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mmu_circPrkar1a_360
Basic information of circular RNA
PanCircBase ID:
mmu_circPrkar1a_360
mm39_Chr. Position ID:
chr11|109551860|109553933|+
Gene name:
Prkar1a
Transcript:
ENSMUST00000106677.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
5,6,7,8
Exon/intron offsets:
0,253,1241,1914
Genomic length:
2073
Exon/intron sizes in nt:
92,62,47,159
Flanking exon/introns:
chr11:109550995-109551860|chr11:109553933-109555584
Splice length:
360
Other database IDs:
circAtlas: mmu-Prkar1a_0029
Human Ortholog IDs:
Mature spliced Sequence:
GTTATTCCAAAAGATTATAAGACAATGGCTGCTTTAGCCAAGGCCATCGAAAAGAATGTGCTGTTTTCACACCTTGATGATAACGAGAGAAGTGACATTTTTGATGCTATGTTTCCAGTCTCCTTTATTGCTGGAGAGACGGTTATTCAGCAAGGTGATGAAGGGGATAACTTCTATGTGATTGATCAAGGAGAAATGGATGTCTATGTCAATAATGAATGGGCAACCAGTGTTGGGGAAGGAGGGAGCTTTGGAGAGCTGGCTTTGATTTATGGAACACCCAGAGCAGCCACTGTCAAAGCAAAGACAAACGTGAAACTGTGGGGCATCGACCGAGACAGCTACCGAAGAATCCTCATG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GAACACCCAGAGCAGCCAC
60.97
TCTTTTCGATGGCCTTGGCT
59.96
141
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CCAGAGCAGCCACTGTCAAA
60.54
GCACATTCTTTTCGATGGCCT
59.53
141
PCR template sequence:
GGCTTTGATTTATGGAACACCCAGAGCAGCCACTGTCAAAGCAAAGACAAACGTGAAACTGTGGGGCATCGACCGAGACAGCTACCGAAGAATCCTCATGGTTATTCCAAAAGATTATAAGACAATGGCTGCTTTAGCCAAGGCCATCGAAAAGAATGTGCTGTTTTCACACCTTGATGATAACGAGAGAAGTGACATTT
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-494-3p(1), mmu-miR-181d-5p(1)
siRNAs for circular RNA silencing
Junction sequence
AAGAATCCTCATGGTTATTCCAAAAG
siRNA sets
TTTTGGAATAACCATGAGG, TTTGGAATAACCATGAGGA, TTGGAATAACCATGAGGAT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCPRKAR1A_360_ORF_1
1.1163
0.276257468
0.951109149
696
ORF sequence:
ATGGCTGCTTTAGCCAAGGCCATCGAAAAGAATGTGCTGTTTTCACACCTTGATGATAACGAGAGAAGTGACATTTTTGATGCTATGTTTCCAGTCTCCTTTATTGCTGGAGAGACGGTTATTCAGCAAGGTGATGAAGGGGATAACTTCTATGTGATTGATCAAGGAGAAATGGATGTCTATGTCAATAATGAATGGGCAACCAGTGTTGGGGAAGGAGGGAGCTTTGGAGAGCTGGCTTTGATTTATGGAACACCCAGAGCAGCCACTGTCAAAGCAAAGACAAACGTGAAACTGTGGGGCATCGACCGAGACAGCTACCGAAGAATCCTCATGGTTATTCCAAAAGATTATAAGACAATGGCTGCTTTAGCCAAGGCCATCGAAAAGAATGTGCTGTTTTCACACCTTGATGATAACGAGAGAAGTGACATTTTTGATGCTATGTTTCCAGTCTCCTTTATTGCTGGAGAGACGGTTATTCAGCAAGGTGATGAAGGGGATAACTTCTATGTGATTGATCAAGGAGAAATGGATGTCTATGTCAATAATGAATGGGCAACCAGTGTTGGGGAAGGAGGGAGCTTTGGAGAGCTGGCTTTGATTTATGGAACACCCAGAGCAGCCACTGTCAAAGCAAAGACAAACGTGAAACTGTGGGGCATCGACCGAGACAGCTACCGAAGAATCCTCATG
Peptide sequence:
MAALAKAIEKNVLFSHLDDNERSDIFDAMFPVSFIAGETVIQQGDEGDNFYVIDQGEMDVYVNNEWATSVGEGGSFGELALIYGTPRAATVKAKTNVKLWGIDRDSYRRILMVIPKDYKTMAALAKAIEKNVLFSHLDDNERSDIFDAMFPVSFIAGETVIQQGDEGDNFYVIDQGEMDVYVNNEWATSVGEGGSFGELALIYGTPRAATVKAKTNVKLWGIDRDSYRRILM
IRESfinder result
IRESfinder score
0.489066299
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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