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mmu_circPbrm1_1283
Basic information of circular RNA
PanCircBase ID:
mmu_circPbrm1_1283
mm39_Chr. Position ID:
chr14|30778192|30796939|+
Gene name:
Pbrm1
Transcript:
ENSMUST00000112098.11
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
16,17,18,19,20
Exon/intron offsets:
0,5233,8510,11086,18535
Genomic length:
18747
Exon/intron sizes in nt:
4,52,77,10,66,43,212
Flanking exon/introns:
chr14:30776212-30778192|chr14:30796939-30804506
Splice length:
1283
Other database IDs:
circAtlas: hsa-PBRM1_0129
Human Ortholog IDs:
Mature spliced Sequence:
GAATACTCATGACAGTGAGATGTTGGGTCTCAGGAGGCTATCCAGTAAAAAGAACATAAGAAAACAGCGAATGAAAATTTTATTCAATGTTGTTCTTGAAGCTCGAGAGCCAGGTTCAGGCAGAAGACTTTGCGATCTATTTATGGTTAAGCCATCCAAGAAGGACTATCCTGATTATTATAAAATCATCTTAGAGCCAATGGACCTGAAAATAATTGAGCATAACATCCGAAATGACAAATATGCAGGTGAAGAAGGAATGATGGAAGACATGAAACTCATGTTCCGCAATGCCAGGCACTACAATGAGGAGGGCTCCCAGGTATACAATGATGCCCATATCCTGGAGAAGTTACTCAAAGATAAAAGGAAAGAGCTGGGCCCTCTGCCTGATGATGATGACATGGCTTCTCCCAAACTTAAATTGAGTAGGAAGAGTGGTGTTTCTCCTAAGAAATCAAAGTACATGACTCCAATGCAGCAGAAACTGAATGAAGTGTATGAAGCTGTAAAGAACTATACTGATAAGAGGGGTCGCCGCCTTAGTGCTATATTTCTAAGACTCCCCTCTAGATCAGAGCTGCCTGACTACTACCTGACCATTAAAAAGCCCATGGACATGGAAAAAATTCGAAGTCACATGATGGCAAACAAGTACCAAGACATAGATTCTATGGTAGAGGACTTTGTCATGATGTTTAATAATGCCTGTACCTACAATGAACCAGAGTCTTTGATCTACAAAGATGCCCTTGTACTGCATAAAGTCCTCCTTGAGACTCGGAGAGACCTGGAGGGAGATGAGGATTCTCATGTCCCTAATGTGACGTTGCTGATTCAAGAGCTCATCCATAACCTTTTTGTGTCAGTCATGAGTCATCAGGATGACGAAGGGAGGTGTTACAGCGACTCCTTAGCAGAAATTCCTGCTGTGGATCCCAACTCTCCCAATAAACCTCCCCTTACATTTGACATTATCAGGAAAAATGTTGAAAGTAATCGGTATCGGCGACTTGATTTATTTCAGGAGCATATGTTTGAAGTATTGGAACGGGCAAGAAGGATGAACCGGACAGATTCCGAAATATATGAGGATGCTGTAGAACTTCAGCAGTTTTTTATTAGAATTCGTGATGAACTCTGCAAAAATGGAGAGATCCTTCTTTCTCCAGCACTCAGCTATACCACAAAACACTTGCATAACGATGTGGAAAAAGAAAAAAAGGAAAAATTGCCTAAAGAAATAGAGGAAGATAAACTAAAACGCGAAGAAGAAAAAAGAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
ACCACAAAACACTTGCATAACGA
59.62
GGATAGCCTCCTGAGACCCA
60.11
143
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
ACCACAAAACACTTGCATAACGA
59.62
TGGATAGCCTCCTGAGACCC
60.11
144
PCR template sequence:
ACCACAAAACACTTGCATAACGATGTGGAAAAAGAAAAAAAGGAAAAATTGCCTAAAGAAATAGAGGAAGATAAACTAAAACGCGAAGAAGAAAAAAGAGGAATACTCATGACAGTGAGATGTTGGGTCTCAGGAGGCTATCCAGTAAAAAGAACATAAGAAAACAGCGAATGAAAATTTTATTCAATGTTGTTCTTGAA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
