top of page
mmu_circPhf20_1143
Basic information of circular RNA
PanCircBase ID:
mmu_circPhf20_1143
mm39_Chr. Position ID:
chr2|156065254|156115791|+
Gene name:
Phf20
Transcript:
ENSMUST00000037401.10
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
7
Exon/intron indexes:
2,3,4,5,6,7,8
Exon/intron offsets:
0,28441,30891,40946,43820,49207,50348
Genomic length:
50537
Exon/intron sizes in nt:
11,51,72,85,80,38,81,10,000
Flanking exon/introns:
chr2:156038717-156065254|chr2:156115791-156118408
Splice length:
1143
Other database IDs:
CIRCpedia: MMU_CIRCpedia_218404, circAtlas: mmu-Phf20_0033
Human Ortholog IDs:
Mature spliced Sequence:
GAGGATAAAAGCAGCCCTGTTGATGACTGAAAATGACCAAGCACCCACCTAACAGACGAGGAATCAGCTTTGAAGTGGGAGCCCAGTTGGAAGCTCGGGACCGTTTAAAAAACTGGTATCCAGCTCATATTGAAGACATTGACTACGAAGAAGGGAGAGTTCTCATCCATTTCAAGCGTTGGAACCATCGTTACGATGAGTGGTTTTGCTGGGACAGTCCTTATCTGCGCCCTTTAGAGAAGATCCAGCTGAGGAAAGAGGGTTTACATGATGAGGATGGCTCTTCTGAATTTCAAATAAACCAGCAAGTGCTTGCTTGCTGGTCTGACTGTCGATTTTATCCAGCCAGAGTCACTGCTGTGAACAAGGATGGTACTTACACTGTGAAATTTTATGATGGAGTAGTTCAAACTGTCAAACATATTCATGTCAAAGCTTTTTCCAAAGATCAGAATATTGTGGGTAATGCTAGGCCTAAAGAAACAGACCACAAAAGTCTTTCATCGTCTCCTGAGAAACGAGAGAAGTTTAAAGAACAGAGAAAAGTCACGGTCAATGTGAAGAAAGACAAAGTGGAAAAAGCCTTAAAGACAGAAAAGCGGCCCAAGCAACCTGACAAAGAGGGAAAGCTGATCTGCTCAGAAAAAGGCAAAGTGTCAGAGAAAAGCCTTCCTAAGAACGAAAAGGAAGATAAGGAGAACATTTCCGAGAACGAGCGGGAGTACTCCGGGGATGCCCAGGTGGAAAAGAAGCCTGAGAAGGACCTTGTGAAGAACCCACAAGAGAACCTGAAGGAGCCAAAAAGAAAACGAGGCAGACCCCCTTCCATAACTCCTACGGCTGTGGATTCAAACTCTCAAACTTTGCAACCAATAACATTGGAATTGAGAAGACGGAAAATATCAAAACGAAGTGACACCCCATTAAAGCGTCCCAGACTCGACAAAAATTCACCCCAGGAACAGTCAAAAAAACGCTCTGAAAATAGTGACAAAGACTTATCCAGGAGACGGTCCTCCAGGCTGTCCACTAATGGGACCCGTGAGATCCTAGATCCTGACTCGATTGTACCTGATCTGGTTCATACGGTTGATACAAACCCTCTACCAGACAAGTCACCCAGTGCCAAGGATTCTGCTGAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
ACCTGATCTGGTTCATACGGT
58.53
ACTGGGCTCCCACTTCAAAG
59.89
161
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
ACCTGATCTGGTTCATACGGT
58.53
CAACTGGGCTCCCACTTCAA
60.18
163
PCR template sequence:
GAGATCCTAGATCCTGACTCGATTGTACCTGATCTGGTTCATACGGTTGATACAAACCCTCTACCAGACAAGTCACCCAGTGCCAAGGATTCTGCTGAAGGAGGATAAAAGCAGCCCTGTTGATGACTGAAAATGACCAAGCACCCACCTAACAGACGAGGAATCAGCTTTGAAGTGGGAGCCCAGTTGGAAGCTCGGGA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
