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mmu_circPkd2_1189
Basic information of circular RNA
PanCircBase ID:
mmu_circPkd2_1189
mm39_Chr. Position ID:
chr5|104624908|104637280|+
Gene name:
Pkd2
Transcript:
ENSMUST00000086831.4
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
6
Exon/intron indexes:
3,4,5,6,7,8
Exon/intron offsets:
0,1748,3107,5982,9604,12190
Genomic length:
12372
Exon/intron sizes in nt:
1,34,25,12,25,22,91,68,000
Flanking exon/introns:
chr5:104614862-104624908|chr5:104637280-104638509
Splice length:
1189
Other database IDs:
circBase: hsa_circ_0070401, circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_49532
Human Ortholog IDs:
Mature spliced Sequence:
TGACCTACGGCATGATGAGCTCCAATGTGTACTACTACACTCGGACACTGTCACAGCTATTCATAGACACCCCAGTGTCGAAAACAGAGAAAACCAACTTTAAAACTCTTTCTTCCATGGAGGACTTCTGGAAGTTCACCGAAGGCTCCTTCCTGGATGGGCTGTACTGGAAGGCACAGACCAGCAACCACACGCAAGCTGACAACCGAAGCTTTATCTTCTATGAGAACCTGCTGCTAGGAGTGCCGCGTCTACGCCAACTCCGAGTCAGAAACGGATCCTGCTCCATCCCTCAGGACCTGCGAGATGAAATTAAAGAGTGCTATGACGTCTACTCCGTCAGCAGTGAGGACAGAGCTCCATTTGGACCGCGGAATGGAACTGCGTGGATGTACACAAGTGAGAAGGAGCTGAATGGGAGCAGTCACTGGGGGATCATTGCGTCGTACAGTGGAGCGGGTTACTACCTGGATCTGTCCAGAACCAGGGAGGAGACAGCAGCCCAGCTTGCTGGCCTCAGGAGGAACTTCTGGCTGGACCGGGGCACGCGGGCAGCTTTTATAGACTTCTCGGTGTATAACGCAAACATTAACCTGTTCTGTGTGGTCAGGTTATTGGCGGAGTTCCCAGCAACGGGTGGCGTGGTACCCTCTTGGCAGTTTCAGCCTGTAAAACTGATCCGCTATGTCACAGCCTTTGATTTCTTCCTGGCAGCCTGTGAGATCATCTTTTGTTTCTTTATCATTTACTATGTGGTGGAAGAGATATTGGAAATTCGGATTCACAGACTGAGCTATTTCAGGAGTTTCTGGAATTGTCTGGATGTTGTGATTGTCGTGTTATCTGTAGTAGCTATGGTGATTAACATTTACCGAATGTCAAATGCAGAGGGGCTGCTACAGTTTCTTGAAGATCAAAATTCTTTCCCCAACTTTGAGCATGTGGCATACTGGCAAATACAGTTCAACAATATAAGTGCTGTCATGGTATTTTTGGTCTGGATTAAGCTCTTCAAATTCATCAATTTTAATAGGACCATGAGCCAGCTCTCCACAACCATGTCTCGATGTGCCAAAGACCTCTTCGGCTTCACCATAATGTTCTCCATCATCTTCTTGGCATACGCACAGCTGGCATACCTTGTCTTCGGCACCCAGGTCGATGACTTCAGCACTTTCCAAGAATGTAT
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CTTCTTGGCATACGCACAGC
59.9
TCTGTTTTCGACACTGGGGT
59.17
166
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
ATACCTTGTCTTCGGCACCC
59.75
TCTGTTTTCGACACTGGGGT
59.17
142
PCR template sequence:
TCACCATAATGTTCTCCATCATCTTCTTGGCATACGCACAGCTGGCATACCTTGTCTTCGGCACCCAGGTCGATGACTTCAGCACTTTCCAAGAATGTATTGACCTACGGCATGATGAGCTCCAATGTGTACTACTACACTCGGACACTGTCACAGCTATTCATAGACACCCCAGTGTCGAAAACAGAGAAAACCAACTT
