top of page
mmu_circCacna2d3_538
Basic information of circular RNA
PanCircBase ID:
mmu_circCacna2d3_538
mm39_Chr. Position ID:
chr14|28665513|28704330|-
Gene name:
Cacna2d3
Transcript:
ENSMUST00000022567.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
8
Exon/intron indexes:
35,34,33,32,31,30,29,28
Exon/intron offsets:
0,8685,10324,13235,25601,28659,37600,38755
Genomic length:
38817
Exon/intron sizes in nt:
112,56,53,76,71,63,45,62
Flanking exon/introns:
chr14:28630355-28665513|chr14:28704330-28765457
Splice length:
538
Other database IDs:
CIRCpedia: MMU_CIRCpedia_15328, circAtlas: mmu-Cac2d3_0003
circBase: hsa_circ_0124248, circAtlas: hsa-CAC2D3_0005, CIRCpedia: HSA_CIRCpedia_138368
Human Ortholog IDs:
Mature spliced Sequence:
CTGTAGGCATTCAGATGAAACTTGAATTCTTCCAAAGGAAGTTCTGGACTGCCAGCAGACAGTGTGCCTCCCTGGATGGCAAATGCTCCATAAGCTGCGATGACGAGACTGTGAACTGTTACCTTATAGACAATAACGGATTCATTCTGGTGTCTGAAGACTACACACAGACTGGAGATTTTTTTGGTGAGGTGGAAGGAGCTGTCATGAACAAGTTGTTAACAATGGGTTCCTTTAAAAGAATAACCTTGTACGACTACCAAGCCATGTGTAGAGCCAACAAGGAGAGCAGTGACAGTGCCCATGGACTTCTGGACCCCTATAAGGCCTTTCTCTCTGCAGCCAAGTGGATAATGACGGAACTTGTCTTGTTCCTGGTGGAGTTTAACCTGTGCAGTTGGTGGCACTCCGACATGACAGCTAAAGCCCAGAAACTGAAACAGACCCTGGAACCTTGTGATACTGAATACCCAGCCTTTGTTTCTGAACGCACCATCAAGGAGACCACAGGGAACATTGCTTGCGAAGACTGCTCCAA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AACGCACCATCAAGGAGACC
60.32
GAGCATTTGCCATCCAGGGA
60.4
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AACGCACCATCAAGGAGACC
60.32
TGGAGCATTTGCCATCCAGG
60.69
142
PCR template sequence:
AACAGACCCTGGAACCTTGTGATACTGAATACCCAGCCTTTGTTTCTGAACGCACCATCAAGGAGACCACAGGGAACATTGCTTGCGAAGACTGCTCCAACTGTAGGCATTCAGATGAAACTTGAATTCTTCCAAAGGAAGTTCTGGACTGCCAGCAGACAGTGTGCCTCCCTGGATGGCAAATGCTCCATAAGCTGCGA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
2
Interacting miRNAs (#binding sites)
mmu-miR-135a-5p(1), mmu-miR-452-3p(1)
siRNAs for circular RNA silencing
Junction sequence
AAGACTGCTCCAACTGTAGGCATTCA
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCCACNA2D3_538_ORF_1
0.9064
0.198881329
0.767135906
549
ORF sequence:
ATGAAACTTGAATTCTTCCAAAGGAAGTTCTGGACTGCCAGCAGACAGTGTGCCTCCCTGGATGGCAAATGCTCCATAAGCTGCGATGACGAGACTGTGAACTGTTACCTTATAGACAATAACGGATTCATTCTGGTGTCTGAAGACTACACACAGACTGGAGATTTTTTTGGTGAGGTGGAAGGAGCTGTCATGAACAAGTTGTTAACAATGGGTTCCTTTAAAAGAATAACCTTGTACGACTACCAAGCCATGTGTAGAGCCAACAAGGAGAGCAGTGACAGTGCCCATGGACTTCTGGACCCCTATAAGGCCTTTCTCTCTGCAGCCAAGTGGATAATGACGGAACTTGTCTTGTTCCTGGTGGAGTTTAACCTGTGCAGTTGGTGGCACTCCGACATGACAGCTAAAGCCCAGAAACTGAAACAGACCCTGGAACCTTGTGATACTGAATACCCAGCCTTTGTTTCTGAACGCACCATCAAGGAGACCACAGGGAACATTGCTTGCGAAGACTGCTCCAACTGTAGGCATTCAGATGAAACTTGA
Peptide sequence:
MKLEFFQRKFWTASRQCASLDGKCSISCDDETVNCYLIDNNGFILVSEDYTQTGDFFGEVEGAVMNKLLTMGSFKRITLYDYQAMCRANKESSDSAHGLLDPYKAFLSAAKWIMTELVLFLVEFNLCSWWHSDMTAKAQKLKQTLEPCDTEYPAFVSERTIKETTGNIACEDCSNCRHSDET
IRESfinder result
IRESfinder score
0.537928208
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
bottom of page