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mmu_circPhldb2_947
Basic information of circular RNA
PanCircBase ID:
mmu_circPhldb2_947
mm39_Chr. Position ID:
chr16|45583272|45601820|-
Gene name:
Phldb2
Transcript:
ENSMUST00000036355.13
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
7
Exon/intron indexes:
13,12,11,10,9,8,7
Exon/intron offsets:
0,7762,9225,12034,14803,17346,18392
Genomic length:
18548
Exon/intron sizes in nt:
2,05,10,01,41,14,49,01,00,000
Flanking exon/introns:
chr16:45578570-45583272|chr16:45601820-45609351
Splice length:
947
Other database IDs:
circBase: hsa_circ_0004125, circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_24377
Human Ortholog IDs:
Mature spliced Sequence:
GATGCCGACCTGTTGGATGTTGAGAGCAAACACTTTGAAGACTTGGAATTCCAGCAGCTTGAGCATGAGAGCCGCCTAGATGAGGAAAAGGAGAACTTGACTCAACAGCTCCTGCGGGAGGTGGCAGAGTATCAGCGGAACATCGTGGCTAGGAAGGAAAAAATTTCTGCATTGAAAAAGCAAGCCAGTCACATCGTTCAGCAGGCTCAGAGGGAACAAGATCACTTTGTGAAAGAGAAGAACAATCTAATAATGATGCTCCAAAGAGAAAAAGAGAATCTTTGCAATTTGGAAAAGAAATACTCCAGTCTCACTGGTGGGAAAGGGTTCCCTATTAACCCCAATACTCTGAAAGAGGGCTATATCAGTGTAAATGAGATTAATGAGTCATGTGGCAATTCCACGAATCTATCCCCTTCCACTCAGTTCCCTGCTGATGCTGATGCTGCTGTCACTGAGCCTGCCTTGGCTGTGCCGGTGAGCCAGCCCCAGAGTTCAGAGCACTTTAGAAGCCTGGAAGAAAGGAAAAAGCAGCACAAAGAAGGCCTCTACCTGAGTGACACTCTGCCTCGAAAGAAAACCACCCCTTCCCTGTCCCCACACTTCAGCAGTGCCACAATGGGGAGGAGCACCACCCCGAAGGCTCACCTCCCTCTGGGGCAGAGCAATAGCTGTGGCAGTGTGCTCCCTCACTCACTGGCGACCATGACCAAAGACTCTGAGTCTCGGAGGATGCTCAGAGGTTATAATCACCAACAGATGAGTGAAGGACAAAGACAGAAACCCGAATTTTACAGCCGCACAGCATCTGAGTCAAACGTCTACTTGAATAGTTTCCATTACCCAGATCGCAGCTACAAGGATCAGGCCTATGACACGTTGAGCCTGGACAGCTCTGACAGCATGGAGACCAGCATCTCTGCCTGTTCACCGGACAATATATCAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GCCTATGACACGTTGAGCCT
60.11
TCATGCTCAAGCTGCTGGAA
59.96
148
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AGGCCTATGACACGTTGAGC
60.11
TCATGCTCAAGCTGCTGGAA
59.96
150
PCR template sequence:
ATCGCAGCTACAAGGATCAGGCCTATGACACGTTGAGCCTGGACAGCTCTGACAGCATGGAGACCAGCATCTCTGCCTGTTCACCGGACAATATATCAAGGATGCCGACCTGTTGGATGTTGAGAGCAAACACTTTGAAGACTTGGAATTCCAGCAGCTTGAGCATGAGAGCCGCCTAGATGAGGAAAAGGAGAACTTGA
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-9-5p(1), mmu-miR-20b-5p(1), mmu-miR-134-5p(1), mmu-miR-106a-5p(1), mmu-miR-93-5p(1), mmu-miR-20a-5p(1), mmu-miR-17-5p(1), mmu-miR-181a-5p(1), mmu-miR-15b-5p(1), mmu-miR-709(1), mmu-miR-214-3p(1), mmu-miR-24-3p(1), mmu-miR-362-5p(1), mmu-miR-324-3p(1), mmu-miR-384-3p(1), mmu-miR-29b-2-5p(1), mmu-miR-484(1)
siRNAs for circular RNA silencing
Junction sequence
ACAATATATCAAGGATGCCGACCTGT
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCPHLDB2_947_ORF_1
0.8778
0.174349442
0.933595835
774
ORF sequence:
ATGATGCTCCAAAGAGAAAAAGAGAATCTTTGCAATTTGGAAAAGAAATACTCCAGTCTCACTGGTGGGAAAGGGTTCCCTATTAACCCCAATACTCTGAAAGAGGGCTATATCAGTGTAAATGAGATTAATGAGTCATGTGGCAATTCCACGAATCTATCCCCTTCCACTCAGTTCCCTGCTGATGCTGATGCTGCTGTCACTGAGCCTGCCTTGGCTGTGCCGGTGAGCCAGCCCCAGAGTTCAGAGCACTTTAGAAGCCTGGAAGAAAGGAAAAAGCAGCACAAAGAAGGCCTCTACCTGAGTGACACTCTGCCTCGAAAGAAAACCACCCCTTCCCTGTCCCCACACTTCAGCAGTGCCACAATGGGGAGGAGCACCACCCCGAAGGCTCACCTCCCTCTGGGGCAGAGCAATAGCTGTGGCAGTGTGCTCCCTCACTCACTGGCGACCATGACCAAAGACTCTGAGTCTCGGAGGATGCTCAGAGGTTATAATCACCAACAGATGAGTGAAGGACAAAGACAGAAACCCGAATTTTACAGCCGCACAGCATCTGAGTCAAACGTCTACTTGAATAGTTTCCATTACCCAGATCGCAGCTACAAGGATCAGGCCTATGACACGTTGAGCCTGGACAGCTCTGACAGCATGGAGACCAGCATCTCTGCCTGTTCACCGGACAATATATCAAGGATGCCGACCTGTTGGATGTTGAGAGCAAACACTTTGAAGACTTGGAATTCCAGCAGCTTGAGCATGAGAGCCGCCTAG
Peptide sequence:
MMLQREKENLCNLEKKYSSLTGGKGFPINPNTLKEGYISVNEINESCGNSTNLSPSTQFPADADAAVTEPALAVPVSQPQSSEHFRSLEERKKQHKEGLYLSDTLPRKKTTPSLSPHFSSATMGRSTTPKAHLPLGQSNSCGSVLPHSLATMTKDSESRRMLRGYNHQQMSEGQRQKPEFYSRTASESNVYLNSFHYPDRSYKDQAYDTLSLDSSDSMETSISACSPDNISRMPTCWMLRANTLKTWNSSSLSMRAA
IRESfinder result
IRESfinder score
0.565309173
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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