGTATAACGGTCCAACCTGTCTTCCTGTGAATCCTGCCTCTAGTCAAGAATTTGACCCAGTTTTGTTTCAGCAAGATGCAGCTCTTTCTAGTTTAGTAAATCTTGGCTGTCAACCACTGTCACCAATACCATTTCATTCTTCAAATTCAGATGCGACAGGACATCTCTTAGCACATTCACCTCATTCTGTGCAAACCCCACCTCATCTGCAGTCAATGGGATACCATTGTTCAAATGCAGGACAAACAGCTCTTTCTTCTCCAGTGGCAGACCAGATCACAGGTCAGCCTTCTTCTCATTTACAGCCTATTACATATTGTCCTTCACACCCAGGATCTGCTACAGCAGCTTCCCCAGCAGCCTCTCATCCTCTGGCTAGTTCACCGATTTCTGGGCCATCATCCCCTCAGCTGCAGCCTATGCCTTATCAATCTCCTAGCTCAGGAACTGCCTCATCACCATCTCCAACTACCAGAATGCATTCTGGACAGCACTCAACTCAAGCACAAAGTACAGGCCAAGGAGGCCTTTCTGTTCCTTCATCCTTAGTATGTCACAGTTTGTGTGACCCAGCGTCATTTCCGCCTGGTGGTGCAACTGTGAGCATTAAACCTGAACCTGAAGATCAAGAACCTAACTTTGCAACCATTGGTCTACAGGATATCACCTTAGATGATGATGGAAGACCTCATTGGGAGGCTGAAGGAAAAATAATCAGAGAAAAATGTCAAGGGGCTCACATTGTCCTTGAAGTTCCTCCCTATCATAACCCAGCAGTTACATCTGCCGTGCAGGTGCACTTTTATCTTTGCAATGGCAAGAGGAAAAAAAGCCAGTCTCAACGTTTTACTTACACACCAGTTTTGATGAAGCAAGAACAAAGAGAAGACACAGATTTGCCTTCAGTTCCATCTTTGCCTGTGCCTCATTCTGCCCAGGCCCAGAGGCCCTCCTCAGAGACAGGGCACCCCCATGACCGTGCGATGTCAGCACCGGGAAGCCTGCTTTGTCAAGTGCAGCCAGCATATACATCTATGGTAGCCTCCACCCATTTGCCACAGTTGCAGTGTAGGGATGAAGGTGCTGGTAAAGAGCAGCACATAGCAACATCTTCAGTCATGCACCAGCCTTTCCAAGTTACACCAACATCTCCTATAGGGTCTTCCTATCAGTCTATACAAACTAGTATGTATAACGGTCCAACCTGTCTTCCTGTGAATCCTGCCTCTAGTCAAGAATTTGACCCAGTTTTGTTTCAGCAAGATGCAGCTCTTTCTAGTTTAGTAAATCTTGGCTGTCAACCACTGTCACCAATACCATTTCATTCTTCAAATTCAGATGCGACAGGACATCTCTTAGCACATTCACCTCATTCTGTGCAAACCCCACCTCATCTGCAGTCAATGGGATACCATTGTTCAAATGCAGGACAAACAGCTCTTTCTTCTCCAGTGGCAGACCAGATCACAGGTCAGCCTTCTTCTCATTTACAGCCTATTACATATTGTCCTTCACACCCAGGATCTGCTACAGCAGCTTCCCCAGCAGCCTCTCATCCTCTGGCTAGTTCACCGATTTCTGGGCCATCATCCCCTCAGCTGCAGCCTATGCCTTATCAATCTCCTAGCTCAGGAACTGCCTCATCACCATCTCCAACTACCAGAATGCATTCTGGACAGCACTCAACTCAAGCACAAAGTACAGGCCAAGGAGGCCTTTCTGTTCCTTCATCCTTAGTATGTCACAGTTTGTGTGACCCAGCGTCATTTCCGCCTGGTGGTGCAACTGTGAGCATTAAACCTGAACCTGAAGATCAAGAACCTAACTTTGCAACCATTGGTCTACAGGATATCACCTTAGATGAT
Peptide sequence:
MKQEQREDTDLPSVPSLPVPHSAQAQRPSSETGHPHDRAMSAPGSLLCQVQPAYTSMVASTHLPQLQCRDEGAGKEQHIATSSVMHQPFQVTPTSPIGSSYQSIQTSMYNGPTCLPVNPASSQEFDPVLFQQDAALSSLVNLGCQPLSPIPFHSSNSDATGHLLAHSPHSVQTPPHLQSMGYHCSNAGQTALSSPVADQITGQPSSHLQPITYCPSHPGSATAASPAASHPLASSPISGPSSPQLQPMPYQSPSSGTASSPSPTTRMHSGQHSTQAQSTGQGGLSVPSSLVCHSLCDPASFPPGGATVSIKPEPEDQEPNFATIGLQDITLDDDGRPHWEAEGKIIREKCQGAHIVLEVPPYHNPAVTSAVQVHFYLCNGKRKKSQSQRFTYTPVLMKQEQREDTDLPSVPSLPVPHSAQAQRPSSETGHPHDRAMSAPGSLLCQVQPAYTSMVASTHLPQLQCRDEGAGKEQHIATSSVMHQPFQVTPTSPIGSSYQSIQTSMYNGPTCLPVNPASSQEFDPVLFQQDAALSSLVNLGCQPLSPIPFHSSNSDATGHLLAHSPHSVQTPPHLQSMGYHCSNAGQTALSSPVADQITGQPSSHLQPITYCPSHPGSATAASPAASHPLASSPISGPSSPQLQPMPYQSPSSGTASSPSPTTRMHSGQHSTQAQSTGQGGLSVPSSLVCHSLCDPASFPPGGATVSIKPEPEDQEPNFATIGLQDITLDD
IRESfinder result
IRESfinder score
0.75511457
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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