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mmu_circPrpf40a_783
Basic information of circular RNA
PanCircBase ID:
mmu_circPrpf40a_783
mm39_Chr. Position ID:
chr2|53043975|53050898|-
Gene name:
Prpf40a
Transcript:
ENSMUST00000076313.14
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
6
Exon/intron indexes:
11,10,9,8,7,6
Exon/intron offsets:
0,2659,3929,5299,5594,6812
Genomic length:
6923
Exon/intron sizes in nt:
1,09,36,32,55,41,21,110
Flanking exon/introns:
chr2:53043540-53043975|chr2:53050898-53065027
Splice length:
783
Other database IDs:
CIRCpedia: MMU_CIRCpedia_222929, circAtlas: mmu-Prpf40a_0003
circAtlas: hsa-SCAF8_0001
Human Ortholog IDs:
Mature spliced Sequence:
AAATCAATGTGGACAGAACATAAATCACCTGATGGAAGGACTTATTATTACAATACTGAAACAAAACAGTCTACCTGGGAAAAGCCAGATGATCTTAAAACACCTGCTGAGCAACTATTGTCTAAATGCCCATGGAAAGAGTACAAATCTGATTCCGGGAAGCCTTATTACTATAATTCTCAAACAAAGGAGTCCCGCTGGGCCAAACCTAAGGAACTTGAAGATCTTGAAGGATACCAGAATACCATTGTTGCTGGAGGTCTTATTACAAAATCAAACCTGCATGCCATGATCAAAGCTGAAGAAAGCAGCAAGCAAGAAGAATGTACTACAGCATCAACAGCCCCAGTTCCTACAACAGAAATTCCTACCACTATGAGCACCATGGCTGCTGCAGAAGCAGCGGCTGCTGTTGTTGCAGCTGCTGCAGCTGCTGCAGCAGCAGCTAATGCCAATACTTCCACCACACCTACTAATACTGTGGGAAGTGTTCCAGTTGCTCCTGAACCTGAGGTTACTTCCATTGTTGCTACTGCTGTAGATAATGAAAATACAGTAACTGTATCAACTGAAGAGCAAGCACAGCTTGCTAATACCACAGCTATTCAAGATCTCAGTGGTGATATATCCAGTAACACTGGAGAGGAACCAGCTAAACAAGAAACTGTCTCCGATTTTACTCCTAAAAAAGAAGAGGAAGAGAGCCAACCAGCAAAAAAAACATATACTTGGAATACAAAGGAGGAGGCAAAGCAAGCATTTAAAGAATTATTGAAAGAAAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GGAAGAGAGCCAACCAGCAA
60.25
GGCTTTTCCCAGGTAGACTGT
59.65
174
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GAGGAAGAGAGCCAACCAGC
60.39
GGCTTTTCCCAGGTAGACTGT
59.65
176
PCR template sequence:
TAAAAAAGAAGAGGAAGAGAGCCAACCAGCAAAAAAAACATATACTTGGAATACAAAGGAGGAGGCAAAGCAAGCATTTAAAGAATTATTGAAAGAAAAGAAATCAATGTGGACAGAACATAAATCACCTGATGGAAGGACTTATTATTACAATACTGAAACAAAACAGTCTACCTGGGAAAAGCCAGATGATCTTAAAA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
4
Interacting miRNAs (#binding sites)
mmu-miR-218-5p(1), mmu-miR-499-5p(1), mmu-miR-129-5p(1), mmu-miR-335-3p(1)
siRNAs for circular RNA silencing
Junction sequence
ATTGAAAGAAAAGAAATCAATGTGGA
siRNA sets
CATTGATTTCTTTTCTTTC, ATTGATTTCTTTTCTTTCA, TTGATTTCTTTTCTTTCAA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCPRPF40A_783_ORF_1
