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mmu_circRims2_642
Basic information of circular RNA
PanCircBase ID:
mmu_circRims2_642
mm39_Chr. Position ID:
chr15|39138370|39209016|+
Gene name:
Rims2
Transcript:
ENSMUST00000082054.12
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
2,3,4,5
Exon/intron offsets:
0,438,17126,70335
Genomic length:
70646
Exon/intron sizes in nt:
33,87,211,311
Flanking exon/introns:
chr15:39061933-39138370|chr15:39209016-39300392
Splice length:
642
Other database IDs:
CIRCpedia: MMU_CIRCpedia_19099, circAtlas: mmu-Rims2_0010
circAtlas: hsa-RIMS2_0026, CIRCpedia: HSA_CIRCpedia_348232
Human Ortholog IDs:
Mature spliced Sequence:
GATCAAAGAAGAACACAAAGCACAACCGACACAGTGGTTTCCCTTTAGTGGGATCACTGAACTGGTAAATAACGTTCTGCAGCCCCAGCAAAAACAACCCAATGAGAAGGAGCCCCAGACAAAGCTGCACCAACAATTTGAAATGTATAAGGAGCAAGTCAAGAAGATGGGAGAGGAATCGCAGCAGCAGCAAGAGCAGAAGGGTGATGCCCCGACCTGTGGCATCTGCCACAAGACAAAATTTGCAGATGGATGCGGCCATAATTGTTCCTATTGCCAAACCAAGTTCTGTGCTCGATGTGGAGGTCGAGTGTCTTTACGCTCAAACAAGGTTATGTGGGTGTGTAATTTGTGCCGAAAACAACAAGAAATCCTCACTAAATCAGGAGCATGGTTTTATAATAGTGGGTCTAACACACTGCAGCAACCTGATCAAAAGGTTCCTCGAGGGCTTCGAAATGAGGAAGCCCCTCAGGAGAAGAAAGCAAAACTACACGAGCAGCCCCAGTTCCAAGGAGCCCCAGGTGACTTATCAGTACCTGCAGTTGAGAAAGGCCGAGCTCATGGGCTCACAAGACAGGATACTATTAAAAATGGATCAGGAGTGAAGCACCAGATTGCCAGTGACATGCCTTCAGACAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AGCTCATGGGCTCACAAGAC
60.04
TGGGGCTGCAGAACGTTATT
59.96
171
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GCTCATGGGCTCACAAGACA
60.32
TGGGGCTGCAGAACGTTATT
59.96
170
PCR template sequence:
CAGTTGAGAAAGGCCGAGCTCATGGGCTCACAAGACAGGATACTATTAAAAATGGATCAGGAGTGAAGCACCAGATTGCCAGTGACATGCCTTCAGACAGGATCAAAGAAGAACACAAAGCACAACCGACACAGTGGTTTCCCTTTAGTGGGATCACTGAACTGGTAAATAACGTTCTGCAGCCCCAGCAAAAACAACCC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
6
Interacting miRNAs (#binding sites)
mmu-miR-182-5p(1), mmu-miR-340-5p(1), mmu-miR-224-5p(1), mmu-miR-129-5p(1), mmu-miR-207(1), mmu-miR-1904(1)
siRNAs for circular RNA silencing
Junction sequence
TGCCTTCAGACAGGATCAAAGAAGAA
siRNA sets
CTTCTTTGATCCTGTCTGA, TTCTTCTTTGATCCTGTCT, TCTTCTTTGATCCTGTCTG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCRIMS2_642_ORF_1
0.8293
0.18222715
0.994731485
1140
ORF sequence:
ATGTATAAGGAGCAAGTCAAGAAGATGGGAGAGGAATCGCAGCAGCAGCAAGAGCAGAAGGGTGATGCCCCGACCTGTGGCATCTGCCACAAGACAAAATTTGCAGATGGATGCGGCCATAATTGTTCCTATTGCCAAACCAAGTTCTGTGCTCGATGTGGAGGTCGAGTGTCTTTACGCTCAAACAAGGTTATGTGGGTGTGTAATTTGTGCCGAAAACAACAAGAAATCCTCACTAAATCAGGAGCATGGTTTTATAATAGTGGGTCTAACACACTGCAGCAACCTGATCAAAAGGTTCCTCGAGGGCTTCGAAATGAGGAAGCCCCTCAGGAGAAGAAAGCAAAACTACACGAGCAGCCCCAGTTCCAAGGAGCCCCAGGTGACTTATCAGTACCTGCAGTTGAGAAAGGCCGAGCTCATGGGCTCACAAGACAGGATACTATTAAAAATGGATCAGGAGTGAAGCACCAGATTGCCAGTGACATGCCTTCAGACAGGATCAAAGAAGAACACAAAGCACAACCGACACAGTGGTTTCCCTTTAGTGGGATCACTGAACTGGTAAATAACGTTCTGCAGCCCCAGCAAAAACAACCCAATGAGAAGGAGCCCCAGACAAAGCTGCACCAACAATTTGAAATGTATAAGGAGCAAGTCAAGAAGATGGGAGAGGAATCGCAGCAGCAGCAAGAGCAGAAGGGTGATGCCCCGACCTGTGGCATCTGCCACAAGACAAAATTTGCAGATGGATGCGGCCATAATTGTTCCTATTGCCAAACCAAGTTCTGTGCTCGATGTGGAGGTCGAGTGTCTTTACGCTCAAACAAGGTTATGTGGGTGTGTAATTTGTGCCGAAAACAACAAGAAATCCTCACTAAATCAGGAGCATGGTTTTATAATAGTGGGTCTAACACACTGCAGCAACCTGATCAAAAGGTTCCTCGAGGGCTTCGAAATGAGGAAGCCCCTCAGGAGAAGAAAGCAAAACTACACGAGCAGCCCCAGTTCCAAGGAGCCCCAGGTGACTTATCAGTACCTGCAGTTGAGAAAGGCCGAGCTCATGGGCTCACAAGACAGGATACTATTAAAAATGGATCAGGAGTGAAGCACCAGATTGCCAGTGACATGCCTTCAGAC
Peptide sequence:
MYKEQVKKMGEESQQQQEQKGDAPTCGICHKTKFADGCGHNCSYCQTKFCARCGGRVSLRSNKVMWVCNLCRKQQEILTKSGAWFYNSGSNTLQQPDQKVPRGLRNEEAPQEKKAKLHEQPQFQGAPGDLSVPAVEKGRAHGLTRQDTIKNGSGVKHQIASDMPSDRIKEEHKAQPTQWFPFSGITELVNNVLQPQQKQPNEKEPQTKLHQQFEMYKEQVKKMGEESQQQQEQKGDAPTCGICHKTKFADGCGHNCSYCQTKFCARCGGRVSLRSNKVMWVCNLCRKQQEILTKSGAWFYNSGSNTLQQPDQKVPRGLRNEEAPQEKKAKLHEQPQFQGAPGDLSVPAVEKGRAHGLTRQDTIKNGSGVKHQIASDMPSD
IRESfinder result
IRESfinder score
0.490151542
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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