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mmu_circPrpf40a_1122
Basic information of circular RNA
PanCircBase ID:
mmu_circPrpf40a_1122
mm39_Chr. Position ID:
chr2|53042457|53050898|-
Gene name:
Prpf40a
Transcript:
ENSMUST00000076313.14
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
9
Exon/intron indexes:
14,13,12,11,10,9,8,7,6
Exon/intron offsets:
0,512,1018,1518,4177,5447,6817,7112,8330
Genomic length:
8441
Exon/intron sizes in nt:
1,09,16,56,51,09,36,32,00,00,00,000
Flanking exon/introns:
chr2:53041841-53042457|chr2:53050898-53065027
Splice length:
1122
Other database IDs:
circAtlas: mmu-Prpf40a_0022
circBase: hsa_circ_0056749
Human Ortholog IDs:
Mature spliced Sequence:
AAATCAATGTGGACAGAACATAAATCACCTGATGGAAGGACTTATTATTACAATACTGAAACAAAACAGTCTACCTGGGAAAAGCCAGATGATCTTAAAACACCTGCTGAGCAACTATTGTCTAAATGCCCATGGAAAGAGTACAAATCTGATTCCGGGAAGCCTTATTACTATAATTCTCAAACAAAGGAGTCCCGCTGGGCCAAACCTAAGGAACTTGAAGATCTTGAAGGATACCAGAATACCATTGTTGCTGGAGGTCTTATTACAAAATCAAACCTGCATGCCATGATCAAAGCTGAAGAAAGCAGCAAGCAAGAAGAATGTACTACAGCATCAACAGCCCCAGTTCCTACAACAGAAATTCCTACCACTATGAGCACCATGGCTGCTGCAGAAGCAGCGGCTGCTGTTGTTGCAGCTGCTGCAGCTGCTGCAGCAGCAGCTAATGCCAATACTTCCACCACACCTACTAATACTGTGGGAAGTGTTCCAGTTGCTCCTGAACCTGAGGTTACTTCCATTGTTGCTACTGCTGTAGATAATGAAAATACAGTAACTGTATCAACTGAAGAGCAAGCACAGCTTGCTAATACCACAGCTATTCAAGATCTCAGTGGTGATATATCCAGTAACACTGGAGAGGAACCAGCTAAACAAGAAACTGTCTCCGATTTTACTCCTAAAAAAGAAGAGGAAGAGAGCCAACCAGCAAAAAAAACATATACTTGGAATACAAAGGAGGAGGCAAAGCAAGCATTTAAAGAATTATTGAAAGAAAAGCGGGTGCCCTCCAATGCTTCATGGGAGCAGGCTATGAAAATGATCATAAATGATCCTCGGTACAGTGCTTTAGCAAAGCTGAGTGAGAAAAAGCAGGCCTTTAATGCCTATAAAGTCCAGACGGAGAAAGAGGAAAAAGAAGAAGCAAGATCAAAATACAAAGAAGCTAAGGAATCTTTTCAGCGTTTTCTTGAAAATCATGAGAAAATGACTTCCACAACCAGATACAAAAAAGCTGAGCAAATGTTTGGGGAGATGGAAGTTTGGAATGCAATTTCAGAGCGTGATCGTCTAGAAATCTATGAAGATGTTTTGTTCTTCCTTTCAAAGAAAGAAAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TGCAATTTCAGAGCGTGATCG
59.61
GGCTTTTCCCAGGTAGACTGT
59.65
156
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GCAATTTCAGAGCGTGATCGT
59.61
GGCTTTTCCCAGGTAGACTGT
59.65
155
PCR template sequence:
GCAAATGTTTGGGGAGATGGAAGTTTGGAATGCAATTTCAGAGCGTGATCGTCTAGAAATCTATGAAGATGTTTTGTTCTTCCTTTCAAAGAAAGAAAAGAAATCAATGTGGACAGAACATAAATCACCTGATGGAAGGACTTATTATTACAATACTGAAACAAAACAGTCTACCTGGGAAAAGCCAGATGATCTTAAAA
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-335-3p(2), mmu-miR-218-5p(1), mmu-miR-499-5p(1), mmu-miR-129-5p(1)
siRNAs for circular RNA silencing
Junction sequence
AAAGAAAGAAAAGAAATCAATGTGGA
siRNA sets
CATTGATTTCTTTTCTTTC, ATTGATTTCTTTTCTTTCT, TTGATTTCTTTTCTTTCTT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCPRPF40A_1122_ORF_1
1.0186
0.110743743
0.999998152
2238
ORF sequence:
ATGTGGACAGAACATAAATCACCTGATGGAAGGACTTATTATTACAATACTGAAACAAAACAGTCTACCTGGGAAAAGCCAGATGATCTTAAAACACCTGCTGAGCAACTATTGTCTAAATGCCCATGGAAAGAGTACAAATCTGATTCCGGGAAGCCTTATTACTATAATTCTCAAACAAAGGAGTCCCGCTGGGCCAAACCTAAGGAACTTGAAGATCTTGAAGGATACCAGAATACCATTGTTGCTGGAGGTCTTATTACAAAATCAAACCTGCATGCCATGATCAAAGCTGAAGAAAGCAGCAAGCAAGAAGAATGTACTACAGCATCAACAGCCCCAGTTCCTACAACAGAAATTCCTACCACTATGAGCACCATGGCTGCTGCAGAAGCAGCGGCTGCTGTTGTTGCAGCTGCTGCAGCTGCTGCAGCAGCAGCTAATGCCAATACTTCCACCACACCTACTAATACTGTGGGAAGTGTTCCAGTTGCTCCTGAACCTGAGGTTACTTCCATTGTTGCTACTGCTGTAGATAATGAAAATACAGTAACTGTATCAACTGAAGAGCAAGCACAGCTTGCTAATACCACAGCTATTCAAGATCTCAGTGGTGATATATCCAGTAACACTGGAGAGGAACCAGCTAAACAAGAAACTGTCTCCGATTTTACTCCTAAAAAAGAAGAGGAAGAGAGCCAACCAGCAAAAAAAACATATACTTGGAATACAAAGGAGGAGGCAAAGCAAGCATTTAAAGAATTATTGAAAGAAAAGCGGGTGCCCTCCAATGCTTCATGGGAGCAGGCTATGAAAATGATCATAAATGATCCTCGGTACAGTGCTTTAGCAAAGCTGAGTGAGAAAAAGCAGGCCTTTAATGCCTATAAAGTCCAGACGGAGAAAGAGGAAAAAGAAGAAGCAAGATCAAAATACAAAGAAGCTAAGGAATCTTTTCAGCGTTTTCTTGAAAATCATGAGAAAATGACTTCCACAACCAGATACAAAAAAGCTGAGCAAATGTTTGGGGAGATGGAAGTTTGGAATGCAATTTCAGAGCGTGATCGTCTAGAAATCTATGAAGATGTTTTGTTCTTCCTTTCAAAGAAAGAAAAGAAATCAATGTGGACAGAACATAAATCACCTGATGGAAGGACTTATTATTACAATACTGAAACAAAACAGTCTACCTGGGAAAAGCCAGATGATCTTAAAACACCTGCTGAGCAACTATTGTCTAAATGCCCATGGAAAGAGTACAAATCTGATTCCGGGAAGCCTTATTACTATAATTCTCAAACAAAGGAGTCCCGCTGGGCCAAACCTAAGGAACTTGAAGATCTTGAAGGATACCAGAATACCATTGTTGCTGGAGGTCTTATTACAAAATCAAACCTGCATGCCATGATCAAAGCTGAAGAAAGCAGCAAGCAAGAAGAATGTACTACAGCATCAACAGCCCCAGTTCCTACAACAGAAATTCCTACCACTATGAGCACCATGGCTGCTGCAGAAGCAGCGGCTGCTGTTGTTGCAGCTGCTGCAGCTGCTGCAGCAGCAGCTAATGCCAATACTTCCACCACACCTACTAATACTGTGGGAAGTGTTCCAGTTGCTCCTGAACCTGAGGTTACTTCCATTGTTGCTACTGCTGTAGATAATGAAAATACAGTAACTGTATCAACTGAAGAGCAAGCACAGCTTGCTAATACCACAGCTATTCAAGATCTCAGTGGTGATATATCCAGTAACACTGGAGAGGAACCAGCTAAACAAGAAACTGTCTCCGATTTTACTCCTAAAAAAGAAGAGGAAGAGAGCCAACCAGCAAAAAAAACATATACTTGGAATACAAAGGAGGAGGCAAAGCAAGCATTTAAAGAATTATTGAAAGAAAAGCGGGTGCCCTCCAATGCTTCATGGGAGCAGGCTATGAAAATGATCATAAATGATCCTCGGTACAGTGCTTTAGCAAAGCTGAGTGAGAAAAAGCAGGCCTTTAATGCCTATAAAGTCCAGACGGAGAAAGAGGAAAAAGAAGAAGCAAGATCAAAATACAAAGAAGCTAAGGAATCTTTTCAGCGTTTTCTTGAAAATCATGAGAAAATGACTTCCACAACCAGATACAAAAAAGCTGAGCAAATGTTTGGGGAGATGGAAGTTTGGAATGCAATTTCAGAGCGTGATCGTCTAGAAATCTATGAAGATGTTTTGTTCTTCCTTTCAAAGAAAGAAAAG
Peptide sequence:
MWTEHKSPDGRTYYYNTETKQSTWEKPDDLKTPAEQLLSKCPWKEYKSDSGKPYYYNSQTKESRWAKPKELEDLEGYQNTIVAGGLITKSNLHAMIKAEESSKQEECTTASTAPVPTTEIPTTMSTMAAAEAAAAVVAAAAAAAAAANANTSTTPTNTVGSVPVAPEPEVTSIVATAVDNENTVTVSTEEQAQLANTTAIQDLSGDISSNTGEEPAKQETVSDFTPKKEEEESQPAKKTYTWNTKEEAKQAFKELLKEKRVPSNASWEQAMKMIINDPRYSALAKLSEKKQAFNAYKVQTEKEEKEEARSKYKEAKESFQRFLENHEKMTSTTRYKKAEQMFGEMEVWNAISERDRLEIYEDVLFFLSKKEKKSMWTEHKSPDGRTYYYNTETKQSTWEKPDDLKTPAEQLLSKCPWKEYKSDSGKPYYYNSQTKESRWAKPKELEDLEGYQNTIVAGGLITKSNLHAMIKAEESSKQEECTTASTAPVPTTEIPTTMSTMAAAEAAAAVVAAAAAAAAAANANTSTTPTNTVGSVPVAPEPEVTSIVATAVDNENTVTVSTEEQAQLANTTAIQDLSGDISSNTGEEPAKQETVSDFTPKKEEEESQPAKKTYTWNTKEEAKQAFKELLKEKRVPSNASWEQAMKMIINDPRYSALAKLSEKKQAFNAYKVQTEKEEKEEARSKYKEAKESFQRFLENHEKMTSTTRYKKAEQMFGEMEVWNAISERDRLEIYEDVLFFLSKKEK
IRESfinder result
IRESfinder score
0.503674069
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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