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mmu_circHspd1_526
Basic information of circular RNA
PanCircBase ID:
mmu_circHspd1_526
mm39_Chr. Position ID:
chr1|55121216|55123944|-
Gene name:
Hspd1
Transcript:
ENSMUST00000027123.15
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
6,5,4,3
Exon/intron offsets:
0,1009,1667,2475
Genomic length:
2728
Exon/intron sizes in nt:
94,96,83,253
Flanking exon/introns:
chr1:55120987-55121216|chr1:55123944-55125924
Splice length:
526
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GGAAGAACTGTGATTATTGAACAGAGTTGGGGAAGTCCCAAAGTAACAAAAGATGGGGTCACTGTTGCAAAGTCAATTGATTTAAAGGATAAATACAAAAATATTGGAGCTAAACTTGTTCAGGACGTTGCCAATAACACAAACGAAGAGGCTGGGGATGGCACCACCACTGCCACTGTTCTGGCACGATCTATTGCCAAGGAGGGCTTTGAGAAGATCAGCAAAGGGGCTAATCCAGTGGAAATCCGGAGAGGTGTGATGTTGGCTGTGGATGCTGTAATTGCTGAACTTAAGAAACAGTCTAAACCTGTGACAACCCCTGAAGAAATTGCTCAGGTTGCTACAATTTCTGCAAATGGAGACAAAGACATTGGGAACATCATTTCTGATGCAATGAAAAAGGTTGGAAGAAAGGGTGTCATCACAGTGAAGGATGGAAAAACCCTGAATGATGAGCTAGAAATTATTGAAGGCATGAAGTTTGATAGAGGATATATTTCCCCGTATTTTATTAACACATCAAAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GTGAAGGATGGAAAAACCCTGA
58.5
ACTTTGCAACAGTGACCCCA
60.03
173
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TGGAAAAACCCTGAATGATGAGC
59.49
ACTTTGCAACAGTGACCCCA
60.03
165
PCR template sequence:
GTGAAGGATGGAAAAACCCTGAATGATGAGCTAGAAATTATTGAAGGCATGAAGTTTGATAGAGGATATATTTCCCCGTATTTTATTAACACATCAAAAGGGAAGAACTGTGATTATTGAACAGAGTTGGGGAAGTCCCAAAGTAACAAAAGATGGGGTCACTGTTGCAAAGTCAATTGATTTAAAGGATAAATACAAAA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
7
Interacting miRNAs (#binding sites)
mmu-miR-182-5p(2), mmu-miR-136-5p(1), mmu-miR-433-5p(1), mmu-miR-676-3p(1), mmu-miR-382-3p(1), mmu-miR-194-5p(1), mmu-miR-425-5p(1)
siRNAs for circular RNA silencing
Junction sequence
AACACATCAAAAGGGAAGAACTGTGA
siRNA sets
GTTCTTCCCTTTTGATGTG,AGTTCTTCCCTTTTGATGT,TTCTTCCCTTTTGATGTGT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCHSPD1_526_ORF_1
1.1242
0.174524858
0.404867472
288
ORF sequence:
ATGTTGGCTGTGGATGCTGTAATTGCTGAACTTAAGAAACAGTCTAAACCTGTGACAACCCCTGAAGAAATTGCTCAGGTTGCTACAATTTCTGCAAATGGAGACAAAGACATTGGGAACATCATTTCTGATGCAATGAAAAAGGTTGGAAGAAAGGGTGTCATCACAGTGAAGGATGGAAAAACCCTGAATGATGAGCTAGAAATTATTGAAGGCATGAAGTTTGATAGAGGATATATTTCCCCGTATTTTATTAACACATCAAAAGGGAAGAACTGTGATTATTGA
Peptide sequence:
MLAVDAVIAELKKQSKPVTTPEEIAQVATISANGDKDIGNIISDAMKKVGRKGVITVKDGKTLNDELEIIEGMKFDRGYISPYFINTSKGKNCDY
IRESfinder result
IRESfinder score
0.516955567
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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