12
Interacting miRNAs (#binding sites)
mmu-miR-136-5p(2), mmu-miR-211-5p(1), 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-125b-5p(1), mmu-miR-23a-3p(1), mmu-miR-149-5p(1), mmu-miR-207(1), mmu-miR-1904(1)
siRNAs for circular RNA silencing
Junction sequence
GAAGAAAAAAGAGGAATACTCATGAC
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCPBRM1_1283_ORF_1
1.1178
0.17818513
0.999134525
1323
ORF sequence:
ATGTTGGGTCTCAGGAGGCTATCCAGTAAAAAGAACATAAGAAAACAGCGAATGAAAATTTTATTCAATGTTGTTCTTGAAGCTCGAGAGCCAGGTTCAGGCAGAAGACTTTGCGATCTATTTATGGTTAAGCCATCCAAGAAGGACTATCCTGATTATTATAAAATCATCTTAGAGCCAATGGACCTGAAAATAATTGAGCATAACATCCGAAATGACAAATATGCAGGTGAAGAAGGAATGATGGAAGACATGAAACTCATGTTCCGCAATGCCAGGCACTACAATGAGGAGGGCTCCCAGGTATACAATGATGCCCATATCCTGGAGAAGTTACTCAAAGATAAAAGGAAAGAGCTGGGCCCTCTGCCTGATGATGATGACATGGCTTCTCCCAAACTTAAATTGAGTAGGAAGAGTGGTGTTTCTCCTAAGAAATCAAAGTACATGACTCCAATGCAGCAGAAACTGAATGAAGTGTATGAAGCTGTAAAGAACTATACTGATAAGAGGGGTCGCCGCCTTAGTGCTATATTTCTAAGACTCCCCTCTAGATCAGAGCTGCCTGACTACTACCTGACCATTAAAAAGCCCATGGACATGGAAAAAATTCGAAGTCACATGATGGCAAACAAGTACCAAGACATAGATTCTATGGTAGAGGACTTTGTCATGATGTTTAATAATGCCTGTACCTACAATGAACCAGAGTCTTTGATCTACAAAGATGCCCTTGTACTGCATAAAGTCCTCCTTGAGACTCGGAGAGACCTGGAGGGAGATGAGGATTCTCATGTCCCTAATGTGACGTTGCTGATTCAAGAGCTCATCCATAACCTTTTTGTGTCAGTCATGAGTCATCAGGATGACGAAGGGAGGTGTTACAGCGACTCCTTAGCAGAAATTCCTGCTGTGGATCCCAACTCTCCCAATAAACCTCCCCTTACATTTGACATTATCAGGAAAAATGTTGAAAGTAATCGGTATCGGCGACTTGATTTATTTCAGGAGCATATGTTTGAAGTATTGGAACGGGCAAGAAGGATGAACCGGACAGATTCCGAAATATATGAGGATGCTGTAGAACTTCAGCAGTTTTTTATTAGAATTCGTGATGAACTCTGCAAAAATGGAGAGATCCTTCTTTCTCCAGCACTCAGCTATACCACAAAACACTTGCATAACGATGTGGAAAAAGAAAAAAAGGAAAAATTGCCTAAAGAAATAGAGGAAGATAAACTAAAACGCGAAGAAGAAAAAAGAGGAATACTCATGACAGTGAGATGTTGGGTCTCAGGAGGCTATCCAGTAAAAAGAACATAA
Peptide sequence:
MLGLRRLSSKKNIRKQRMKILFNVVLEAREPGSGRRLCDLFMVKPSKKDYPDYYKIILEPMDLKIIEHNIRNDKYAGEEGMMEDMKLMFRNARHYNEEGSQVYNDAHILEKLLKDKRKELGPLPDDDDMASPKLKLSRKSGVSPKKSKYMTPMQQKLNEVYEAVKNYTDKRGRRLSAIFLRLPSRSELPDYYLTIKKPMDMEKIRSHMMANKYQDIDSMVEDFVMMFNNACTYNEPESLIYKDALVLHKVLLETRRDLEGDEDSHVPNVTLLIQELIHNLFVSVMSHQDDEGRCYSDSLAEIPAVDPNSPNKPPLTFDIIRKNVESNRYRRLDLFQEHMFEVLERARRMNRTDSEIYEDAVELQQFFIRIRDELCKNGEILLSPALSYTTKHLHNDVEKEKKEKLPKEIEEDKLKREEEKRGILMTVRCWVSGGYPVKRT
IRESfinder result
IRESfinder score
0.450964347
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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