1.0226
0.08050618
0.999727771
1560
ORF sequence:
ATGTGGACAGAACATAAATCACCTGATGGAAGGACTTATTATTACAATACTGAAACAAAACAGTCTACCTGGGAAAAGCCAGATGATCTTAAAACACCTGCTGAGCAACTATTGTCTAAATGCCCATGGAAAGAGTACAAATCTGATTCCGGGAAGCCTTATTACTATAATTCTCAAACAAAGGAGTCCCGCTGGGCCAAACCTAAGGAACTTGAAGATCTTGAAGGATACCAGAATACCATTGTTGCTGGAGGTCTTATTACAAAATCAAACCTGCATGCCATGATCAAAGCTGAAGAAAGCAGCAAGCAAGAAGAATGTACTACAGCATCAACAGCCCCAGTTCCTACAACAGAAATTCCTACCACTATGAGCACCATGGCTGCTGCAGAAGCAGCGGCTGCTGTTGTTGCAGCTGCTGCAGCTGCTGCAGCAGCAGCTAATGCCAATACTTCCACCACACCTACTAATACTGTGGGAAGTGTTCCAGTTGCTCCTGAACCTGAGGTTACTTCCATTGTTGCTACTGCTGTAGATAATGAAAATACAGTAACTGTATCAACTGAAGAGCAAGCACAGCTTGCTAATACCACAGCTATTCAAGATCTCAGTGGTGATATATCCAGTAACACTGGAGAGGAACCAGCTAAACAAGAAACTGTCTCCGATTTTACTCCTAAAAAAGAAGAGGAAGAGAGCCAACCAGCAAAAAAAACATATACTTGGAATACAAAGGAGGAGGCAAAGCAAGCATTTAAAGAATTATTGAAAGAAAAGAAATCAATGTGGACAGAACATAAATCACCTGATGGAAGGACTTATTATTACAATACTGAAACAAAACAGTCTACCTGGGAAAAGCCAGATGATCTTAAAACACCTGCTGAGCAACTATTGTCTAAATGCCCATGGAAAGAGTACAAATCTGATTCCGGGAAGCCTTATTACTATAATTCTCAAACAAAGGAGTCCCGCTGGGCCAAACCTAAGGAACTTGAAGATCTTGAAGGATACCAGAATACCATTGTTGCTGGAGGTCTTATTACAAAATCAAACCTGCATGCCATGATCAAAGCTGAAGAAAGCAGCAAGCAAGAAGAATGTACTACAGCATCAACAGCCCCAGTTCCTACAACAGAAATTCCTACCACTATGAGCACCATGGCTGCTGCAGAAGCAGCGGCTGCTGTTGTTGCAGCTGCTGCAGCTGCTGCAGCAGCAGCTAATGCCAATACTTCCACCACACCTACTAATACTGTGGGAAGTGTTCCAGTTGCTCCTGAACCTGAGGTTACTTCCATTGTTGCTACTGCTGTAGATAATGAAAATACAGTAACTGTATCAACTGAAGAGCAAGCACAGCTTGCTAATACCACAGCTATTCAAGATCTCAGTGGTGATATATCCAGTAACACTGGAGAGGAACCAGCTAAACAAGAAACTGTCTCCGATTTTACTCCTAAAAAAGAAGAGGAAGAGAGCCAACCAGCAAAAAAAACATATACTTGGAATACAAAGGAGGAGGCAAAGCAAGCATTTAAAGAATTATTGAAAGAAAAG
Peptide sequence:
MWTEHKSPDGRTYYYNTETKQSTWEKPDDLKTPAEQLLSKCPWKEYKSDSGKPYYYNSQTKESRWAKPKELEDLEGYQNTIVAGGLITKSNLHAMIKAEESSKQEECTTASTAPVPTTEIPTTMSTMAAAEAAAAVVAAAAAAAAAANANTSTTPTNTVGSVPVAPEPEVTSIVATAVDNENTVTVSTEEQAQLANTTAIQDLSGDISSNTGEEPAKQETVSDFTPKKEEEESQPAKKTYTWNTKEEAKQAFKELLKEKKSMWTEHKSPDGRTYYYNTETKQSTWEKPDDLKTPAEQLLSKCPWKEYKSDSGKPYYYNSQTKESRWAKPKELEDLEGYQNTIVAGGLITKSNLHAMIKAEESSKQEECTTASTAPVPTTEIPTTMSTMAAAEAAAAVVAAAAAAAAAANANTSTTPTNTVGSVPVAPEPEVTSIVATAVDNENTVTVSTEEQAQLANTTAIQDLSGDISSNTGEEPAKQETVSDFTPKKEEEESQPAKKTYTWNTKEEAKQAFKELLKEK
IRESfinder result
IRESfinder score
0.500670406
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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