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mmu_circRttn_1499
Basic information of circular RNA
PanCircBase ID:
mmu_circRttn_1499
mm39_Chr. Position ID:
chr18|89071643|89113770|+
Gene name:
Rttn
Transcript:
ENSMUST00000023828.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
11
Exon/intron indexes:
28,29,30,31,32,33,34,35,36,37,38
Exon/intron offsets:
0,6841,7232,10581,12327,20025,21907,28374,36907,38296,41973
Genomic length:
42127
Exon/intron sizes in nt:
22,01,29,11,11,59,72,10,00,00,00,00,00,000
Flanking exon/introns:
chr18:89066644-89071643|chr18:89113770-89119754
Splice length:
1499
Other database IDs:
circAtlas: mmu-Rttn_0056
Human Ortholog IDs:
Mature spliced Sequence:
GAAATGCTTGGAACTGTTTTACGTTTTCCAAACACAGCTGTCTCTGAAGCTACTCCAGTGCCTCAGAGTCACAGATGCTCCCCATTTCTATGGCTTACCTTCATTGGAGAGGACCTTAGCAGGGATGGCTCACCTCACTGCCTTCCCTGGGTGGAGTGCACACTCTCCTCTTTCAAAGCCACTTGAGATTTGTGGGAAGTACTTGTCCGGTCTCCTGGAGGTCATTACTTCCTTTTATGTTGAACGGGGAGGAAATGCTATGTCCTTCATGGGGAAAGGCGTTACAAAGAGCACAGGTCTTTGCTTACTTCACTTATCCCATGAGATGATAGTCCAGGCACCAGGCTCGGAGTGGATGCCGCTTTGGTTCTTGCCTTTGGGTAGTCACAGTGAAGAACATGCCCCTACTCAGCAAGGATTGGCCTGGCTAATTCCCTTATGGGTTGATAGAGACCCAGAGGTGAGATTCACTTCACTGGGGTTGGGATCAGCACTGACTACTATTGAAGCTGGCTGTGTGGCCTTGGCAAACAGTTGTCAGAATATTTCTGGTGGGCTCTGGGGAACCGTGGTGAACATTCTTCTGGATCAATCAGAATGCAGTCTGGTGCGCCGGGAGGCTGCATTTATTCTTCAGAATCTCCTTGTAATTCCAATGCCTTCAGAAATTATAAAGGATTATACTTGGCAGGGCCCCTGTGTCCATGATGAGGATTCTGGCCTGTCACTTTCAGGAAAACCTGCCCTTCAGGCTCTTTTATATCACTGTCGTTTCTATGAACATTTGACTCACATGGTGAAACATTGTTATGTAGGAAGATATATCTTTGATTTTAATTTTTCTGCTTTTACTGAAACTTCAGAATACAGTGATTTAAATGGTTTAGACGACTCATTCAAGTTTTGGAGGGCCCCTTCTGGGACATCTACTCAGGATCATGAGCCAAGCTCTCTTTCCACCTCAGAAACAATGGTGGCTGCCTCGGTGGTCAGTTCTGAGATTCAGCCCCTGCTGCCGTCAACACTTCTTCCTGAAACTGCCCTTGACCAGTTTGTGACGCAAGGTCAACGTGAAATGAGACCAGTGCGACCTCGTGACTCATTGCTGTCTACTTCCCTGAACAGGCAGTATGTGTTTGTTACTCCGTCTCTGCTGTCAGCAGTCTGTAGCCTTTTAGACAACCTCTTGGCAGTTACTCCAAGAGATGCTGCAAATGCTTTTCAACAAGCTCATCTCATAGAACTCCTCTGTAGCACGGTGGATGCTTCCCTCATAGAAATGTGCATCCAAGAACTCAAGACCCCACTGCCTTTACCATCTGCTGTTGAACATATTCAGGCTCAGGCTTCCTTTTTCTTGGAATACCTATCCTCTTTGTCCCAGCTCTTGAAGTCCTGTCTGTTGGTAGAGCCTAAACTTGTGACACAAGATGAGCTCTTGAAACCTCTTATCACTAATGTCATCCGAGTTCTCATTGTGTGTCCCAAAGATGTATTAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TGTGACACAAGATGAGCTCT
56.49
TCTGAGGCACTGGAGTAGCT
59.96
147
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TGGTAGAGCCTAAACTTGTGACA
59.36
TCTGAGGCACTGGAGTAGCT
59.96
163
PCR template sequence:
CTGTTGGTAGAGCCTAAACTTGTGACACAAGATGAGCTCTTGAAACCTCTTATCACTAATGTCATCCGAGTTCTCATTGTGTGTCCCAAAGATGTATTAGGAAATGCTTGGAACTGTTTTACGTTTTCCAAACACAGCTGTCTCTGAAGCTACTCCAGTGCCTCAGAGTCACAGATGCTCCCCATTTCTATGGCTTACCT
