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mmu_circPam_894
Basic information of circular RNA
PanCircBase ID:
mmu_circPam_894
mm39_Chr. Position ID:
chr1|97811850|97862463|-
Gene name:
Pam
Transcript:
ENSMUST00000058762.15
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
10
Exon/intron indexes:
14,13,12,11,10,9,8,7,6,5
Exon/intron offsets:
0,1476,10235,11506,11843,13082,14215,38968,40305,50525
Genomic length:
50613
Exon/intron sizes in nt:
72,185,104,77,81,68,49,84,86,88
Flanking exon/introns:
chr1:97792245-97811850|chr1:97862463-97872344
Splice length:
894
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
TTGACTTCAAGCCTCGGGCCAGCATGGACACTGTCCACCATATGCTGCTGTTTGGATGCAACATGCCCTCATCCACTGGGAGTTACTGGTTTTGTGATGAAGGAACCTGTACAGATAAAGCCAATATTCTATATGCCTGGGCAAGAAATGCTCCCCCCACCCGGCTCCCTAAAGGTGTTGGATTCAGAGTTGGAGGGGAAACTGGAAGCAAATACTTCGTCCTTCAAGTTCACTATGGGGACATCAGTGCTTTTCGAGATAATCACAAAGACTGTTCCGGTGTGTCCTTACATCTCACACGTGTGCCACAGCCTTTGATTGCGGGCATGTACCTTATGATGTCTGTCAACACTGTTATACCCCCAGGAGAGAAAGTAGTGAATTCTGACATTTCGTGCCATTACAAAATGTATCCAATGCATGTGTTTGCCTACCGAGTCCATACTCACCATTTAGGTAAGGTAGTGAGTGGATACAGAGTAAGAAACGGACAGTGGACGCTGATTGGACGCCAGAGCCCCCAGCTGCCACAGGCTTTTTACCCAGTGGAACACCCAGTAGATGTTGCTTTTGGTGATATACTGGCAGCCAGATGTGTGTTCACTGGTGAGGGGAGGACCGAAGCCACCCACATCGGCGGCACATCTAGTGATGAAATGTGCAACTTGTACATTATGTATTACATGGAAGCCAAGCATGCAGTTTCCTTCATGACCTGTACACAGAATGTGGCTCCAGATATGTTCAGAACTATCCCAGAAGAGGCCAATATTCCAATTCCTGTAAAATCCGACATGGTTATGATCCATGGGCATCACAAAGAAACAGAAAACAAAGAAAAGAGTGCTTTAATACAGCAGCCAAAGCAGGGAGAGGAGGAAGCCTTCGAGCAGG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TGATCCATGGGCATCACAAAGA
60.03
GTTGCATCCAAACAGCAGCA
59.97
155
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TGATCCATGGGCATCACAAAGA
60.03
TGTTGCATCCAAACAGCAGC
59.97
156
PCR template sequence:
ATGGTTATGATCCATGGGCATCACAAAGAAACAGAAAACAAAGAAAAGAGTGCTTTAATACAGCAGCCAAAGCAGGGAGAGGAGGAAGCCTTCGAGCAGGTTGACTTCAAGCCTCGGGCCAGCATGGACACTGTCCACCATATGCTGCTGTTTGGATGCAACATGCCCTCATCCACTGGGAGTTACTGGTTTTGTGATGA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
10
Interacting miRNAs (#binding sites)
mmu-miR-15a-5p(1), mmu-miR-103-3p(1), mmu-miR-34a-5p(1), mmu-miR-15b-5p(1), mmu-miR-33-5p(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)
siRNAs for circular RNA silencing
Junction sequence
GCCTTCGAGCAGGTTGACTTCAAGCC
siRNA sets
TTGAAGTCAACCTGCTCGA, GAAGTCAACCTGCTCGAAG, CTTGAAGTCAACCTGCTCG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCPAM_894_ORF_1
0.9568
0.129663318
0.99994195
1764
ORF sequence:
