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mmu_circTogaram1_1189
Basic information of circular RNA
PanCircBase ID:
mmu_circTogaram1_1189
mm39_Chr. Position ID:
chr12|65023468|65033264|+
Gene name:
Togaram1
Transcript:
ENSMUST00000066296.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
6
Exon/intron indexes:
2,3,4,5,6,7
Exon/intron offsets:
0,1474,3888,5751,6633,9698
Genomic length:
9796
Exon/intron sizes in nt:
157,135,297,263,239,98
Flanking exon/introns:
chr12:65014802-65023468|chr12:65033264-65039318
Splice length:
1189
Other database IDs:
circBase: mmu_circ_0004112, CIRCpedia: MMU_CIRCpedia_25978, circAtlas: mmu-Fam179b_0001
circBase: hsa_circ_0101837, circAtlas: hsa-FAM179B_0001, CIRCpedia: HSA_CIRCpedia_12147
Human Ortholog IDs:
Mature spliced Sequence:
TTTTCAGCTCATGACCTTATCCCGTCTCCAAAATTAAAGCCCTCTCAAGGAATGCCAGCCAGTGATGATTTATGTTTTAGCAAAAAAAGGTCATCAAGAAACTTATTTCAGAGTAGTCGGGACTTTAACTCAGAGTCAGTTCCTACATGTGGTGCTGGTAATACTGCAGATCTTCAGACAAATCTTCCCGGGAAATGTGGGCAGCTTGGATTGTCACAGATAGGTTGTAGAACTGGCAGTGTGGGTTCTGACTTACAGTTTTTGGGGACAGCCAATGGCCATCAAGATAAAGTATATGCTAGCATTGATTTTGGCAGTAAGACACAGCAAACATTTGGTAGTCAATCAGAACGAACTTCTTCATACTCTGGTTCAAATGCAAGTCCAGGATCCTTCATCCTTCCATCCTATCCTCTCGCATCACCTCGAACTAGTCCAAAGCACACATCTCCTCTTTCTGTAGCACCAAAGAAGTCGCAAGATAATTCCATTAGTTTCTCAAATTCTTGGCCTCTTAAGAGCTTCGAAGGACTGTCAAAGCCAAGTCCACAGAAAAAGCTTGCCAACCAGAAATCATCTGACCCTACAGGAGAAAATTTTCAAGAAAAAACTACTGCAGTTCAACTTACACCTGCCTTGGTGCGATCACCTTCTTCCCGAAGAGGCCTAAATGGGACCAAACCTGTTCCTCCCATACCAAGGGGGATAAACCTCTTGCCTGATAAAGCTGACTTAAGCACAATGGGACACATGAAGAAACAGCCTGATGATATTTGGAAAAGTGAAAAAGATAATCTTACAATTGATCTTTCAGAATTGAATTTCAGAGATAAAGATTTGGATCAGGAAGAGATGCACAGCTCTCTTAGGTCCCTTCGAAATAGTGCAGCTAAGAAAAGAGCCAAACTCAGTGGCAGCAGCAGCACCTCTGATGTTGACAGTCCCGACTCTGCCATGAAGCTTGAGCTGACCATTGACTCCCCGTCCCGAGCTTCCTCTCCAAACATCAGCTCTTACAGTGAAAGTGGAGTGTATAGCCAAGAATCGTTGACCTCTTCTCTTTCTACAACGCCTCAGGGGAAGAGAATAATGTCAGACATATTTCCAACATTTGGATCAAAACCTTGCTCAACAAGGCTTTCTTCTGCAAAGAAAACCTCCCATGCTGCTGAACAGAGTCCCAGTGCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TGGATCAAAACCTTGCTCAACA
58.7
ACTGGCTGGCATTCCTTGAG
60.32
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TGGATCAAAACCTTGCTCAACA
58.7
ATCACTGGCTGGCATTCCTT
59.67
143
PCR template sequence:
ATGTCAGACATATTTCCAACATTTGGATCAAAACCTTGCTCAACAAGGCTTTCTTCTGCAAAGAAAACCTCCCATGCTGCTGAACAGAGTCCCAGTGCAGTTTTCAGCTCATGACCTTATCCCGTCTCCAAAATTAAAGCCCTCTCAAGGAATGCCAGCCAGTGATGATTTATGTTTTAGCAAAAAAAGGTCATCAAGAA
