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mmu_circRftn2_795
Basic information of circular RNA
PanCircBase ID:
mmu_circRftn2_795
mm39_Chr. Position ID:
chr1|55224108|55245774|-
Gene name:
Rftn2
Transcript:
ENSMUST00000027121.15
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
8,7,6,5,4
Exon/intron offsets:
0,9294,10566,19233,21386
Genomic length:
21666
Exon/intron sizes in nt:
7,91,04,12,22,10,280
Flanking exon/introns:
chr1:55211241-55224108|chr1:55245774-55250308
Splice length:
795
Other database IDs:
circAtlas: mmu-Rftn2_0016
circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_158066
Human Ortholog IDs:
Mature spliced Sequence:
ATTAATGCCGCTGCTAAAAGAGGGATGAAGTTTGTTGGGCTGGTCTCCCAGTGCTACTTGCCATCTATGCACTGTAATGGAGCCAGCCACGATGGAGTTGCAGAGTCGGGGCTACACGTGAGACAAGATTCACAAGACAACTGCAAAGGCTGGAATGAAGGAGCCCTTGGTGGACACTTGTCTGAAAGTGGAGTGGAGGAGGAACCTCAGCATGAAAGTGGACAGCATCAGACAGAGAGGAACAGCAGCCCCAGCTACGCTAACCCAAAGCGGGGAGAAGCCCCAGATGGTAAGCTGTACATGGTCTTCAATGCTTTTGAGGAAGATGCGGCCAGCTGGGCCTATCAGGAAGGTGTCCTGTCCATGAAAGTGACGCGGAAGGGAGCTGTCATCAGCGCTCTGGACGCCAACTGGCTAGAACTAACGACATTTTACTATAAGCAAGGCTTCTCTTTAATTGACTCTTTTGTGTGCTGGGAGACACCTAAAGGGGACCAGTTACCTAAATCTTTGGAAGGCTTTTTTATCTACGAAGAAGAAGGATCTGGAGTCCCAGGTTCTAACAGGAGAGGAAACGACGCCATTGTGGTGGAGCAGTGGACAGTCATTGAGGGCTGTGAAATTAAAACAGATTACGGCCCCCTGCTGCACACCCTGGCTGAGTTTGGATGGCTTCTGACAAGCGTGTTGCCTACCCCGATATTGAGACATGACAGTGAAGGGAATTTGGCTACCAAGCAAGTCGTATTTCTCCAAAGGCCGGTTACGTGGAACTCAGCTGCTCAAACCCCAGAA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TTCTCCAAAGGCCGGTTACG
60.32
ATCGTGGCTGGCTCCATTAC
60.18
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TTCTCCAAAGGCCGGTTACG
60.32
CATCGTGGCTGGCTCCATTA
60.18
141
PCR template sequence:
CCCGATATTGAGACATGACAGTGAAGGGAATTTGGCTACCAAGCAAGTCGTATTTCTCCAAAGGCCGGTTACGTGGAACTCAGCTGCTCAAACCCCAGAAATTAATGCCGCTGCTAAAAGAGGGATGAAGTTTGTTGGGCTGGTCTCCCAGTGCTACTTGCCATCTATGCACTGTAATGGAGCCAGCCACGATGGAGTTG
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-205-5p(1), mmu-miR-495-3p(1), mmu-miR-503-5p(1), mmu-miR-149-5p(1), mmu-miR-207(1), mmu-miR-673-5p(1), mmu-miR-539-5p(1), mmu-miR-490-3p(1), mmu-miR-376a-3p(1)
siRNAs for circular RNA silencing
Junction sequence
TCAAACCCCAGAAATTAATGCCGCTG
siRNA sets
ATTAATTTCTGGGGTTTGA, AGCGGCATTAATTTCTGGG, GCGGCATTAATTTCTGGGG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCRFTN2_795_ORF_1
