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mmu_circAtp2c1_738
Basic information of circular RNA
PanCircBase ID:
mmu_circAtp2c1_738
mm39_Chr. Position ID:
chr9|105312250|105326087|-
Gene name:
Atp2c1
Transcript:
ENSMUST00000177293.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
7
Exon/intron indexes:
12,11,10,9,8,7,6
Exon/intron offsets:
0,4289,7714,7894,10166,11000,13770
Genomic length:
13837
Exon/intron sizes in nt:
157,105,90,96,98,125,67
Flanking exon/introns:
chr9:105310023-105312250|chr9:105326087-105329002
Splice length:
738
Other database IDs:
circAtlas: mmu-Atp2c1_0002
circAtlas: hsa-ATP2C1_0003, CIRCpedia: HSA_CIRCpedia_43545
Human Ortholog IDs:
Mature spliced Sequence:
GTATCATCATGTTGGTTGGCTGGTTACTAGGAAAAGACATTCTGGAAATGTTCACTATTAGTGTAAGCTTGGCTGTAGCTGCAATTCCTGAAGGCCTGCCTATTGTGGTCACGGTGACTCTAGCCCTTGGTGTTATGAGAATGGTGAAGAAAAGGGCTATTGTAAAGAAATTGCCTATTGTGGAAACACTGGGCTGCTGTAATGTGATTTGTTCAGATAAAACTGGAACCCTGACGAAGAACGAGATGACTGTTACTCACATCCTCACTTCCGATGGCCTGCATGCTGAGGTCACTGGAGTTGGCTATAATCAGTTTGGTGAAGTGATCGTTGATGGTGATGTTGTTCATGGATTTTATAACCCAGCTGTTAGCAGAATTGTTGAGGCAGGCTGTGTGTGCAATGATGCTGTAATTAGGAACAACACTCTGATGGGAAAGCCAACTGAAGGAGCCTTAATCGCTCTTGCTATGAAGATGGGTCTTGATGGACTGCAACAAGACTACATCAGGAAAGCTGAATACCCTTTTAGTTCTGAGCAGAAGTGGATGGCTGTTAAGTGTGTGCACCGAACACAGCAGGACAGACCAGAGATTTGTTTTATGAAGGGTGCTTATGAGCAGGTGATTAAGTATTGTACTACATACAACAGCAAAGGGCAGACTTTGGCACTTACCCAGCAGCAGAGAGATTTGTATCAACAAGAGAAGGCACGGATGGGCTCAGCGGGACTCAGAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
ACTTTGGCACTTACCCAGCA
59.82
AGGAATTGCAGCTACAGCCA
59.67
165
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
ACTTTGGCACTTACCCAGCA
59.82
AATTGCAGCTACAGCCAAGC
59.47
162
PCR template sequence:
ACTACATACAACAGCAAAGGGCAGACTTTGGCACTTACCCAGCAGCAGAGAGATTTGTATCAACAAGAGAAGGCACGGATGGGCTCAGCGGGACTCAGAGGTATCATCATGTTGGTTGGCTGGTTACTAGGAAAAGACATTCTGGAAATGTTCACTATTAGTGTAAGCTTGGCTGTAGCTGCAATTCCTGAAGGCCTGCC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
11
Interacting miRNAs (#binding sites)
mmu-miR-7a-1-3p(2), mmu-miR-9-5p(1), mmu-miR-199a-5p(1), mmu-miR-92a-3p(1), mmu-miR-335-5p(1), mmu-miR-194-5p(1), mmu-miR-297a-5p(1), mmu-miR-384-3p(1), mmu-miR-1199-5p(1), mmu-miR-1904(1), mmu-miR-323-3p(1)
siRNAs for circular RNA silencing
Junction sequence
GCGGGACTCAGAGGTATCATCATGTT
siRNA sets
