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mmu_circHps3_1022
Basic information of circular RNA
PanCircBase ID:
mmu_circHps3_1022
mm39_Chr. Position ID:
chr3|20076921|20084969|-
Gene name:
Hps3
Transcript:
ENSMUST00000012580.13
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
6,5,4,3,2
Exon/intron offsets:
0,2973,6202,6389,7556
Genomic length:
8048
Exon/intron sizes in nt:
82,190,86,172,492
Flanking exon/introns:
chr3:20074121-20076921|chr3:20084969-20089212
Splice length:
1022
Other database IDs:
CIRCpedia: MMU_CIRCpedia_12796, circAtlas: mmu-Hps3_0006
circAtlas: hsa-HPS3_0003, CIRCpedia: HSA_CIRCpedia_124653
Human Ortholog IDs:
Mature spliced Sequence:
GAGACTATCTGGTAGCAATTGAGGAGAAAAACAAAACTATATTCCTGCGTGCTTACGTGAATTGGAGGAGTAAGAGGAGCGACAACTCCCGTGTGTGCATTCGAATGGTTGGCCACAATGTGGAGGCATCCTTCTGTGAAAGCTTTAGAGACCAGATGTCTATAATTGAGATGCCAATGTCTGAGGCCCCTTTGTGCTTTTCGTGTTGTCCTGTGAAAGGAGATCTTCTTGTTGGATGTACAAATAAGTTAGTGTTATTTACTTTGAAGTATGATATCATTAATGAGGAATTCTCAATATTGAACTTTGAACGTTCATTAATTATACACATAGATAATATCACTCCTGTTGAAATCTCTTTTTGTGTTGGATATGTTGCTGTCATGTCTGATTTAGAAGTCTTACTCCTAAAACTGGAGTCAGACCCTATACATGGAGAGAGTGTTGACCACCACCCACAAGAAACCAGCAATCCATTGAAAGAGGCGGAAGGTGTCAGTAATGAAACTTCACAACTTGAGTCAGAAGATTTTGTTATCTGTCTAAAACCCATGGAACTCATTGGTGAAAAATGTGAACAGTCTGGGATATCTGTTAAACTGGAGTCCACAGGATTAGAAGATGAAAAAGTAAAATATTTACGTGTTCGGCATCTATTGTATAGACGTTTTGCTCCAGATATTTCGTCCTATGTCTTGTCTGATAACATCAAGTTACATTCCCTTCAGCTGCTACCCATTCACCAAAGTGGTTTTCATCCTGATGAAAATGATTTATCGCCGAAAAAAGAGATGCCAAATCTCTTCTGTTTCTTCTCGTTACCTCATGTGGGCTATCTGTACATGGTTGTGAAGTCTGTTGAATTAATGTCAGTCTATTGGTATCCTGAGAAGTCTCAACAAGCCGTGCTCACACCACAGTTCTTGCATGTCATCACAAGCCAAAGCCTGCAGTGTTTCACGGTGCGATGCAGTGCAGCGGTGGCACATGAGGAAGACCTATACATGGATACTACGCTAAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CAGTGTTTCACGGTGCGATG
60.11
TCGCTCCTCTTACTCCTCCA
59.38
154
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CAGTGTTTCACGGTGCGATG
60.11
ATGCACACACGGGAGTTGTC
60.88
172
PCR template sequence:
CTTGCATGTCATCACAAGCCAAAGCCTGCAGTGTTTCACGGTGCGATGCAGTGCAGCGGTGGCACATGAGGAAGACCTATACATGGATACTACGCTAAAGGAGACTATCTGGTAGCAATTGAGGAGAAAAACAAAACTATATTCCTGCGTGCTTACGTGAATTGGAGGAGTAAGAGGAGCGACAACTCCCGTGTGTGCAT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
8
Interacting miRNAs (#binding sites)
mmu-miR-1a-3p(1), mmu-miR-206-3p(1), mmu-miR-122-5p(1), mmu-miR-217-5p(1), mmu-miR-23a-3p(1), mmu-miR-29b-1-5p(1), mmu-miR-29b-2-5p(1), mmu-miR-335-3p(1)
siRNAs for circular RNA silencing
Junction sequence
TACTACGCTAAAGGAGACTATCTGGT
siRNA sets
ATAGTCTCCTTTAGCGTAG, CAGATAGTCTCCTTTAGCG, TAGTCTCCTTTAGCGTAGT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCHPS3_1022_ORF_1
0.8366
0.012137762
0.95466801
933
ORF sequence:
ATGGTTGGCCACAATGTGGAGGCATCCTTCTGTGAAAGCTTTAGAGACCAGATGTCTATAATTGAGATGCCAATGTCTGAGGCCCCTTTGTGCTTTTCGTGTTGTCCTGTGAAAGGAGATCTTCTTGTTGGATGTACAAATAAGTTAGTGTTATTTACTTTGAAGTATGATATCATTAATGAGGAATTCTCAATATTGAACTTTGAACGTTCATTAATTATACACATAGATAATATCACTCCTGTTGAAATCTCTTTTTGTGTTGGATATGTTGCTGTCATGTCTGATTTAGAAGTCTTACTCCTAAAACTGGAGTCAGACCCTATACATGGAGAGAGTGTTGACCACCACCCACAAGAAACCAGCAATCCATTGAAAGAGGCGGAAGGTGTCAGTAATGAAACTTCACAACTTGAGTCAGAAGATTTTGTTATCTGTCTAAAACCCATGGAACTCATTGGTGAAAAATGTGAACAGTCTGGGATATCTGTTAAACTGGAGTCCACAGGATTAGAAGATGAAAAAGTAAAATATTTACGTGTTCGGCATCTATTGTATAGACGTTTTGCTCCAGATATTTCGTCCTATGTCTTGTCTGATAACATCAAGTTACATTCCCTTCAGCTGCTACCCATTCACCAAAGTGGTTTTCATCCTGATGAAAATGATTTATCGCCGAAAAAAGAGATGCCAAATCTCTTCTGTTTCTTCTCGTTACCTCATGTGGGCTATCTGTACATGGTTGTGAAGTCTGTTGAATTAATGTCAGTCTATTGGTATCCTGAGAAGTCTCAACAAGCCGTGCTCACACCACAGTTCTTGCATGTCATCACAAGCCAAAGCCTGCAGTGTTTCACGGTGCGATGCAGTGCAGCGGTGGCACATGAGGAAGACCTATACATGGATACTACGCTAAAGGAGACTATCTGGTAG
Peptide sequence:
MVGHNVEASFCESFRDQMSIIEMPMSEAPLCFSCCPVKGDLLVGCTNKLVLFTLKYDIINEEFSILNFERSLIIHIDNITPVEISFCVGYVAVMSDLEVLLLKLESDPIHGESVDHHPQETSNPLKEAEGVSNETSQLESEDFVICLKPMELIGEKCEQSGISVKLESTGLEDEKVKYLRVRHLLYRRFAPDISSYVLSDNIKLHSLQLLPIHQSGFHPDENDLSPKKEMPNLFCFFSLPHVGYLYMVVKSVELMSVYWYPEKSQQAVLTPQFLHVITSQSLQCFTVRCSAAVAHEEDLYMDTTLKETIW
IRESfinder result
IRESfinder score
0.681550025
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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