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-210-3p(1), mmu-miR-20b-5p(1), mmu-miR-16-5p(1), mmu-miR-106a-5p(1), mmu-miR-93-5p(1), mmu-miR-20a-5p(1), mmu-miR-17-5p(1), mmu-miR-106b-5p(1), mmu-miR-149-5p(1), mmu-miR-127-5p(1), mmu-miR-96-5p(1), mmu-miR-669d-5p(1)
siRNAs for circular RNA silencing
Junction sequence
TCCAAGAATGTATTGACCTACGGCAT
siRNA sets
AGGTCAATACATTCTTGGA, GTAGGTCAATACATTCTTG, ATGCCGTAGGTCAATACAT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCPKD2_1189_ORF_1
1.0203
0.225418985
0.998847266
1281
ORF sequence:
ATGATGAGCTCCAATGTGTACTACTACACTCGGACACTGTCACAGCTATTCATAGACACCCCAGTGTCGAAAACAGAGAAAACCAACTTTAAAACTCTTTCTTCCATGGAGGACTTCTGGAAGTTCACCGAAGGCTCCTTCCTGGATGGGCTGTACTGGAAGGCACAGACCAGCAACCACACGCAAGCTGACAACCGAAGCTTTATCTTCTATGAGAACCTGCTGCTAGGAGTGCCGCGTCTACGCCAACTCCGAGTCAGAAACGGATCCTGCTCCATCCCTCAGGACCTGCGAGATGAAATTAAAGAGTGCTATGACGTCTACTCCGTCAGCAGTGAGGACAGAGCTCCATTTGGACCGCGGAATGGAACTGCGTGGATGTACACAAGTGAGAAGGAGCTGAATGGGAGCAGTCACTGGGGGATCATTGCGTCGTACAGTGGAGCGGGTTACTACCTGGATCTGTCCAGAACCAGGGAGGAGACAGCAGCCCAGCTTGCTGGCCTCAGGAGGAACTTCTGGCTGGACCGGGGCACGCGGGCAGCTTTTATAGACTTCTCGGTGTATAACGCAAACATTAACCTGTTCTGTGTGGTCAGGTTATTGGCGGAGTTCCCAGCAACGGGTGGCGTGGTACCCTCTTGGCAGTTTCAGCCTGTAAAACTGATCCGCTATGTCACAGCCTTTGATTTCTTCCTGGCAGCCTGTGAGATCATCTTTTGTTTCTTTATCATTTACTATGTGGTGGAAGAGATATTGGAAATTCGGATTCACAGACTGAGCTATTTCAGGAGTTTCTGGAATTGTCTGGATGTTGTGATTGTCGTGTTATCTGTAGTAGCTATGGTGATTAACATTTACCGAATGTCAAATGCAGAGGGGCTGCTACAGTTTCTTGAAGATCAAAATTCTTTCCCCAACTTTGAGCATGTGGCATACTGGCAAATACAGTTCAACAATATAAGTGCTGTCATGGTATTTTTGGTCTGGATTAAGCTCTTCAAATTCATCAATTTTAATAGGACCATGAGCCAGCTCTCCACAACCATGTCTCGATGTGCCAAAGACCTCTTCGGCTTCACCATAATGTTCTCCATCATCTTCTTGGCATACGCACAGCTGGCATACCTTGTCTTCGGCACCCAGGTCGATGACTTCAGCACTTTCCAAGAATGTATTGACCTACGGCATGATGAGCTCCAATGTGTACTACTACACTCGGACACTGTCACAGCTATTCATAGACACCCCAGTGTCGAAAACAGAGAAAACCAACTTTAA
Peptide sequence:
MMSSNVYYYTRTLSQLFIDTPVSKTEKTNFKTLSSMEDFWKFTEGSFLDGLYWKAQTSNHTQADNRSFIFYENLLLGVPRLRQLRVRNGSCSIPQDLRDEIKECYDVYSVSSEDRAPFGPRNGTAWMYTSEKELNGSSHWGIIASYSGAGYYLDLSRTREETAAQLAGLRRNFWLDRGTRAAFIDFSVYNANINLFCVVRLLAEFPATGGVVPSWQFQPVKLIRYVTAFDFFLAACEIIFCFFIIYYVVEEILEIRIHRLSYFRSFWNCLDVVIVVLSVVAMVINIYRMSNAEGLLQFLEDQNSFPNFEHVAYWQIQFNNISAVMVFLVWIKLFKFINFNRTMSQLSTTMSRCAKDLFGFTIMFSIIFLAYAQLAYLVFGTQVDDFSTFQECIDLRHDELQCVLLHSDTVTAIHRHPSVENRENQL
IRESfinder result
IRESfinder score
0.630340052
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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