top of page
mmu_circPhf20_2341
Basic information of circular RNA
PanCircBase ID:
mmu_circPhf20_2341
mm39_Chr. Position ID:
chr2|156065254|156140636|+
Gene name:
Phf20
Transcript:
ENSMUST00000037401.10
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
14
Exon/intron indexes:
2,3,4,5,6,7,8,9,10,11,12,13,14,15
Exon/intron offsets:
0,28441,30891,40946,43820,49207,50348,53154,64466,69131,70079,70762,73314,75186
Genomic length:
75382
Exon/intron sizes in nt:
11,51,72,85,80,38,81,10,00,00,00,00,00,00,00,00,00,00,000
Flanking exon/introns:
chr2:156038717-156065254|chr2:156140636-156144702
Splice length:
2341
Other database IDs:
circAtlas: mmu-Phf20_0024
circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_33977
Human Ortholog IDs:
Mature spliced Sequence:
GAGGATAAAAGCAGCCCTGTTGATGACTGAAAATGACCAAGCACCCACCTAACAGACGAGGAATCAGCTTTGAAGTGGGAGCCCAGTTGGAAGCTCGGGACCGTTTAAAAAACTGGTATCCAGCTCATATTGAAGACATTGACTACGAAGAAGGGAGAGTTCTCATCCATTTCAAGCGTTGGAACCATCGTTACGATGAGTGGTTTTGCTGGGACAGTCCTTATCTGCGCCCTTTAGAGAAGATCCAGCTGAGGAAAGAGGGTTTACATGATGAGGATGGCTCTTCTGAATTTCAAATAAACCAGCAAGTGCTTGCTTGCTGGTCTGACTGTCGATTTTATCCAGCCAGAGTCACTGCTGTGAACAAGGATGGTACTTACACTGTGAAATTTTATGATGGAGTAGTTCAAACTGTCAAACATATTCATGTCAAAGCTTTTTCCAAAGATCAGAATATTGTGGGTAATGCTAGGCCTAAAGAAACAGACCACAAAAGTCTTTCATCGTCTCCTGAGAAACGAGAGAAGTTTAAAGAACAGAGAAAAGTCACGGTCAATGTGAAGAAAGACAAAGTGGAAAAAGCCTTAAAGACAGAAAAGCGGCCCAAGCAACCTGACAAAGAGGGAAAGCTGATCTGCTCAGAAAAAGGCAAAGTGTCAGAGAAAAGCCTTCCTAAGAACGAAAAGGAAGATAAGGAGAACATTTCCGAGAACGAGCGGGAGTACTCCGGGGATGCCCAGGTGGAAAAGAAGCCTGAGAAGGACCTTGTGAAGAACCCACAAGAGAACCTGAAGGAGCCAAAAAGAAAACGAGGCAGACCCCCTTCCATAACTCCTACGGCTGTGGATTCAAACTCTCAAACTTTGCAACCAATAACATTGGAATTGAGAAGACGGAAAATATCAAAACGAAGTGACACCCCATTAAAGCGTCCCAGACTCGACAAAAATTCACCCCAGGAACAGTCAAAAAAACGCTCTGAAAATAGTGACAAAGACTTATCCAGGAGACGGTCCTCCAGGCTGTCCACTAATGGGACCCGTGAGATCCTAGATCCTGACTCGATTGTACCTGATCTGGTTCATACGGTTGATACAAACCCTCTACCAGACAAGTCACCCAGTGCCAAGGATTCTGCTGAAGGTCAGTTGAAGTCTCCATTGGAAGCTGGCCAGGTCTCTTCTGCATTAACTTGCCACCCCATTGGGGATGGCCTGGGGGCAGCAGATTTGGAGTTGAATTGCAAGTCAATGGGAGAAAACACGATGAAAACAGAACCTGTTTCTCCTCTTGCTGAGGTGCAGGAAGTTTCAACTGTTGAAGTTCCAAATACTTTGAAGAAAGTTGATGACTCTGTGACGTTGAATGTGCCAGCTGTGGACCTAGACCACAAGTTTCGATGCAAGGTTCTGGACTGTTTGAAATTTTTCCGCAAGGCTAAATTGCTGCACTATCATATGAAGTATTTCCATGGGATGGAGAAGTCACCAGAGCCAGAGGAGGGCCCAGGGAAGACGCATGTACAGACTCGGGGCTCTGCGGTGCCTGACAAGACAAGCCAGGAGAGCCTAACCAGGAAGCGGGTCTCTGCCAGTTCCCCCACTGCAAAAGAGAAGGAAAAGACTAAAGAGAAGAAATTCAAAGAACTTGTGAGAGTGAAGCCAAAGAAGAAAAAGAAAAAGAAAAAGAAAACCAAGCCTGAATGTCCCTGCAGTGAGGACATCAGTGATACTTCCCAGGAACCTTCTCCACCCAAAACATTTGCTGTCACCAGGTGTGGGTCCTCACACAAGCCTGGGGTCCATATGAGCCCGCAGCTCCATGGTTCAGATAATGGAAACCACAAAGGGAAATTGAAAACCTGTGAGGAGGATAATTTGAGTGAGTCCTCTTCCGAGAGCTTTCTTTGGAGTGATGAGGAATATGGTCAAGATGTTGATGTGACCACCAACCCAGATGAGGAGCTTGAGGGCGACGACCGCTATGATTTTGAGGTGGTCCGCTGCATCTGTGAAGTGCAGGAGGAAAATGACTTCATGATTCAGTGTGAAGAGTGCCAGTGCTGGCAGCACGGGGTCTGCATGGGCTTACTGGAAGAAAACGTGCCTGAGAAATACACCTGCTATGTTTGCCAAGACCCTCCAGGTCAGAGGCCTGGCTTCAAGTACTGGTATGACAAGGAGTGGCTGAGCCGGGGACACATGCATGGTCTGGCATTTCTGGATCAGAACTACTCCCACCAGAATGCCAGGAAGATCGTGGCCACCCACCAGCTGCTCGGGGACGTGCAGAGAGTGATCCAAGTGCTGCACGGCCTGCAGCTCAAGATGAGCATTCTGCA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GGACGTGCAGAGAGTGATCC
60.18
ACTGGGCTCCCACTTCAAAG
59.89
147
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GGGACGTGCAGAGAGTGATC
60.18
ACTGGGCTCCCACTTCAAAG
59.89
148
PCR template sequence:
AGAATGCCAGGAAGATCGTGGCCACCCACCAGCTGCTCGGGGACGTGCAGAGAGTGATCCAAGTGCTGCACGGCCTGCAGCTCAAGATGAGCATTCTGCAGAGGATAAAAGCAGCCCTGTTGATGACTGAAAATGACCAAGCACCCACCTAACAGACGAGGAATCAGCTTTGAAGTGGGAGCCCAGTTGGAAGCTCGGGA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
26
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-181a-5p(1), mmu-miR-34a-5p(1), mmu-miR-211-5p(1), mmu-miR-204-5p(1), mmu-miR-322-5p(1), mmu-miR-298-5p(1), mmu-miR-132-3p(1), mmu-miR-203-3p(1), mmu-miR-324-5p(1), mmu-miR-326-3p(1), mmu-miR-23a-3p(1), mmu-miR-149-5p(1), mmu-miR-29b-1-5p(1), mmu-miR-96-5p(1), mmu-miR-182-5p(1), mmu-miR-1198-5p(1), mmu-miR-190b-5p(1), mmu-miR-673-5p(1), mmu-miR-335-3p(1), mmu-miR-669d-5p(1), mmu-miR-181d-5p(1)
siRNAs for circular RNA silencing
Junction sequence
TGAGCATTCTGCAGAGGATAAAAGCA
siRNA sets
TTTATCCTCTGCAGAATGC, TTATCCTCTGCAGAATGCT, TTTTATCCTCTGCAGAATG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCPHF20_2341_ORF_1
0.9161
0.260489916
0.999999472
2361
ORF sequence:
ATGACCAAGCACCCACCTAACAGACGAGGAATCAGCTTTGAAGTGGGAGCCCAGTTGGAAGCTCGGGACCGTTTAAAAAACTGGTATCCAGCTCATATTGAAGACATTGACTACGAAGAAGGGAGAGTTCTCATCCATTTCAAGCGTTGGAACCATCGTTACGATGAGTGGTTTTGCTGGGACAGTCCTTATCTGCGCCCTTTAGAGAAGATCCAGCTGAGGAAAGAGGGTTTACATGATGAGGATGGCTCTTCTGAATTTCAAATAAACCAGCAAGTGCTTGCTTGCTGGTCTGACTGTCGATTTTATCCAGCCAGAGTCACTGCTGTGAACAAGGATGGTACTTACACTGTGAAATTTTATGATGGAGTAGTTCAAACTGTCAAACATATTCATGTCAAAGCTTTTTCCAAAGATCAGAATATTGTGGGTAATGCTAGGCCTAAAGAAACAGACCACAAAAGTCTTTCATCGTCTCCTGAGAAACGAGAGAAGTTTAAAGAACAGAGAAAAGTCACGGTCAATGTGAAGAAAGACAAAGTGGAAAAAGCCTTAAAGACAGAAAAGCGGCCCAAGCAACCTGACAAAGAGGGAAAGCTGATCTGCTCAGAAAAAGGCAAAGTGTCAGAGAAAAGCCTTCCTAAGAACGAAAAGGAAGATAAGGAGAACATTTCCGAGAACGAGCGGGAGTACTCCGGGGATGCCCAGGTGGAAAAGAAGCCTGAGAAGGACCTTGTGAAGAACCCACAAGAGAACCTGAAGGAGCCAAAAAGAAAACGAGGCAGACCCCCTTCCATAACTCCTACGGCTGTGGATTCAAACTCTCAAACTTTGCAACCAATAACATTGGAATTGAGAAGACGGAAAATATCAAAACGAAGTGACACCCCATTAAAGCGTCCCAGACTCGACAAAAATTCACCCCAGGAACAGTCAAAAAAACGCTCTGAAAATAGTGACAAAGACTTATCCAGGAGACGGTCCTCCAGGCTGTCCACTAATGGGACCCGTGAGATCCTAGATCCTGACTCGATTGTACCTGATCTGGTTCATACGGTTGATACAAACCCTCTACCAGACAAGTCACCCAGTGCCAAGGATTCTGCTGAAGGTCAGTTGAAGTCTCCATTGGAAGCTGGCCAGGTCTCTTCTGCATTAACTTGCCACCCCATTGGGGATGGCCTGGGGGCAGCAGATTTGGAGTTGAATTGCAAGTCAATGGGAGAAAACACGATGAAAACAGAACCTGTTTCTCCTCTTGCTGAGGTGCAGGAAGTTTCAACTGTTGAAGTTCCAAATACTTTGAAGAAAGTTGATGACTCTGTGACGTTGAATGTGCCAGCTGTGGACCTAGACCACAAGTTTCGATGCAAGGTTCTGGACTGTTTGAAATTTTTCCGCAAGGCTAAATTGCTGCACTATCATATGAAGTATTTCCATGGGATGGAGAAGTCACCAGAGCCAGAGGAGGGCCCAGGGAAGACGCATGTACAGACTCGGGGCTCTGCGGTGCCTGACAAGACAAGCCAGGAGAGCCTAACCAGGAAGCGGGTCTCTGCCAGTTCCCCCACTGCAAAAGAGAAGGAAAAGACTAAAGAGAAGAAATTCAAAGAACTTGTGAGAGTGAAGCCAAAGAAGAAAAAGAAAAAGAAAAAGAAAACCAAGCCTGAATGTCCCTGCAGTGAGGACATCAGTGATACTTCCCAGGAACCTTCTCCACCCAAAACATTTGCTGTCACCAGGTGTGGGTCCTCACACAAGCCTGGGGTCCATATGAGCCCGCAGCTCCATGGTTCAGATAATGGAAACCACAAAGGGAAATTGAAAACCTGTGAGGAGGATAATTTGAGTGAGTCCTCTTCCGAGAGCTTTCTTTGGAGTGATGAGGAATATGGTCAAGATGTTGATGTGACCACCAACCCAGATGAGGAGCTTGAGGGCGACGACCGCTATGATTTTGAGGTGGTCCGCTGCATCTGTGAAGTGCAGGAGGAAAATGACTTCATGATTCAGTGTGAAGAGTGCCAGTGCTGGCAGCACGGGGTCTGCATGGGCTTACTGGAAGAAAACGTGCCTGAGAAATACACCTGCTATGTTTGCCAAGACCCTCCAGGTCAGAGGCCTGGCTTCAAGTACTGGTATGACAAGGAGTGGCTGAGCCGGGGACACATGCATGGTCTGGCATTTCTGGATCAGAACTACTCCCACCAGAATGCCAGGAAGATCGTGGCCACCCACCAGCTGCTCGGGGACGTGCAGAGAGTGATCCAAGTGCTGCACGGCCTGCAGCTCAAGATGAGCATTCTGCAGAGGATAAAAGCAGCCCTGTTGATGACTGAAAATGACCAAGCACCCACCTAA
Peptide sequence:
MTKHPPNRRGISFEVGAQLEARDRLKNWYPAHIEDIDYEEGRVLIHFKRWNHRYDEWFCWDSPYLRPLEKIQLRKEGLHDEDGSSEFQINQQVLACWSDCRFYPARVTAVNKDGTYTVKFYDGVVQTVKHIHVKAFSKDQNIVGNARPKETDHKSLSSSPEKREKFKEQRKVTVNVKKDKVEKALKTEKRPKQPDKEGKLICSEKGKVSEKSLPKNEKEDKENISENEREYSGDAQVEKKPEKDLVKNPQENLKEPKRKRGRPPSITPTAVDSNSQTLQPITLELRRRKISKRSDTPLKRPRLDKNSPQEQSKKRSENSDKDLSRRRSSRLSTNGTREILDPDSIVPDLVHTVDTNPLPDKSPSAKDSAEGQLKSPLEAGQVSSALTCHPIGDGLGAADLELNCKSMGENTMKTEPVSPLAEVQEVSTVEVPNTLKKVDDSVTLNVPAVDLDHKFRCKVLDCLKFFRKAKLLHYHMKYFHGMEKSPEPEEGPGKTHVQTRGSAVPDKTSQESLTRKRVSASSPTAKEKEKTKEKKFKELVRVKPKKKKKKKKKTKPECPCSEDISDTSQEPSPPKTFAVTRCGSSHKPGVHMSPQLHGSDNGNHKGKLKTCEEDNLSESSSESFLWSDEEYGQDVDVTTNPDEELEGDDRYDFEVVRCICEVQEENDFMIQCEECQCWQHGVCMGLLEENVPEKYTCYVCQDPPGQRPGFKYWYDKEWLSRGHMHGLAFLDQNYSHQNARKIVATHQLLGDVQRVIQVLHGLQLKMSILQRIKAALLMTENDQAPT
IRESfinder result
IRESfinder score
0.498132637
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
bottom of page