ATGATGATACCTCTGAGTC,TGATACCTCTGAGTCCCGC,TGATGATACCTCTGAGTCC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCATP2C1_738_ORF_1
1.154
0.118009588
0.999642951
1467
ORF sequence:
ATGTTGGTTGGCTGGTTACTAGGAAAAGACATTCTGGAAATGTTCACTATTAGTGTAAGCTTGGCTGTAGCTGCAATTCCTGAAGGCCTGCCTATTGTGGTCACGGTGACTCTAGCCCTTGGTGTTATGAGAATGGTGAAGAAAAGGGCTATTGTAAAGAAATTGCCTATTGTGGAAACACTGGGCTGCTGTAATGTGATTTGTTCAGATAAAACTGGAACCCTGACGAAGAACGAGATGACTGTTACTCACATCCTCACTTCCGATGGCCTGCATGCTGAGGTCACTGGAGTTGGCTATAATCAGTTTGGTGAAGTGATCGTTGATGGTGATGTTGTTCATGGATTTTATAACCCAGCTGTTAGCAGAATTGTTGAGGCAGGCTGTGTGTGCAATGATGCTGTAATTAGGAACAACACTCTGATGGGAAAGCCAACTGAAGGAGCCTTAATCGCTCTTGCTATGAAGATGGGTCTTGATGGACTGCAACAAGACTACATCAGGAAAGCTGAATACCCTTTTAGTTCTGAGCAGAAGTGGATGGCTGTTAAGTGTGTGCACCGAACACAGCAGGACAGACCAGAGATTTGTTTTATGAAGGGTGCTTATGAGCAGGTGATTAAGTATTGTACTACATACAACAGCAAAGGGCAGACTTTGGCACTTACCCAGCAGCAGAGAGATTTGTATCAACAAGAGAAGGCACGGATGGGCTCAGCGGGACTCAGAGGTATCATCATGTTGGTTGGCTGGTTACTAGGAAAAGACATTCTGGAAATGTTCACTATTAGTGTAAGCTTGGCTGTAGCTGCAATTCCTGAAGGCCTGCCTATTGTGGTCACGGTGACTCTAGCCCTTGGTGTTATGAGAATGGTGAAGAAAAGGGCTATTGTAAAGAAATTGCCTATTGTGGAAACACTGGGCTGCTGTAATGTGATTTGTTCAGATAAAACTGGAACCCTGACGAAGAACGAGATGACTGTTACTCACATCCTCACTTCCGATGGCCTGCATGCTGAGGTCACTGGAGTTGGCTATAATCAGTTTGGTGAAGTGATCGTTGATGGTGATGTTGTTCATGGATTTTATAACCCAGCTGTTAGCAGAATTGTTGAGGCAGGCTGTGTGTGCAATGATGCTGTAATTAGGAACAACACTCTGATGGGAAAGCCAACTGAAGGAGCCTTAATCGCTCTTGCTATGAAGATGGGTCTTGATGGACTGCAACAAGACTACATCAGGAAAGCTGAATACCCTTTTAGTTCTGAGCAGAAGTGGATGGCTGTTAAGTGTGTGCACCGAACACAGCAGGACAGACCAGAGATTTGTTTTATGAAGGGTGCTTATGAGCAGGTGATTAAGTATTGTACTACATACAACAGCAAAGGGCAGACTTTGGCACTTACCCAGCAGCAGAGAGATTTGTATCAACAAGAGAAGGCACGGATGGGCTCAGCGGGACTCAGA
Peptide sequence:
MLVGWLLGKDILEMFTISVSLAVAAIPEGLPIVVTVTLALGVMRMVKKRAIVKKLPIVETLGCCNVICSDKTGTLTKNEMTVTHILTSDGLHAEVTGVGYNQFGEVIVDGDVVHGFYNPAVSRIVEAGCVCNDAVIRNNTLMGKPTEGALIALAMKMGLDGLQQDYIRKAEYPFSSEQKWMAVKCVHRTQQDRPEICFMKGAYEQVIKYCTTYNSKGQTLALTQQQRDLYQQEKARMGSAGLRGIIMLVGWLLGKDILEMFTISVSLAVAAIPEGLPIVVTVTLALGVMRMVKKRAIVKKLPIVETLGCCNVICSDKTGTLTKNEMTVTHILTSDGLHAEVTGVGYNQFGEVIVDGDVVHGFYNPAVSRIVEAGCVCNDAVIRNNTLMGKPTEGALIALAMKMGLDGLQQDYIRKAEYPFSSEQKWMAVKCVHRTQQDRPEICFMKGAYEQVIKYCTTYNSKGQTLALTQQQRDLYQQEKARMGSAGLR
IRESfinder result
IRESfinder score
0.44682467
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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