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mmu_circPpwd1_773
Basic information of circular RNA
PanCircBase ID:
mmu_circPpwd1_773
mm39_Chr. Position ID:
chr13|104356544|104361960|-
Gene name:
Ppwd1
Transcript:
ENSMUST00000022226.6
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
5,4,3,2
Exon/intron offsets:
0,2801,3055,5313
Genomic length:
5416
Exon/intron sizes in nt:
4,48,12,11,01,103
Flanking exon/introns:
chr13:104353787-104356544|chr13:104361960-104365113
Splice length:
773
Other database IDs:
CIRCpedia: MMU_CIRCpedia_225764
circBase: hsa_circ_0072697, circAtlas: hsa-PPWD1_0007, CIRCpedia: HSA_CIRCpedia_52200
Human Ortholog IDs:
Mature spliced Sequence:
TTCTGGAGTTCGAAAGAGTCTACCTTGATAATCTCCCCAGTGCATCCATGTATGAGCGCAGTTACATGCACAGAGATGTTATCACACATGTGGTATGTACCAAAACAGATTTTATTATCACTGCCAGTCATGATGGACATGTTAAATTTTGGAAAAAAATAGAAGAAGGAATTGAGTTTGTTAAACATTTTCGTAGTCACCTTGGAGTTATTGAGAGTATTGCAGTTAGCTCTGAGGGAGCGTTGTTCTGCTCTGTCGGTGATGATAAAGCGATGAAGGTGTTTGATGTGGTGAACTTTGACATGATCAACATGCTGAAGCTCGGCTATTTTCCTGGACAGTGTGAGTGGATATATTGCCCAGGAGATGCCATATCTTCAGTTGCTGCTTCTGAGAAGAGTACAGGAAAAATTTTCATTTATGATGGACGAGGAGATAACCAGCCACTTCATATTTTTGACAAACTCCATGTATCCCCTCTTACTCAAATAAGACTAAACCCAGTTTACAAAGCAGTGGTGTCTTCTGACAAATCCGGGATGATTGAGTACTGGACTGGACCGCCGCACGAATATAAGTTCCCTAAAAATGTGAACTGGGAGTATAAGACAGACACAGACTTATATGAATTTGCCAAGTGTAAGGCATATCCAACCAGCATATGTTTTTCACCTGATGGGAAGAAAATAGCAACCATTGGATCAGACAGAAAAGTTAGAATTTTCAGGTTTTTAACTGGAAAACTCATGAGGGTCTTTGATGAATCATTAAGT
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AGCAACCATTGGATCAGACAGA
59.69
TGCGCTCATACATGGATGCA
60.18
145
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AGCAACCATTGGATCAGACAGA
59.69
GCGCTCATACATGGATGCAC
59.76
144
PCR template sequence:
TGATGGGAAGAAAATAGCAACCATTGGATCAGACAGAAAAGTTAGAATTTTCAGGTTTTTAACTGGAAAACTCATGAGGGTCTTTGATGAATCATTAAGTTTCTGGAGTTCGAAAGAGTCTACCTTGATAATCTCCCCAGTGCATCCATGTATGAGCGCAGTTACATGCACAGAGATGTTATCACACATGTGGTATGTAC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
17
Interacting miRNAs (#binding sites)
mmu-miR-23b-3p(2), mmu-miR-23a-3p(2), mmu-miR-210-3p(1), mmu-miR-16-5p(1), mmu-miR-15a-5p(1), mmu-miR-141-3p(1), mmu-miR-34c-5p(1), mmu-miR-322-5p(1), mmu-miR-15b-5p(1), mmu-miR-495-3p(1), mmu-miR-182-5p(1), mmu-miR-34b-5p(1), mmu-miR-680(1), mmu-miR-466a-5p(1), mmu-miR-1187(1), mmu-miR-466p-5p(1), mmu-miR-190b-5p(1)
siRNAs for circular RNA silencing
Junction sequence
TGAATCATTAAGTTTCTGGAGTTCGA
siRNA sets
GAACTCCAGAAACTTAATG,AACTCCAGAAACTTAATGA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCPPWD1_773_ORF_1
0.7432
-0.03287316
0.915019591
888
ORF sequence:
ATGTATGAGCGCAGTTACATGCACAGAGATGTTATCACACATGTGGTATGTACCAAAACAGATTTTATTATCACTGCCAGTCATGATGGACATGTTAAATTTTGGAAAAAAATAGAAGAAGGAATTGAGTTTGTTAAACATTTTCGTAGTCACCTTGGAGTTATTGAGAGTATTGCAGTTAGCTCTGAGGGAGCGTTGTTCTGCTCTGTCGGTGATGATAAAGCGATGAAGGTGTTTGATGTGGTGAACTTTGACATGATCAACATGCTGAAGCTCGGCTATTTTCCTGGACAGTGTGAGTGGATATATTGCCCAGGAGATGCCATATCTTCAGTTGCTGCTTCTGAGAAGAGTACAGGAAAAATTTTCATTTATGATGGACGAGGAGATAACCAGCCACTTCATATTTTTGACAAACTCCATGTATCCCCTCTTACTCAAATAAGACTAAACCCAGTTTACAAAGCAGTGGTGTCTTCTGACAAATCCGGGATGATTGAGTACTGGACTGGACCGCCGCACGAATATAAGTTCCCTAAAAATGTGAACTGGGAGTATAAGACAGACACAGACTTATATGAATTTGCCAAGTGTAAGGCATATCCAACCAGCATATGTTTTTCACCTGATGGGAAGAAAATAGCAACCATTGGATCAGACAGAAAAGTTAGAATTTTCAGGTTTTTAACTGGAAAACTCATGAGGGTCTTTGATGAATCATTAAGTTTCTGGAGTTCGAAAGAGTCTACCTTGATAATCTCCCCAGTGCATCCATGTATGAGCGCAGTTACATGCACAGAGATGTTATCACACATGTGGTATGTACCAAAACAGATTTTATTATCACTGCCAGTCATGATGGACATGTTAAATTTTGGAAAAAAATAG
Peptide sequence:
MYERSYMHRDVITHVVCTKTDFIITASHDGHVKFWKKIEEGIEFVKHFRSHLGVIESIAVSSEGALFCSVGDDKAMKVFDVVNFDMINMLKLGYFPGQCEWIYCPGDAISSVAASEKSTGKIFIYDGRGDNQPLHIFDKLHVSPLTQIRLNPVYKAVVSSDKSGMIEYWTGPPHEYKFPKNVNWEYKTDTDLYEFAKCKAYPTSICFSPDGKKIATIGSDRKVRIFRFLTGKLMRVFDESLSFWSSKESTLIISPVHPCMSAVTCTEMLSHMWYVPKQILLSLPVMMDMLNFGKK
IRESfinder result
IRESfinder score
0.705880213
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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