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mmu_circDhx9_653
Basic information of circular RNA
PanCircBase ID:
mmu_circDhx9_653
mm39_Chr. Position ID:
chr1|153347971|153352308|-
Gene name:
Dhx9
Transcript:
ENSMUST00000190544.7
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
6
Exon/intron indexes:
7,6,5,4,3,2
Exon/intron offsets:
0,175,446,921,3437,4198
Genomic length:
4337
Exon/intron sizes in nt:
78,16,29,01,37,47,139
Flanking exon/introns:
chr1:153347557-153347971|chr1:153352308-153353786
Splice length:
653
Other database IDs:
circAtlas: mmu-Dhx9_0008
Human Ortholog IDs:
Mature spliced Sequence:
GTGGAGGAGAATGAGATTGAGTGCTGACTTTAAGCCTGGCTGAGAAACATACTGTCATCGGTGTCATTAATGAAAGGGTGGATGTTGTTCCCCTGAAAGCCAGTGGCCTTTGACCCCCTTGAAGCCCTTGTGCCTGAAGGAGCTTTATTGCAGAAATGACCATTTATATCAAGCAGCTTGGCAGAAGGATTTTCGCACGTGAACATGGATCTAATAAGAAATTAGCAGCACAGTCATGTGCCCTCTCACTTGTCCGACAGCTCTATCATCTTGGAGTGATTGAGGCTTACTCTGGGCTTACAAAGAAGAAAGAAGGAGAGAGAGTGGAGCCTTACAAAGTTTTCCTTTCTCCAGATTTGGAGCTTCAGCTGCAAAATGTGGTTCAAGAGCTAGATCTTGAAATTGTGCCCCCACCTGTTGATCCTTCTATGCCAGTTATACTTAACATTGGGAAATTGGCTCATTTTGAACCATCTCAGAGACAAAATGCAGTGGGAGTGGTTCCTTGGTCACCTCCACAATCCAACTGGAATCCTTGGACAAGTAGCAACATTGATGAGGGACCCCTTGCTTATGCTTCTACAGAACAAATAAGCATGGACCTTAAGAATGAATTAACATACCAGATGGAACAAGATCATAATTTACAAAGT
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GGGACCCCTTGCTTATGCTT
60.03
AGTATGTTTCTCAGCCAGGCT
59.09
147
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GGGACCCCTTGCTTATGCTT
60.03
CAGTATGTTTCTCAGCCAGGC
58.99
148
PCR template sequence:
TGATGAGGGACCCCTTGCTTATGCTTCTACAGAACAAATAAGCATGGACCTTAAGAATGAATTAACATACCAGATGGAACAAGATCATAATTTACAAAGTGTGGAGGAGAATGAGATTGAGTGCTGACTTTAAGCCTGGCTGAGAAACATACTGTCATCGGTGTCATTAATGAAAGGGTGGATGTTGTTCCCCTGAAAGC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
5
Interacting miRNAs (#binding sites)
mmu-miR-199a-5p(1), mmu-miR-127-5p(1), mmu-miR-425-5p(1), mmu-miR-5101(1), mmu-miR-335-3p(1)
siRNAs for circular RNA silencing
Junction sequence
TAATTTACAAAGTGTGGAGGAGAATG
siRNA sets
ATTCTCCTCCACACTTTGT, TTCTCCTCCACACTTTGTA, CATTCTCCTCCACACTTTG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCDHX9_653_ORF_1
1.0998
0.052182064
0.684284921
525
ORF sequence:
ATGACCATTTATATCAAGCAGCTTGGCAGAAGGATTTTCGCACGTGAACATGGATCTAATAAGAAATTAGCAGCACAGTCATGTGCCCTCTCACTTGTCCGACAGCTCTATCATCTTGGAGTGATTGAGGCTTACTCTGGGCTTACAAAGAAGAAAGAAGGAGAGAGAGTGGAGCCTTACAAAGTTTTCCTTTCTCCAGATTTGGAGCTTCAGCTGCAAAATGTGGTTCAAGAGCTAGATCTTGAAATTGTGCCCCCACCTGTTGATCCTTCTATGCCAGTTATACTTAACATTGGGAAATTGGCTCATTTTGAACCATCTCAGAGACAAAATGCAGTGGGAGTGGTTCCTTGGTCACCTCCACAATCCAACTGGAATCCTTGGACAAGTAGCAACATTGATGAGGGACCCCTTGCTTATGCTTCTACAGAACAAATAAGCATGGACCTTAAGAATGAATTAACATACCAGATGGAACAAGATCATAATTTACAAAGTGTGGAGGAGAATGAGATTGAGTGCTGA
Peptide sequence:
MTIYIKQLGRRIFAREHGSNKKLAAQSCALSLVRQLYHLGVIEAYSGLTKKKEGERVEPYKVFLSPDLELQLQNVVQELDLEIVPPPVDPSMPVILNIGKLAHFEPSQRQNAVGVVPWSPPQSNWNPWTSSNIDEGPLAYASTEQISMDLKNELTYQMEQDHNLQSVEENEIEC
IRESfinder result
IRESfinder score
0.795410563
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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