13
Interacting miRNAs (#binding sites)
mmu-miR-362-5p(2), mmu-miR-23b-3p(1), mmu-miR-27b-3p(1), mmu-miR-27a-3p(1), mmu-miR-7b-5p(1), mmu-miR-34a-5p(1), mmu-miR-203-3p(1), mmu-miR-324-5p(1), mmu-miR-23a-3p(1), mmu-miR-29b-1-5p(1), mmu-miR-96-5p(1), mmu-miR-190b-5p(1), mmu-miR-673-5p(1)
siRNAs for circular RNA silencing
Junction sequence
GATTCTGCTGAAGGAGGATAAAAGCA
siRNA sets
TTTATCCTCCTTCAGCAGA,ATCCTCCTTCAGCAGAATC,CTTTTATCCTCCTTCAGCA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCPHF20_1143_ORF_1
0.9605
0.215529724
0.995704681
1119
ORF sequence:
ATGACCAAGCACCCACCTAACAGACGAGGAATCAGCTTTGAAGTGGGAGCCCAGTTGGAAGCTCGGGACCGTTTAAAAAACTGGTATCCAGCTCATATTGAAGACATTGACTACGAAGAAGGGAGAGTTCTCATCCATTTCAAGCGTTGGAACCATCGTTACGATGAGTGGTTTTGCTGGGACAGTCCTTATCTGCGCCCTTTAGAGAAGATCCAGCTGAGGAAAGAGGGTTTACATGATGAGGATGGCTCTTCTGAATTTCAAATAAACCAGCAAGTGCTTGCTTGCTGGTCTGACTGTCGATTTTATCCAGCCAGAGTCACTGCTGTGAACAAGGATGGTACTTACACTGTGAAATTTTATGATGGAGTAGTTCAAACTGTCAAACATATTCATGTCAAAGCTTTTTCCAAAGATCAGAATATTGTGGGTAATGCTAGGCCTAAAGAAACAGACCACAAAAGTCTTTCATCGTCTCCTGAGAAACGAGAGAAGTTTAAAGAACAGAGAAAAGTCACGGTCAATGTGAAGAAAGACAAAGTGGAAAAAGCCTTAAAGACAGAAAAGCGGCCCAAGCAACCTGACAAAGAGGGAAAGCTGATCTGCTCAGAAAAAGGCAAAGTGTCAGAGAAAAGCCTTCCTAAGAACGAAAAGGAAGATAAGGAGAACATTTCCGAGAACGAGCGGGAGTACTCCGGGGATGCCCAGGTGGAAAAGAAGCCTGAGAAGGACCTTGTGAAGAACCCACAAGAGAACCTGAAGGAGCCAAAAAGAAAACGAGGCAGACCCCCTTCCATAACTCCTACGGCTGTGGATTCAAACTCTCAAACTTTGCAACCAATAACATTGGAATTGAGAAGACGGAAAATATCAAAACGAAGTGACACCCCATTAAAGCGTCCCAGACTCGACAAAAATTCACCCCAGGAACAGTCAAAAAAACGCTCTGAAAATAGTGACAAAGACTTATCCAGGAGACGGTCCTCCAGGCTGTCCACTAATGGGACCCGTGAGATCCTAGATCCTGACTCGATTGTACCTGATCTGGTTCATACGGTTGATACAAACCCTCTACCAGACAAGTCACCCAGTGCCAAGGATTCTGCTGAAGGAGGATAA
Peptide sequence:
MTKHPPNRRGISFEVGAQLEARDRLKNWYPAHIEDIDYEEGRVLIHFKRWNHRYDEWFCWDSPYLRPLEKIQLRKEGLHDEDGSSEFQINQQVLACWSDCRFYPARVTAVNKDGTYTVKFYDGVVQTVKHIHVKAFSKDQNIVGNARPKETDHKSLSSSPEKREKFKEQRKVTVNVKKDKVEKALKTEKRPKQPDKEGKLICSEKGKVSEKSLPKNEKEDKENISENEREYSGDAQVEKKPEKDLVKNPQENLKEPKRKRGRPPSITPTAVDSNSQTLQPITLELRRRKISKRSDTPLKRPRLDKNSPQEQSKKRSENSDKDLSRRRSSRLSTNGTREILDPDSIVPDLVHTVDTNPLPDKSPSAKDSAEGG
IRESfinder result
IRESfinder score
0.518590301
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
bottom of page