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-322-5p(1), mmu-miR-29b-3p(1), mmu-miR-29a-3p(1), mmu-miR-29c-3p(1), mmu-miR-298-5p(1), mmu-miR-217-5p(1), mmu-miR-483-5p(1), mmu-miR-1187(1), mmu-miR-190b-5p(1)
siRNAs for circular RNA silencing
Junction sequence
AGTCCCAGTGCAGTTTTCAGCTCATG
siRNA sets
CTGAAAACTGCACTGGGAC, CATGAGCTGAAAACTGCAC, GAGCTGAAAACTGCACTGG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCTOGARAM1_1189_ORF_1
0.8197
0.013031051
0.993611043
1215
ORF sequence:
ATGCTGCTGAACAGAGTCCCAGTGCAGTTTTCAGCTCATGACCTTATCCCGTCTCCAAAATTAAAGCCCTCTCAAGGAATGCCAGCCAGTGATGATTTATGTTTTAGCAAAAAAAGGTCATCAAGAAACTTATTTCAGAGTAGTCGGGACTTTAACTCAGAGTCAGTTCCTACATGTGGTGCTGGTAATACTGCAGATCTTCAGACAAATCTTCCCGGGAAATGTGGGCAGCTTGGATTGTCACAGATAGGTTGTAGAACTGGCAGTGTGGGTTCTGACTTACAGTTTTTGGGGACAGCCAATGGCCATCAAGATAAAGTATATGCTAGCATTGATTTTGGCAGTAAGACACAGCAAACATTTGGTAGTCAATCAGAACGAACTTCTTCATACTCTGGTTCAAATGCAAGTCCAGGATCCTTCATCCTTCCATCCTATCCTCTCGCATCACCTCGAACTAGTCCAAAGCACACATCTCCTCTTTCTGTAGCACCAAAGAAGTCGCAAGATAATTCCATTAGTTTCTCAAATTCTTGGCCTCTTAAGAGCTTCGAAGGACTGTCAAAGCCAAGTCCACAGAAAAAGCTTGCCAACCAGAAATCATCTGACCCTACAGGAGAAAATTTTCAAGAAAAAACTACTGCAGTTCAACTTACACCTGCCTTGGTGCGATCACCTTCTTCCCGAAGAGGCCTAAATGGGACCAAACCTGTTCCTCCCATACCAAGGGGGATAAACCTCTTGCCTGATAAAGCTGACTTAAGCACAATGGGACACATGAAGAAACAGCCTGATGATATTTGGAAAAGTGAAAAAGATAATCTTACAATTGATCTTTCAGAATTGAATTTCAGAGATAAAGATTTGGATCAGGAAGAGATGCACAGCTCTCTTAGGTCCCTTCGAAATAGTGCAGCTAAGAAAAGAGCCAAACTCAGTGGCAGCAGCAGCACCTCTGATGTTGACAGTCCCGACTCTGCCATGAAGCTTGAGCTGACCATTGACTCCCCGTCCCGAGCTTCCTCTCCAAACATCAGCTCTTACAGTGAAAGTGGAGTGTATAGCCAAGAATCGTTGACCTCTTCTCTTTCTACAACGCCTCAGGGGAAGAGAATAATGTCAGACATATTTCCAACATTTGGATCAAAACCTTGCTCAACAAGGCTTTCTTCTGCAAAGAAAACCTCCCATGCTGCTGAACAGAGTCCCAGTGCA
Peptide sequence:
MLLNRVPVQFSAHDLIPSPKLKPSQGMPASDDLCFSKKRSSRNLFQSSRDFNSESVPTCGAGNTADLQTNLPGKCGQLGLSQIGCRTGSVGSDLQFLGTANGHQDKVYASIDFGSKTQQTFGSQSERTSSYSGSNASPGSFILPSYPLASPRTSPKHTSPLSVAPKKSQDNSISFSNSWPLKSFEGLSKPSPQKKLANQKSSDPTGENFQEKTTAVQLTPALVRSPSSRRGLNGTKPVPPIPRGINLLPDKADLSTMGHMKKQPDDIWKSEKDNLTIDLSELNFRDKDLDQEEMHSSLRSLRNSAAKKRAKLSGSSSTSDVDSPDSAMKLELTIDSPSRASSPNISSYSESGVYSQESLTSSLSTTPQGKRIMSDIFPTFGSKPCSTRLSSAKKTSHAAEQSPSA
IRESfinder result
IRESfinder score
0.750268325
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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