top of page
mmu_circPam_1521
Basic information of circular RNA
PanCircBase ID:
mmu_circPam_1521
mm39_Chr. Position ID:
chr1|97780827|97903630|-
Gene name:
Pam
Transcript:
ENSMUST00000058762.15
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
14
Exon/intron indexes:
16,15,14,13,12,11,10,9,8,7,6,5,4,3
Exon/intron offsets:
0,11100,31023,32499,41258,42529,42866,44105,45238,69991,71328,81548,91517,122682
Genomic length:
122803
Exon/intron sizes in nt:
13,03,18,72,18,51,04,70,00,00,00,00,00,00,00,000
Flanking exon/introns:
chr1:97772437-97780827|chr1:97903630-97904581
Splice length:
1521
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GTTTAAAGAAACTACCAGATCATTTTCCAATGAATGCCTTGGTACCACCAGACCCATCACTCCTATTGATTCTTCGGATTTTACACTGGATATTCGCATGCCTGGGGTCACACCTAAAGAGTCTGACACGTACTTCTGCATGTCCATGCGTCTGCCTGTGGATGAGGAAGCCTTCGTGATTGACTTCAAGCCTCGGGCCAGCATGGACACTGTCCACCATATGCTGCTGTTTGGATGCAACATGCCCTCATCCACTGGGAGTTACTGGTTTTGTGATGAAGGAACCTGTACAGATAAAGCCAATATTCTATATGCCTGGGCAAGAAATGCTCCCCCCACCCGGCTCCCTAAAGGTGTTGGATTCAGAGTTGGAGGGGAAACTGGAAGCAAATACTTCGTCCTTCAAGTTCACTATGGGGACATCAGTGCTTTTCGAGATAATCACAAAGACTGTTCCGGTGTGTCCTTACATCTCACACGTGTGCCACAGCCTTTGATTGCGGGCATGTACCTTATGATGTCTGTCAACACTGTTATACCCCCAGGAGAGAAAGTAGTGAATTCTGACATTTCGTGCCATTACAAAATGTATCCAATGCATGTGTTTGCCTACCGAGTCCATACTCACCATTTAGGTAAGGTAGTGAGTGGATACAGAGTAAGAAACGGACAGTGGACGCTGATTGGACGCCAGAGCCCCCAGCTGCCACAGGCTTTTTACCCAGTGGAACACCCAGTAGATGTTGCTTTTGGTGATATACTGGCAGCCAGATGTGTGTTCACTGGTGAGGGGAGGACCGAAGCCACCCACATCGGCGGCACATCTAGTGATGAAATGTGCAACTTGTACATTATGTATTACATGGAAGCCAAGCATGCAGTTTCCTTCATGACCTGTACACAGAATGTGGCTCCAGATATGTTCAGAACTATCCCAGAAGAGGCCAATATTCCAATTCCTGTAAAATCCGACATGGTTATGATCCATGGGCATCACAAAGAAACAGAAAACAAAGAAAAGAGTGCTTTAATACAGCAGCCAAAGCAGGGAGAGGAGGAAGCCTTCGAGCAGGGTGATTTCTATTCACTACTTTCCAAGCTGCTAGGAGAAAGGGAAGATGTTGTTCATGTGCACAAATATAATCCTACAGAAAAGACAGAATCTGGGTCAGACCTGGTAGCTGAGATTGCAAACGTAGTCCAGAAAAAGGACCTTGGTCGGTCTGACGCCAGAGAGGGAGCGGAGCATGAGGAAGGGGGTAATGCTATCCTGGTCAGAGACAGGATCCACAAATTCCACAGGCTAGAGTCAACCTTGAGGCCAGCTGAGAGCAGAGCTCTATCCTTCCAGCAGCCTGGTGAAGGTCCTTGGGAACCAGAACTCGCAGGAGATTTCCATGTGGAAGAAGCACTGGAGTGGCCTGGAGTGTACTTGTTACCAGGCCAGGTTTCTGGGGTGGCCCTGGATTCTAAGAATAACCTTGTGATTTTCCACAGAGGTGACCATGTTTGGGATGGAAA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
ACTTGTTACCAGGCCAGGTT
59.15
GTGATGGGTCTGGTGGTACC
59.75
151
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TGTTACCAGGCCAGGTTTCT
58.85
GTGATGGGTCTGGTGGTACC
59.75
148
PCR template sequence:
CTGGAGTGTACTTGTTACCAGGCCAGGTTTCTGGGGTGGCCCTGGATTCTAAGAATAACCTTGTGATTTTCCACAGAGGTGACCATGTTTGGGATGGAAAGTTTAAAGAAACTACCAGATCATTTTCCAATGAATGCCTTGGTACCACCAGACCCATCACTCCTATTGATTCTTCGGATTTTACACTGGATATTCGCATG
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-15a-5p(1), mmu-miR-103-3p(1), mmu-miR-34a-5p(1), mmu-miR-204-5p(1), mmu-miR-15b-5p(1), mmu-miR-33-5p(1), mmu-miR-216a-5p(1), mmu-miR-183-5p(1), mmu-miR-541-5p(1), mmu-miR-107-3p(1), mmu-miR-466d-3p(1), mmu-miR-350-3p(1), mmu-miR-7a-2-3p(1)
siRNAs for circular RNA silencing
Junction sequence
TTTGGGATGGAAAGTTTAAAGAAACT
siRNA sets
TTCTTTAAACTTTCCATCC, TTTCTTTAAACTTTCCATC, TCTTTAAACTTTCCATCCC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCPAM_1521_ORF_1
0.9875
0.15632119
0.99999999
2943
ORF sequence:
ATGCCTGGGGTCACACCTAAAGAGTCTGACACGTACTTCTGCATGTCCATGCGTCTGCCTGTGGATGAGGAAGCCTTCGTGATTGACTTCAAGCCTCGGGCCAGCATGGACACTGTCCACCATATGCTGCTGTTTGGATGCAACATGCCCTCATCCACTGGGAGTTACTGGTTTTGTGATGAAGGAACCTGTACAGATAAAGCCAATATTCTATATGCCTGGGCAAGAAATGCTCCCCCCACCCGGCTCCCTAAAGGTGTTGGATTCAGAGTTGGAGGGGAAACTGGAAGCAAATACTTCGTCCTTCAAGTTCACTATGGGGACATCAGTGCTTTTCGAGATAATCACAAAGACTGTTCCGGTGTGTCCTTACATCTCACACGTGTGCCACAGCCTTTGATTGCGGGCATGTACCTTATGATGTCTGTCAACACTGTTATACCCCCAGGAGAGAAAGTAGTGAATTCTGACATTTCGTGCCATTACAAAATGTATCCAATGCATGTGTTTGCCTACCGAGTCCATACTCACCATTTAGGTAAGGTAGTGAGTGGATACAGAGTAAGAAACGGACAGTGGACGCTGATTGGACGCCAGAGCCCCCAGCTGCCACAGGCTTTTTACCCAGTGGAACACCCAGTAGATGTTGCTTTTGGTGATATACTGGCAGCCAGATGTGTGTTCACTGGTGAGGGGAGGACCGAAGCCACCCACATCGGCGGCACATCTAGTGATGAAATGTGCAACTTGTACATTATGTATTACATGGAAGCCAAGCATGCAGTTTCCTTCATGACCTGTACACAGAATGTGGCTCCAGATATGTTCAGAACTATCCCAGAAGAGGCCAATATTCCAATTCCTGTAAAATCCGACATGGTTATGATCCATGGGCATCACAAAGAAACAGAAAACAAAGAAAAGAGTGCTTTAATACAGCAGCCAAAGCAGGGAGAGGAGGAAGCCTTCGAGCAGGGTGATTTCTATTCACTACTTTCCAAGCTGCTAGGAGAAAGGGAAGATGTTGTTCATGTGCACAAATATAATCCTACAGAAAAGACAGAATCTGGGTCAGACCTGGTAGCTGAGATTGCAAACGTAGTCCAGAAAAAGGACCTTGGTCGGTCTGACGCCAGAGAGGGAGCGGAGCATGAGGAAGGGGGTAATGCTATCCTGGTCAGAGACAGGATCCACAAATTCCACAGGCTAGAGTCAACCTTGAGGCCAGCTGAGAGCAGAGCTCTATCCTTCCAGCAGCCTGGTGAAGGTCCTTGGGAACCAGAACTCGCAGGAGATTTCCATGTGGAAGAAGCACTGGAGTGGCCTGGAGTGTACTTGTTACCAGGCCAGGTTTCTGGGGTGGCCCTGGATTCTAAGAATAACCTTGTGATTTTCCACAGAGGTGACCATGTTTGGGATGGAAAGTTTAAAGAAACTACCAGATCATTTTCCAATGAATGCCTTGGTACCACCAGACCCATCACTCCTATTGATTCTTCGGATTTTACACTGGATATTCGCATGCCTGGGGTCACACCTAAAGAGTCTGACACGTACTTCTGCATGTCCATGCGTCTGCCTGTGGATGAGGAAGCCTTCGTGATTGACTTCAAGCCTCGGGCCAGCATGGACACTGTCCACCATATGCTGCTGTTTGGATGCAACATGCCCTCATCCACTGGGAGTTACTGGTTTTGTGATGAAGGAACCTGTACAGATAAAGCCAATATTCTATATGCCTGGGCAAGAAATGCTCCCCCCACCCGGCTCCCTAAAGGTGTTGGATTCAGAGTTGGAGGGGAAACTGGAAGCAAATACTTCGTCCTTCAAGTTCACTATGGGGACATCAGTGCTTTTCGAGATAATCACAAAGACTGTTCCGGTGTGTCCTTACATCTCACACGTGTGCCACAGCCTTTGATTGCGGGCATGTACCTTATGATGTCTGTCAACACTGTTATACCCCCAGGAGAGAAAGTAGTGAATTCTGACATTTCGTGCCATTACAAAATGTATCCAATGCATGTGTTTGCCTACCGAGTCCATACTCACCATTTAGGTAAGGTAGTGAGTGGATACAGAGTAAGAAACGGACAGTGGACGCTGATTGGACGCCAGAGCCCCCAGCTGCCACAGGCTTTTTACCCAGTGGAACACCCAGTAGATGTTGCTTTTGGTGATATACTGGCAGCCAGATGTGTGTTCACTGGTGAGGGGAGGACCGAAGCCACCCACATCGGCGGCACATCTAGTGATGAAATGTGCAACTTGTACATTATGTATTACATGGAAGCCAAGCATGCAGTTTCCTTCATGACCTGTACACAGAATGTGGCTCCAGATATGTTCAGAACTATCCCAGAAGAGGCCAATATTCCAATTCCTGTAAAATCCGACATGGTTATGATCCATGGGCATCACAAAGAAACAGAAAACAAAGAAAAGAGTGCTTTAATACAGCAGCCAAAGCAGGGAGAGGAGGAAGCCTTCGAGCAGGGTGATTTCTATTCACTACTTTCCAAGCTGCTAGGAGAAAGGGAAGATGTTGTTCATGTGCACAAATATAATCCTACAGAAAAGACAGAATCTGGGTCAGACCTGGTAGCTGAGATTGCAAACGTAGTCCAGAAAAAGGACCTTGGTCGGTCTGACGCCAGAGAGGGAGCGGAGCATGAGGAAGGGGGTAATGCTATCCTGGTCAGAGACAGGATCCACAAATTCCACAGGCTAGAGTCAACCTTGAGGCCAGCTGAGAGCAGAGCTCTATCCTTCCAGCAGCCTGGTGAAGGTCCTTGGGAACCAGAACTCGCAGGAGATTTCCATGTGGAAGAAGCACTGGAGTGGCCTGGAGTGTACTTGTTACCAGGCCAGGTTTCTGGGGTGGCCCTGGATTCTAAGAATAACCTTGTGATTTTCCACAGAGGTGACCATGTTTGGGATGGA
Peptide sequence:
MPGVTPKESDTYFCMSMRLPVDEEAFVIDFKPRASMDTVHHMLLFGCNMPSSTGSYWFCDEGTCTDKANILYAWARNAPPTRLPKGVGFRVGGETGSKYFVLQVHYGDISAFRDNHKDCSGVSLHLTRVPQPLIAGMYLMMSVNTVIPPGEKVVNSDISCHYKMYPMHVFAYRVHTHHLGKVVSGYRVRNGQWTLIGRQSPQLPQAFYPVEHPVDVAFGDILAARCVFTGEGRTEATHIGGTSSDEMCNLYIMYYMEAKHAVSFMTCTQNVAPDMFRTIPEEANIPIPVKSDMVMIHGHHKETENKEKSALIQQPKQGEEEAFEQGDFYSLLSKLLGEREDVVHVHKYNPTEKTESGSDLVAEIANVVQKKDLGRSDAREGAEHEEGGNAILVRDRIHKFHRLESTLRPAESRALSFQQPGEGPWEPELAGDFHVEEALEWPGVYLLPGQVSGVALDSKNNLVIFHRGDHVWDGKFKETTRSFSNECLGTTRPITPIDSSDFTLDIRMPGVTPKESDTYFCMSMRLPVDEEAFVIDFKPRASMDTVHHMLLFGCNMPSSTGSYWFCDEGTCTDKANILYAWARNAPPTRLPKGVGFRVGGETGSKYFVLQVHYGDISAFRDNHKDCSGVSLHLTRVPQPLIAGMYLMMSVNTVIPPGEKVVNSDISCHYKMYPMHVFAYRVHTHHLGKVVSGYRVRNGQWTLIGRQSPQLPQAFYPVEHPVDVAFGDILAARCVFTGEGRTEATHIGGTSSDEMCNLYIMYYMEAKHAVSFMTCTQNVAPDMFRTIPEEANIPIPVKSDMVMIHGHHKETENKEKSALIQQPKQGEEEAFEQGDFYSLLSKLLGEREDVVHVHKYNPTEKTESGSDLVAEIANVVQKKDLGRSDAREGAEHEEGGNAILVRDRIHKFHRLESTLRPAESRALSFQQPGEGPWEPELAGDFHVEEALEWPGVYLLPGQVSGVALDSKNNLVIFHRGDHVWDG
IRESfinder result
IRESfinder score
0.555052672
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
bottom of page