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mmu_circHspd1_695
Basic information of circular RNA
PanCircBase ID:
mmu_circHspd1_695
mm39_Chr. Position ID:
chr1|55120818|55123944|-
Gene name:
Hspd1
Transcript:
ENSMUST00000027123.15
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
7,6,5,4,3
Exon/intron offsets:
0,398,1407,2065,2873
Genomic length:
3126
Exon/intron sizes in nt:
1,69,94,96,83,253
Flanking exon/introns:
chr1:55120331-55120818|chr1:55123944-55125924
Splice length:
695
Other database IDs:
circAtlas: mmu-Hspd1_0001
circBase: hsa_circ_0057676, circAtlas: hsa-SCAF8_0001
Human Ortholog IDs:
Mature spliced Sequence:
GGAAGAACTGTGATTATTGAACAGAGTTGGGGAAGTCCCAAAGTAACAAAAGATGGGGTCACTGTTGCAAAGTCAATTGATTTAAAGGATAAATACAAAAATATTGGAGCTAAACTTGTTCAGGACGTTGCCAATAACACAAACGAAGAGGCTGGGGATGGCACCACCACTGCCACTGTTCTGGCACGATCTATTGCCAAGGAGGGCTTTGAGAAGATCAGCAAAGGGGCTAATCCAGTGGAAATCCGGAGAGGTGTGATGTTGGCTGTGGATGCTGTAATTGCTGAACTTAAGAAACAGTCTAAACCTGTGACAACCCCTGAAGAAATTGCTCAGGTTGCTACAATTTCTGCAAATGGAGACAAAGACATTGGGAACATCATTTCTGATGCAATGAAAAAGGTTGGAAGAAAGGGTGTCATCACAGTGAAGGATGGAAAAACCCTGAATGATGAGCTAGAAATTATTGAAGGCATGAAGTTTGATAGAGGATATATTTCCCCGTATTTTATTAACACATCAAAAGGTCAAAAGTGTGAATTCCAAGATGCCTATGTCTTGTTGAGTGAAAAGAAAATTTCCAGTGTTCAGTCCATTGTCCCTGCTCTTGAAATTGCTAATGCTCATCGGAAGCCATTGGTCATAATCGCCGAAGACGTTGACGGAGAAGCTCTAAGCACGCTGGTTTTGAACAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TCATCGGAAGCCATTGGTCA
59.38
ACTTTGCAACAGTGACCCCA
60.03
145
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TGCTCATCGGAAGCCATTGG
60.75
ACTTTGCAACAGTGACCCCA
60.03
148
PCR template sequence:
TTGTCCCTGCTCTTGAAATTGCTAATGCTCATCGGAAGCCATTGGTCATAATCGCCGAAGACGTTGACGGAGAAGCTCTAAGCACGCTGGTTTTGAACAGGGAAGAACTGTGATTATTGAACAGAGTTGGGGAAGTCCCAAAGTAACAAAAGATGGGGTCACTGTTGCAAAGTCAATTGATTTAAAGGATAAATACAAAA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
9
Interacting miRNAs (#binding sites)
mmu-miR-182-5p(2), mmu-miR-135a-5p(1), mmu-miR-335-5p(1), 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
TGGTTTTGAACAGGGAAGAACTGTGA
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCHSPD1_695_ORF_1
1.1205
0.189396608
0.69632242
450
ORF sequence:
ATGTTGGCTGTGGATGCTGTAATTGCTGAACTTAAGAAACAGTCTAAACCTGTGACAACCCCTGAAGAAATTGCTCAGGTTGCTACAATTTCTGCAAATGGAGACAAAGACATTGGGAACATCATTTCTGATGCAATGAAAAAGGTTGGAAGAAAGGGTGTCATCACAGTGAAGGATGGAAAAACCCTGAATGATGAGCTAGAAATTATTGAAGGCATGAAGTTTGATAGAGGATATATTTCCCCGTATTTTATTAACACATCAAAAGGTCAAAAGTGTGAATTCCAAGATGCCTATGTCTTGTTGAGTGAAAAGAAAATTTCCAGTGTTCAGTCCATTGTCCCTGCTCTTGAAATTGCTAATGCTCATCGGAAGCCATTGGTCATAATCGCCGAAGACGTTGACGGAGAAGCTCTAAGCACGCTGGTTTTGAACAGGGAAGAACTGTGA
Peptide sequence:
MLAVDAVIAELKKQSKPVTTPEEIAQVATISANGDKDIGNIISDAMKKVGRKGVITVKDGKTLNDELEIIEGMKFDRGYISPYFINTSKGQKCEFQDAYVLLSEKKISSVQSIVPALEIANAHRKPLVIIAEDVDGEALSTLVLNREEL
IRESfinder result
IRESfinder score
0.463131777
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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