0.7907
0.205828797
0.999759474
1566
ORF sequence:
ATGAAGTTTGTTGGGCTGGTCTCCCAGTGCTACTTGCCATCTATGCACTGTAATGGAGCCAGCCACGATGGAGTTGCAGAGTCGGGGCTACACGTGAGACAAGATTCACAAGACAACTGCAAAGGCTGGAATGAAGGAGCCCTTGGTGGACACTTGTCTGAAAGTGGAGTGGAGGAGGAACCTCAGCATGAAAGTGGACAGCATCAGACAGAGAGGAACAGCAGCCCCAGCTACGCTAACCCAAAGCGGGGAGAAGCCCCAGATGGTAAGCTGTACATGGTCTTCAATGCTTTTGAGGAAGATGCGGCCAGCTGGGCCTATCAGGAAGGTGTCCTGTCCATGAAAGTGACGCGGAAGGGAGCTGTCATCAGCGCTCTGGACGCCAACTGGCTAGAACTAACGACATTTTACTATAAGCAAGGCTTCTCTTTAATTGACTCTTTTGTGTGCTGGGAGACACCTAAAGGGGACCAGTTACCTAAATCTTTGGAAGGCTTTTTTATCTACGAAGAAGAAGGATCTGGAGTCCCAGGTTCTAACAGGAGAGGAAACGACGCCATTGTGGTGGAGCAGTGGACAGTCATTGAGGGCTGTGAAATTAAAACAGATTACGGCCCCCTGCTGCACACCCTGGCTGAGTTTGGATGGCTTCTGACAAGCGTGTTGCCTACCCCGATATTGAGACATGACAGTGAAGGGAATTTGGCTACCAAGCAAGTCGTATTTCTCCAAAGGCCGGTTACGTGGAACTCAGCTGCTCAAACCCCAGAAATTAATGCCGCTGCTAAAAGAGGGATGAAGTTTGTTGGGCTGGTCTCCCAGTGCTACTTGCCATCTATGCACTGTAATGGAGCCAGCCACGATGGAGTTGCAGAGTCGGGGCTACACGTGAGACAAGATTCACAAGACAACTGCAAAGGCTGGAATGAAGGAGCCCTTGGTGGACACTTGTCTGAAAGTGGAGTGGAGGAGGAACCTCAGCATGAAAGTGGACAGCATCAGACAGAGAGGAACAGCAGCCCCAGCTACGCTAACCCAAAGCGGGGAGAAGCCCCAGATGGTAAGCTGTACATGGTCTTCAATGCTTTTGAGGAAGATGCGGCCAGCTGGGCCTATCAGGAAGGTGTCCTGTCCATGAAAGTGACGCGGAAGGGAGCTGTCATCAGCGCTCTGGACGCCAACTGGCTAGAACTAACGACATTTTACTATAAGCAAGGCTTCTCTTTAATTGACTCTTTTGTGTGCTGGGAGACACCTAAAGGGGACCAGTTACCTAAATCTTTGGAAGGCTTTTTTATCTACGAAGAAGAAGGATCTGGAGTCCCAGGTTCTAACAGGAGAGGAAACGACGCCATTGTGGTGGAGCAGTGGACAGTCATTGAGGGCTGTGAAATTAAAACAGATTACGGCCCCCTGCTGCACACCCTGGCTGAGTTTGGATGGCTTCTGACAAGCGTGTTGCCTACCCCGATATTGAGACATGACAGTGAAGGGAATTTGGCTACCAAGCAAGTCGTATTTCTCCAAAGGCCGGTTACGTGGAACTCAGCTGCTCAAACCCCAGAA
Peptide sequence:
MKFVGLVSQCYLPSMHCNGASHDGVAESGLHVRQDSQDNCKGWNEGALGGHLSESGVEEEPQHESGQHQTERNSSPSYANPKRGEAPDGKLYMVFNAFEEDAASWAYQEGVLSMKVTRKGAVISALDANWLELTTFYYKQGFSLIDSFVCWETPKGDQLPKSLEGFFIYEEEGSGVPGSNRRGNDAIVVEQWTVIEGCEIKTDYGPLLHTLAEFGWLLTSVLPTPILRHDSEGNLATKQVVFLQRPVTWNSAAQTPEINAAAKRGMKFVGLVSQCYLPSMHCNGASHDGVAESGLHVRQDSQDNCKGWNEGALGGHLSESGVEEEPQHESGQHQTERNSSPSYANPKRGEAPDGKLYMVFNAFEEDAASWAYQEGVLSMKVTRKGAVISALDANWLELTTFYYKQGFSLIDSFVCWETPKGDQLPKSLEGFFIYEEEGSGVPGSNRRGNDAIVVEQWTVIEGCEIKTDYGPLLHTLAEFGWLLTSVLPTPILRHDSEGNLATKQVVFLQRPVTWNSAAQTPE
IRESfinder result
IRESfinder score
0.419061008
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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