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mmu_circPam_806
Basic information of circular RNA
PanCircBase ID:
mmu_circPam_806
mm39_Chr. Position ID:
chr1|97811850|97852241|-
Gene name:
Pam
Transcript:
ENSMUST00000058762.15
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
9
Exon/intron indexes:
14,13,12,11,10,9,8,7,6
Exon/intron offsets:
0,1476,10235,11506,11843,13082,14215,38968,40305
Genomic length:
40391
Exon/intron sizes in nt:
72,185,104,77,81,68,49,84,86
Flanking exon/introns:
chr1:97792245-97811850|chr1:97852241-97862375
Splice length:
806
Other database IDs:
CIRCpedia: MMU_CIRCpedia_35673, circAtlas: mmu-Pam_0010
circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_49696
Human Ortholog IDs:
Mature spliced Sequence:
GTTTTGTGATGAAGGAACCTGTACAGATAAAGCCAATATTCTATATGCCTGGGCAAGAAATGCTCCCCCCACCCGGCTCCCTAAAGGTGTTGGATTCAGAGTTGGAGGGGAAACTGGAAGCAAATACTTCGTCCTTCAAGTTCACTATGGGGACATCAGTGCTTTTCGAGATAATCACAAAGACTGTTCCGGTGTGTCCTTACATCTCACACGTGTGCCACAGCCTTTGATTGCGGGCATGTACCTTATGATGTCTGTCAACACTGTTATACCCCCAGGAGAGAAAGTAGTGAATTCTGACATTTCGTGCCATTACAAAATGTATCCAATGCATGTGTTTGCCTACCGAGTCCATACTCACCATTTAGGTAAGGTAGTGAGTGGATACAGAGTAAGAAACGGACAGTGGACGCTGATTGGACGCCAGAGCCCCCAGCTGCCACAGGCTTTTTACCCAGTGGAACACCCAGTAGATGTTGCTTTTGGTGATATACTGGCAGCCAGATGTGTGTTCACTGGTGAGGGGAGGACCGAAGCCACCCACATCGGCGGCACATCTAGTGATGAAATGTGCAACTTGTACATTATGTATTACATGGAAGCCAAGCATGCAGTTTCCTTCATGACCTGTACACAGAATGTGGCTCCAGATATGTTCAGAACTATCCCAGAAGAGGCCAATATTCCAATTCCTGTAAAATCCGACATGGTTATGATCCATGGGCATCACAAAGAAACAGAAAACAAAGAAAAGAGTGCTTTAATACAGCAGCCAAAGCAGGGAGAGGAGGAAGCCTTCGAGCAGG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TTAATACAGCAGCCAAAGCAGG
59.25
TCCAACACCTTTAGGGAGCC
59.3
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AATACAGCAGCCAAAGCAGG
58.82
AATCCAACACCTTTAGGGAGCC
60.29
140
PCR template sequence:
ATGGTTATGATCCATGGGCATCACAAAGAAACAGAAAACAAAGAAAAGAGTGCTTTAATACAGCAGCCAAAGCAGGGAGAGGAGGAAGCCTTCGAGCAGGGTTTTGTGATGAAGGAACCTGTACAGATAAAGCCAATATTCTATATGCCTGGGCAAGAAATGCTCCCCCCACCCGGCTCCCTAAAGGTGTTGGATTCAGA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
4
Interacting miRNAs (#binding sites)
mmu-miR-33-5p(1), mmu-miR-183-5p(1), mmu-miR-541-5p(1), mmu-miR-466d-3p(1)
siRNAs for circular RNA silencing
Junction sequence
GCCTTCGAGCAGGGTTTTGTGATGAA
siRNA sets
TTCATCACAAAACCCTGCT, CATCACAAAACCCTGCTCG, TCATCACAAAACCCTGCTC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCPAM_806_ORF_1
0.9603
0.119555583
0.940052548
798
ORF sequence:
ATGTACCTTATGATGTCTGTCAACACTGTTATACCCCCAGGAGAGAAAGTAGTGAATTCTGACATTTCGTGCCATTACAAAATGTATCCAATGCATGTGTTTGCCTACCGAGTCCATACTCACCATTTAGGTAAGGTAGTGAGTGGATACAGAGTAAGAAACGGACAGTGGACGCTGATTGGACGCCAGAGCCCCCAGCTGCCACAGGCTTTTTACCCAGTGGAACACCCAGTAGATGTTGCTTTTGGTGATATACTGGCAGCCAGATGTGTGTTCACTGGTGAGGGGAGGACCGAAGCCACCCACATCGGCGGCACATCTAGTGATGAAATGTGCAACTTGTACATTATGTATTACATGGAAGCCAAGCATGCAGTTTCCTTCATGACCTGTACACAGAATGTGGCTCCAGATATGTTCAGAACTATCCCAGAAGAGGCCAATATTCCAATTCCTGTAAAATCCGACATGGTTATGATCCATGGGCATCACAAAGAAACAGAAAACAAAGAAAAGAGTGCTTTAATACAGCAGCCAAAGCAGGGAGAGGAGGAAGCCTTCGAGCAGGGTTTTGTGATGAAGGAACCTGTACAGATAAAGCCAATATTCTATATGCCTGGGCAAGAAATGCTCCCCCCACCCGGCTCCCTAAAGGTGTTGGATTCAGAGTTGGAGGGGAAACTGGAAGCAAATACTTCGTCCTTCAAGTTCACTATGGGGACATCAGTGCTTTTCGAGATAATCACAAAGACTGTTCCGGTGTGTCCTTACATCTCACACGTGTGCCACAGCCTTTGA
Peptide sequence:
MYLMMSVNTVIPPGEKVVNSDISCHYKMYPMHVFAYRVHTHHLGKVVSGYRVRNGQWTLIGRQSPQLPQAFYPVEHPVDVAFGDILAARCVFTGEGRTEATHIGGTSSDEMCNLYIMYYMEAKHAVSFMTCTQNVAPDMFRTIPEEANIPIPVKSDMVMIHGHHKETENKEKSALIQQPKQGEEEAFEQGFVMKEPVQIKPIFYMPGQEMLPPPGSLKVLDSELEGKLEANTSSFKFTMGTSVLFEIITKTVPVCPYISHVCHSL
IRESfinder result
IRESfinder score
0.527212677
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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