ATGGACACTGTCCACCATATGCTGCTGTTTGGATGCAACATGCCCTCATCCACTGGGAGTTACTGGTTTTGTGATGAAGGAACCTGTACAGATAAAGCCAATATTCTATATGCCTGGGCAAGAAATGCTCCCCCCACCCGGCTCCCTAAAGGTGTTGGATTCAGAGTTGGAGGGGAAACTGGAAGCAAATACTTCGTCCTTCAAGTTCACTATGGGGACATCAGTGCTTTTCGAGATAATCACAAAGACTGTTCCGGTGTGTCCTTACATCTCACACGTGTGCCACAGCCTTTGATTGCGGGCATGTACCTTATGATGTCTGTCAACACTGTTATACCCCCAGGAGAGAAAGTAGTGAATTCTGACATTTCGTGCCATTACAAAATGTATCCAATGCATGTGTTTGCCTACCGAGTCCATACTCACCATTTAGGTAAGGTAGTGAGTGGATACAGAGTAAGAAACGGACAGTGGACGCTGATTGGACGCCAGAGCCCCCAGCTGCCACAGGCTTTTTACCCAGTGGAACACCCAGTAGATGTTGCTTTTGGTGATATACTGGCAGCCAGATGTGTGTTCACTGGTGAGGGGAGGACCGAAGCCACCCACATCGGCGGCACATCTAGTGATGAAATGTGCAACTTGTACATTATGTATTACATGGAAGCCAAGCATGCAGTTTCCTTCATGACCTGTACACAGAATGTGGCTCCAGATATGTTCAGAACTATCCCAGAAGAGGCCAATATTCCAATTCCTGTAAAATCCGACATGGTTATGATCCATGGGCATCACAAAGAAACAGAAAACAAAGAAAAGAGTGCTTTAATACAGCAGCCAAAGCAGGGAGAGGAGGAAGCCTTCGAGCAGGTTGACTTCAAGCCTCGGGCCAGCATGGACACTGTCCACCATATGCTGCTGTTTGGATGCAACATGCCCTCATCCACTGGGAGTTACTGGTTTTGTGATGAAGGAACCTGTACAGATAAAGCCAATATTCTATATGCCTGGGCAAGAAATGCTCCCCCCACCCGGCTCCCTAAAGGTGTTGGATTCAGAGTTGGAGGGGAAACTGGAAGCAAATACTTCGTCCTTCAAGTTCACTATGGGGACATCAGTGCTTTTCGAGATAATCACAAAGACTGTTCCGGTGTGTCCTTACATCTCACACGTGTGCCACAGCCTTTGATTGCGGGCATGTACCTTATGATGTCTGTCAACACTGTTATACCCCCAGGAGAGAAAGTAGTGAATTCTGACATTTCGTGCCATTACAAAATGTATCCAATGCATGTGTTTGCCTACCGAGTCCATACTCACCATTTAGGTAAGGTAGTGAGTGGATACAGAGTAAGAAACGGACAGTGGACGCTGATTGGACGCCAGAGCCCCCAGCTGCCACAGGCTTTTTACCCAGTGGAACACCCAGTAGATGTTGCTTTTGGTGATATACTGGCAGCCAGATGTGTGTTCACTGGTGAGGGGAGGACCGAAGCCACCCACATCGGCGGCACATCTAGTGATGAAATGTGCAACTTGTACATTATGTATTACATGGAAGCCAAGCATGCAGTTTCCTTCATGACCTGTACACAGAATGTGGCTCCAGATATGTTCAGAACTATCCCAGAAGAGGCCAATATTCCAATTCCTGTAAAATCCGACATGGTTATGATCCATGGGCATCACAAAGAAACAGAAAACAAAGAAAAGAGTGCTTTAATACAGCAGCCAAAGCAGGGAGAGGAGGAAGCCTTCGAGCAG
Peptide sequence:
MDTVHHMLLFGCNMPSSTGSYWFCDEGTCTDKANILYAWARNAPPTRLPKGVGFRVGGETGSKYFVLQVHYGDISAFRDNHKDCSGVSLHLTRVPQPLIAGMYLMMSVNTVIPPGEKVVNSDISCHYKMYPMHVFAYRVHTHHLGKVVSGYRVRNGQWTLIGRQSPQLPQAFYPVEHPVDVAFGDILAARCVFTGEGRTEATHIGGTSSDEMCNLYIMYYMEAKHAVSFMTCTQNVAPDMFRTIPEEANIPIPVKSDMVMIHGHHKETENKEKSALIQQPKQGEEEAFEQVDFKPRASMDTVHHMLLFGCNMPSSTGSYWFCDEGTCTDKANILYAWARNAPPTRLPKGVGFRVGGETGSKYFVLQVHYGDISAFRDNHKDCSGVSLHLTRVPQPLIAGMYLMMSVNTVIPPGEKVVNSDISCHYKMYPMHVFAYRVHTHHLGKVVSGYRVRNGQWTLIGRQSPQLPQAFYPVEHPVDVAFGDILAARCVFTGEGRTEATHIGGTSSDEMCNLYIMYYMEAKHAVSFMTCTQNVAPDMFRTIPEEANIPIPVKSDMVMIHGHHKETENKEKSALIQQPKQGEEEAFEQ
IRESfinder result
IRESfinder score
0.523842165
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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