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mmu_circPbrm1_1992
Basic information of circular RNA
PanCircBase ID:
mmu_circPbrm1_1992
mm39_Chr. Position ID:
chr14|30783425|30809618|+
Gene name:
Pbrm1
Transcript:
ENSMUST00000112098.11
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
8
Exon/intron indexes:
17,18,19,20,21,22,23,24
Exon/intron offsets:
0,3277,5853,13302,21081,22605,23317,26047
Genomic length:
26193
Exon/intron sizes in nt:
2,77,10,66,43,21,21,86,00,00,00,000
Flanking exon/introns:
chr14:30778237-30783425|chr14:30809618-30811421
Splice length:
1992
Other database IDs:
circBase: mmu_circ_0005193, CIRCpedia: MMU_CIRCpedia_16031, circAtlas: mmu-Pbrm1_0047
circAtlas: hsa-PBRM1_0077
Human Ortholog IDs:
Mature spliced Sequence:
TAAAAAGAACATAAGAAAACAGCGAATGAAAATTTTATTCAATGTTGTTCTTGAAGCTCGAGAGCCAGGTTCAGGCAGAAGACTTTGCGATCTATTTATGGTTAAGCCATCCAAGAAGGACTATCCTGATTATTATAAAATCATCTTAGAGCCAATGGACCTGAAAATAATTGAGCATAACATCCGAAATGACAAATATGCAGGTGAAGAAGGAATGATGGAAGACATGAAACTCATGTTCCGCAATGCCAGGCACTACAATGAGGAGGGCTCCCAGGTATACAATGATGCCCATATCCTGGAGAAGTTACTCAAAGATAAAAGGAAAGAGCTGGGCCCTCTGCCTGATGATGATGACATGGCTTCTCCCAAACTTAAATTGAGTAGGAAGAGTGGTGTTTCTCCTAAGAAATCAAAGTACATGACTCCAATGCAGCAGAAACTGAATGAAGTGTATGAAGCTGTAAAGAACTATACTGATAAGAGGGGTCGCCGCCTTAGTGCTATATTTCTAAGACTCCCCTCTAGATCAGAGCTGCCTGACTACTACCTGACCATTAAAAAGCCCATGGACATGGAAAAAATTCGAAGTCACATGATGGCAAACAAGTACCAAGACATAGATTCTATGGTAGAGGACTTTGTCATGATGTTTAATAATGCCTGTACCTACAATGAACCAGAGTCTTTGATCTACAAAGATGCCCTTGTACTGCATAAAGTCCTCCTTGAGACTCGGAGAGACCTGGAGGGAGATGAGGATTCTCATGTCCCTAATGTGACGTTGCTGATTCAAGAGCTCATCCATAACCTTTTTGTGTCAGTCATGAGTCATCAGGATGACGAAGGGAGGTGTTACAGCGACTCCTTAGCAGAAATTCCTGCTGTGGATCCCAACTCTCCCAATAAACCTCCCCTTACATTTGACATTATCAGGAAAAATGTTGAAAGTAATCGGTATCGGCGACTTGATTTATTTCAGGAGCATATGTTTGAAGTATTGGAACGGGCAAGAAGGATGAACCGGACAGATTCCGAAATATATGAGGATGCTGTAGAACTTCAGCAGTTTTTTATTAGAATTCGTGATGAACTCTGCAAAAATGGAGAGATCCTTCTTTCTCCAGCACTCAGCTATACCACAAAACACTTGCATAACGATGTGGAAAAAGAAAAAAAGGAAAAATTGCCTAAAGAAATAGAGGAAGATAAACTAAAACGCGAAGAAGAAAAAAGAGAAGCTGAAAAAAGTGAAGATTCCTCAGGTACTACAGGCCTCTCAGGCTTACATCGTACATACAGCCAGGACTGCAGCTTTAAGAACAGCATGTATCATGTCGGAGATTATGTCTATGTTGAACCTGCGGAGGCCAATCTACAACCACATATAGTGTGTATTGAGAGACTGTGGGAGGATTCAGCTGGTGAAAAATGGTTGTACGGCTGTTGGTTTTATCGGCCAAATGAAACATTCCATTTGGCTACACGAAAATTTCTAGAAAAAGAAGTTTTTAAGAGTGACTACTACAATAAAGTACCTGTTAGTAAAATTCTAGGCAAATGTGTAGTCATGTTTGTCAAGGAATACTTTAAATTATGTCCAGAAAACTTTCGCGATGAGGATGTTTTTGTCTGTGAATCGAGGTATTCTGCCAAAACCAAATCTTTTAAGAAAATTAAACTGTGGACCATGCCCATCAGTTCAGTTAGATTTGTCCCTCGGGATGTGCCTTTGCCTGTGGTCCGAGTGGCCTCTGTGTTTGCAAATGCAGATAAAGGGGATGATGAGAAGAATACAGACAACTCAGATGACAATAGAGCTGAAGACAATTTTAACTTGGAAAAGGAAAAAGAAGATGTTCCTGTGGAGATGTCCAATGGTGAGCCAGGTTGCCACTACTTTGAGCAGCTTCGGTACAATGACATGTGGCTGAAGGTTGGTGATTGTGTCTTCATCAAATCCCACGGCTTGGTGCGCCCTCGTGTGGGCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
ACATGTGGCTGAAGGTTGGT
59.81
TCGCAAAGTCTTCTGCCTGA
59.61
160
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
ACATGTGGCTGAAGGTTGGT
59.81
CTTCTGCCTGAACCTGGCTC
60.68
151
PCR template sequence:
GCCACTACTTTGAGCAGCTTCGGTACAATGACATGTGGCTGAAGGTTGGTGATTGTGTCTTCATCAAATCCCACGGCTTGGTGCGCCCTCGTGTGGGCAGTAAAAAGAACATAAGAAAACAGCGAATGAAAATTTTATTCAATGTTGTTCTTGAAGCTCGAGAGCCAGGTTCAGGCAGAAGACTTTGCGATCTATTTATG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
15
Interacting miRNAs (#binding sites)
mmu-miR-211-5p(2), mmu-miR-23a-3p(2), mmu-miR-136-5p(2), mmu-miR-204-5p(1), mmu-miR-335-5p(1), mmu-miR-33-5p(1), mmu-miR-298-5p(1), mmu-miR-196a-5p(1), mmu-miR-132-3p(1), mmu-miR-495-3p(1), mmu-miR-149-5p(1), mmu-miR-297a-5p(1), mmu-miR-207(1), mmu-miR-697(1), mmu-miR-1904(1)
siRNAs for circular RNA silencing
Junction sequence
CTCGTGTGGGCAGTAAAAAGAACATA
siRNA sets
TTTTTACTGCCCACACGAG,TTCTTTTTACTGCCCACAC,TATGTTCTTTTTACTGCCC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCPBRM1_1992_ORF_1
1.1257
0.188793408
1
3957
ORF sequence:
ATGAAAATTTTATTCAATGTTGTTCTTGAAGCTCGAGAGCCAGGTTCAGGCAGAAGACTTTGCGATCTATTTATGGTTAAGCCATCCAAGAAGGACTATCCTGATTATTATAAAATCATCTTAGAGCCAATGGACCTGAAAATAATTGAGCATAACATCCGAAATGACAAATATGCAGGTGAAGAAGGAATGATGGAAGACATGAAACTCATGTTCCGCAATGCCAGGCACTACAATGAGGAGGGCTCCCAGGTATACAATGATGCCCATATCCTGGAGAAGTTACTCAAAGATAAAAGGAAAGAGCTGGGCCCTCTGCCTGATGATGATGACATGGCTTCTCCCAAACTTAAATTGAGTAGGAAGAGTGGTGTTTCTCCTAAGAAATCAAAGTACATGACTCCAATGCAGCAGAAACTGAATGAAGTGTATGAAGCTGTAAAGAACTATACTGATAAGAGGGGTCGCCGCCTTAGTGCTATATTTCTAAGACTCCCCTCTAGATCAGAGCTGCCTGACTACTACCTGACCATTAAAAAGCCCATGGACATGGAAAAAATTCGAAGTCACATGATGGCAAACAAGTACCAAGACATAGATTCTATGGTAGAGGACTTTGTCATGATGTTTAATAATGCCTGTACCTACAATGAACCAGAGTCTTTGATCTACAAAGATGCCCTTGTACTGCATAAAGTCCTCCTTGAGACTCGGAGAGACCTGGAGGGAGATGAGGATTCTCATGTCCCTAATGTGACGTTGCTGATTCAAGAGCTCATCCATAACCTTTTTGTGTCAGTCATGAGTCATCAGGATGACGAAGGGAGGTGTTACAGCGACTCCTTAGCAGAAATTCCTGCTGTGGATCCCAACTCTCCCAATAAACCTCCCCTTACATTTGACATTATCAGGAAAAATGTTGAAAGTAATCGGTATCGGCGACTTGATTTATTTCAGGAGCATATGTTTGAAGTATTGGAACGGGCAAGAAGGATGAACCGGACAGATTCCGAAATATATGAGGATGCTGTAGAACTTCAGCAGTTTTTTATTAGAATTCGTGATGAACTCTGCAAAAATGGAGAGATCCTTCTTTCTCCAGCACTCAGCTATACCACAAAACACTTGCATAACGATGTGGAAAAAGAAAAAAAGGAAAAATTGCCTAAAGAAATAGAGGAAGATAAACTAAAACGCGAAGAAGAAAAAAGAGAAGCTGAAAAAAGTGAAGATTCCTCAGGTACTACAGGCCTCTCAGGCTTACATCGTACATACAGCCAGGACTGCAGCTTTAAGAACAGCATGTATCATGTCGGAGATTATGTCTATGTTGAACCTGCGGAGGCCAATCTACAACCACATATAGTGTGTATTGAGAGACTGTGGGAGGATTCAGCTGGTGAAAAATGGTTGTACGGCTGTTGGTTTTATCGGCCAAATGAAACATTCCATTTGGCTACACGAAAATTTCTAGAAAAAGAAGTTTTTAAGAGTGACTACTACAATAAAGTACCTGTTAGTAAAATTCTAGGCAAATGTGTAGTCATGTTTGTCAAGGAATACTTTAAATTATGTCCAGAAAACTTTCGCGATGAGGATGTTTTTGTCTGTGAATCGAGGTATTCTGCCAAAACCAAATCTTTTAAGAAAATTAAACTGTGGACCATGCCCATCAGTTCAGTTAGATTTGTCCCTCGGGATGTGCCTTTGCCTGTGGTCCGAGTGGCCTCTGTGTTTGCAAATGCAGATAAAGGGGATGATGAGAAGAATACAGACAACTCAGATGACAATAGAGCTGAAGACAATTTTAACTTGGAAAAGGAAAAAGAAGATGTTCCTGTGGAGATGTCCAATGGTGAGCCAGGTTGCCACTACTTTGAGCAGCTTCGGTACAATGACATGTGGCTGAAGGTTGGTGATTGTGTCTTCATCAAATCCCACGGCTTGGTGCGCCCTCGTGTGGGCAGTAAAAAGAACATAAGAAAACAGCGAATGAAAATTTTATTCAATGTTGTTCTTGAAGCTCGAGAGCCAGGTTCAGGCAGAAGACTTTGCGATCTATTTATGGTTAAGCCATCCAAGAAGGACTATCCTGATTATTATAAAATCATCTTAGAGCCAATGGACCTGAAAATAATTGAGCATAACATCCGAAATGACAAATATGCAGGTGAAGAAGGAATGATGGAAGACATGAAACTCATGTTCCGCAATGCCAGGCACTACAATGAGGAGGGCTCCCAGGTATACAATGATGCCCATATCCTGGAGAAGTTACTCAAAGATAAAAGGAAAGAGCTGGGCCCTCTGCCTGATGATGATGACATGGCTTCTCCCAAACTTAAATTGAGTAGGAAGAGTGGTGTTTCTCCTAAGAAATCAAAGTACATGACTCCAATGCAGCAGAAACTGAATGAAGTGTATGAAGCTGTAAAGAACTATACTGATAAGAGGGGTCGCCGCCTTAGTGCTATATTTCTAAGACTCCCCTCTAGATCAGAGCTGCCTGACTACTACCTGACCATTAAAAAGCCCATGGACATGGAAAAAATTCGAAGTCACATGATGGCAAACAAGTACCAAGACATAGATTCTATGGTAGAGGACTTTGTCATGATGTTTAATAATGCCTGTACCTACAATGAACCAGAGTCTTTGATCTACAAAGATGCCCTTGTACTGCATAAAGTCCTCCTTGAGACTCGGAGAGACCTGGAGGGAGATGAGGATTCTCATGTCCCTAATGTGACGTTGCTGATTCAAGAGCTCATCCATAACCTTTTTGTGTCAGTCATGAGTCATCAGGATGACGAAGGGAGGTGTTACAGCGACTCCTTAGCAGAAATTCCTGCTGTGGATCCCAACTCTCCCAATAAACCTCCCCTTACATTTGACATTATCAGGAAAAATGTTGAAAGTAATCGGTATCGGCGACTTGATTTATTTCAGGAGCATATGTTTGAAGTATTGGAACGGGCAAGAAGGATGAACCGGACAGATTCCGAAATATATGAGGATGCTGTAGAACTTCAGCAGTTTTTTATTAGAATTCGTGATGAACTCTGCAAAAATGGAGAGATCCTTCTTTCTCCAGCACTCAGCTATACCACAAAACACTTGCATAACGATGTGGAAAAAGAAAAAAAGGAAAAATTGCCTAAAGAAATAGAGGAAGATAAACTAAAACGCGAAGAAGAAAAAAGAGAAGCTGAAAAAAGTGAAGATTCCTCAGGTACTACAGGCCTCTCAGGCTTACATCGTACATACAGCCAGGACTGCAGCTTTAAGAACAGCATGTATCATGTCGGAGATTATGTCTATGTTGAACCTGCGGAGGCCAATCTACAACCACATATAGTGTGTATTGAGAGACTGTGGGAGGATTCAGCTGGTGAAAAATGGTTGTACGGCTGTTGGTTTTATCGGCCAAATGAAACATTCCATTTGGCTACACGAAAATTTCTAGAAAAAGAAGTTTTTAAGAGTGACTACTACAATAAAGTACCTGTTAGTAAAATTCTAGGCAAATGTGTAGTCATGTTTGTCAAGGAATACTTTAAATTATGTCCAGAAAACTTTCGCGATGAGGATGTTTTTGTCTGTGAATCGAGGTATTCTGCCAAAACCAAATCTTTTAAGAAAATTAAACTGTGGACCATGCCCATCAGTTCAGTTAGATTTGTCCCTCGGGATGTGCCTTTGCCTGTGGTCCGAGTGGCCTCTGTGTTTGCAAATGCAGATAAAGGGGATGATGAGAAGAATACAGACAACTCAGATGACAATAGAGCTGAAGACAATTTTAACTTGGAAAAGGAAAAAGAAGATGTTCCTGTGGAGATGTCCAATGGTGAGCCAGGTTGCCACTACTTTGAGCAGCTTCGGTACAATGACATGTGGCTGAAGGTTGGTGATTGTGTCTTCATCAAATCCCACGGCTTGGTGCGCCCTCGTGTGGGC
Peptide sequence:
MKILFNVVLEAREPGSGRRLCDLFMVKPSKKDYPDYYKIILEPMDLKIIEHNIRNDKYAGEEGMMEDMKLMFRNARHYNEEGSQVYNDAHILEKLLKDKRKELGPLPDDDDMASPKLKLSRKSGVSPKKSKYMTPMQQKLNEVYEAVKNYTDKRGRRLSAIFLRLPSRSELPDYYLTIKKPMDMEKIRSHMMANKYQDIDSMVEDFVMMFNNACTYNEPESLIYKDALVLHKVLLETRRDLEGDEDSHVPNVTLLIQELIHNLFVSVMSHQDDEGRCYSDSLAEIPAVDPNSPNKPPLTFDIIRKNVESNRYRRLDLFQEHMFEVLERARRMNRTDSEIYEDAVELQQFFIRIRDELCKNGEILLSPALSYTTKHLHNDVEKEKKEKLPKEIEEDKLKREEEKREAEKSEDSSGTTGLSGLHRTYSQDCSFKNSMYHVGDYVYVEPAEANLQPHIVCIERLWEDSAGEKWLYGCWFYRPNETFHLATRKFLEKEVFKSDYYNKVPVSKILGKCVVMFVKEYFKLCPENFRDEDVFVCESRYSAKTKSFKKIKLWTMPISSVRFVPRDVPLPVVRVASVFANADKGDDEKNTDNSDDNRAEDNFNLEKEKEDVPVEMSNGEPGCHYFEQLRYNDMWLKVGDCVFIKSHGLVRPRVGSKKNIRKQRMKILFNVVLEAREPGSGRRLCDLFMVKPSKKDYPDYYKIILEPMDLKIIEHNIRNDKYAGEEGMMEDMKLMFRNARHYNEEGSQVYNDAHILEKLLKDKRKELGPLPDDDDMASPKLKLSRKSGVSPKKSKYMTPMQQKLNEVYEAVKNYTDKRGRRLSAIFLRLPSRSELPDYYLTIKKPMDMEKIRSHMMANKYQDIDSMVEDFVMMFNNACTYNEPESLIYKDALVLHKVLLETRRDLEGDEDSHVPNVTLLIQELIHNLFVSVMSHQDDEGRCYSDSLAEIPAVDPNSPNKPPLTFDIIRKNVESNRYRRLDLFQEHMFEVLERARRMNRTDSEIYEDAVELQQFFIRIRDELCKNGEILLSPALSYTTKHLHNDVEKEKKEKLPKEIEEDKLKREEEKREAEKSEDSSGTTGLSGLHRTYSQDCSFKNSMYHVGDYVYVEPAEANLQPHIVCIERLWEDSAGEKWLYGCWFYRPNETFHLATRKFLEKEVFKSDYYNKVPVSKILGKCVVMFVKEYFKLCPENFRDEDVFVCESRYSAKTKSFKKIKLWTMPISSVRFVPRDVPLPVVRVASVFANADKGDDEKNTDNSDDNRAEDNFNLEKEKEDVPVEMSNGEPGCHYFEQLRYNDMWLKVGDCVFIKSHGLVRPRVG
IRESfinder result
IRESfinder score
0.460940492
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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