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-216a-5p(2), mmu-miR-34c-5p(1), mmu-miR-335-5p(1), mmu-miR-146a-5p(1), mmu-miR-495-3p(1), mmu-miR-34b-5p(1), mmu-miR-190b-5p(1), mmu-miR-669d-5p(1), mmu-miR-146b-5p(1)
siRNAs for circular RNA silencing
Junction sequence
AAAGATGTATTAGGAAATGCTTGGAA
siRNA sets
AAGCATTTCCTAATACATC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCRTTN_1499_ORF_1
0.779
-0.017395743
0.99821398
1422
ORF sequence:
ATGGCTCACCTCACTGCCTTCCCTGGGTGGAGTGCACACTCTCCTCTTTCAAAGCCACTTGAGATTTGTGGGAAGTACTTGTCCGGTCTCCTGGAGGTCATTACTTCCTTTTATGTTGAACGGGGAGGAAATGCTATGTCCTTCATGGGGAAAGGCGTTACAAAGAGCACAGGTCTTTGCTTACTTCACTTATCCCATGAGATGATAGTCCAGGCACCAGGCTCGGAGTGGATGCCGCTTTGGTTCTTGCCTTTGGGTAGTCACAGTGAAGAACATGCCCCTACTCAGCAAGGATTGGCCTGGCTAATTCCCTTATGGGTTGATAGAGACCCAGAGGTGAGATTCACTTCACTGGGGTTGGGATCAGCACTGACTACTATTGAAGCTGGCTGTGTGGCCTTGGCAAACAGTTGTCAGAATATTTCTGGTGGGCTCTGGGGAACCGTGGTGAACATTCTTCTGGATCAATCAGAATGCAGTCTGGTGCGCCGGGAGGCTGCATTTATTCTTCAGAATCTCCTTGTAATTCCAATGCCTTCAGAAATTATAAAGGATTATACTTGGCAGGGCCCCTGTGTCCATGATGAGGATTCTGGCCTGTCACTTTCAGGAAAACCTGCCCTTCAGGCTCTTTTATATCACTGTCGTTTCTATGAACATTTGACTCACATGGTGAAACATTGTTATGTAGGAAGATATATCTTTGATTTTAATTTTTCTGCTTTTACTGAAACTTCAGAATACAGTGATTTAAATGGTTTAGACGACTCATTCAAGTTTTGGAGGGCCCCTTCTGGGACATCTACTCAGGATCATGAGCCAAGCTCTCTTTCCACCTCAGAAACAATGGTGGCTGCCTCGGTGGTCAGTTCTGAGATTCAGCCCCTGCTGCCGTCAACACTTCTTCCTGAAACTGCCCTTGACCAGTTTGTGACGCAAGGTCAACGTGAAATGAGACCAGTGCGACCTCGTGACTCATTGCTGTCTACTTCCCTGAACAGGCAGTATGTGTTTGTTACTCCGTCTCTGCTGTCAGCAGTCTGTAGCCTTTTAGACAACCTCTTGGCAGTTACTCCAAGAGATGCTGCAAATGCTTTTCAACAAGCTCATCTCATAGAACTCCTCTGTAGCACGGTGGATGCTTCCCTCATAGAAATGTGCATCCAAGAACTCAAGACCCCACTGCCTTTACCATCTGCTGTTGAACATATTCAGGCTCAGGCTTCCTTTTTCTTGGAATACCTATCCTCTTTGTCCCAGCTCTTGAAGTCCTGTCTGTTGGTAGAGCCTAAACTTGTGACACAAGATGAGCTCTTGAAACCTCTTATCACTAATGTCATCCGAGTTCTCATTGTGTGTCCCAAAGATGTATTAGGAAATGCTTGGAACTGTTTTACGTTTTCCAAACACAGCTGTCTCTGA
Peptide sequence:
MAHLTAFPGWSAHSPLSKPLEICGKYLSGLLEVITSFYVERGGNAMSFMGKGVTKSTGLCLLHLSHEMIVQAPGSEWMPLWFLPLGSHSEEHAPTQQGLAWLIPLWVDRDPEVRFTSLGLGSALTTIEAGCVALANSCQNISGGLWGTVVNILLDQSECSLVRREAAFILQNLLVIPMPSEIIKDYTWQGPCVHDEDSGLSLSGKPALQALLYHCRFYEHLTHMVKHCYVGRYIFDFNFSAFTETSEYSDLNGLDDSFKFWRAPSGTSTQDHEPSSLSTSETMVAASVVSSEIQPLLPSTLLPETALDQFVTQGQREMRPVRPRDSLLSTSLNRQYVFVTPSLLSAVCSLLDNLLAVTPRDAANAFQQAHLIELLCSTVDASLIEMCIQELKTPLPLPSAVEHIQAQASFFLEYLSSLSQLLKSCLLVEPKLVTQDELLKPLITNVIRVLIVCPKDVLGNAWNCFTFSKHSCL
IRESfinder result
IRESfinder score
0.797171983
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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