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mmu_circGtf2i_801
Basic information of circular RNA
PanCircBase ID:
mmu_circGtf2i_801
mm39_Chr. Position ID:
chr5|134283866|134301440|-
Gene name:
Gtf2i
Transcript:
ENSMUST00000059042.15
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
8
Exon/intron indexes:
19,18,17,16,15,14,13,12
Exon/intron offsets:
0,812,5554,6830,8572,10724,11530,17511
Genomic length:
17574
Exon/intron sizes in nt:
59,184,72,59,184,66,114,63
Flanking exon/introns:
chr5:134280791-134283866|chr5:134301440-134303392
Splice length:
801
Other database IDs:
circAtlas: mmu-Gtf2i_0028
CIRCpedia: HSA_CIRCpedia_369479
Human Ortholog IDs:
Mature spliced Sequence:
ATTCTACTCAACATGTCCCTTCAGAAACCAGTGAGGACCCCGAAGTTGAGGTGACCATTGAAGATGATGACTATTCTCCACCCACCAAGAGGCTAAAGAGCACGGAGCCGCCCCCGCCCCCGCCCGTCCCGGAGCCCGCCAACGCTGGCAAGCGCAAAGTGAGGGAGTTCAACTTTGAGAAATGGAACGCACGCATCACTGACCTACGGAAACAAGTTGAAGAGTTGTTCGAAAGAAAATATGCTCAAGCCATCAAAGCCAAAGGCCCGGTGACGATCCCGTACCCTCTTTTCCAGTCCCATGTTGAAGATCTTTACGTAGAAGGGCTTCCTGAAGGGATTCCTTTTAGAAGGCCGTCGACGTACGGCATTCCTCGCCTTGAGAGGATATTGCTGGCGAAGGAAAGGATCCGCTTCGTGATTAAGAAACATGAGCTTCTGAACTCAACACGAGAAGATTTACAGCTTGATAAACCAGCCTCAGGAGTGAAAGAAGAGTGGTACGCTCGCATCACCAAACTGAGGAAGATGGTTGACCAGCTCTTCTGCAAGAAATTTGCCGAGGCCTTGGGAAGCACGGAAGCCAAGGCTGTACCGTACCAAAAATTTGAGGCCCATCCCAATGATCTCTATGTGGAAGGACTTCCAGAAAACATTCCTTTCCGAAGCCCCTCGTGGTATGGAATCCCAAGACTGGAAAAAATCATCCAAGTGGGCAATCGAATTAAATTTGTTATCAAGAGACCAGAGCTGCTCACTCACAGCACAACTGAAGTGACTCAGCCACGGACAAACACACCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GAGACCAGAGCTGCTCACTC
59.83
TTTAGCCTCTTGGTGGGTGG
59.6
159
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TGCTCACTCACAGCACAACT
59.82
TTTAGCCTCTTGGTGGGTGG
59.6
148
PCR template sequence:
ATCATCCAAGTGGGCAATCGAATTAAATTTGTTATCAAGAGACCAGAGCTGCTCACTCACAGCACAACTGAAGTGACTCAGCCACGGACAAACACACCAGATTCTACTCAACATGTCCCTTCAGAAACCAGTGAGGACCCCGAAGTTGAGGTGACCATTGAAGATGATGACTATTCTCCACCCACCAAGAGGCTAAAGAG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
2
Interacting miRNAs (#binding sites)
mmu-miR-29b-1-5p(1), mmu-miR-29b-2-5p(1)
siRNAs for circular RNA silencing
Junction sequence
ACAAACACACCAGATTCTACTCAACA
siRNA sets
TTGAGTAGAATCTGGTGTG, TGTTGAGTAGAATCTGGTG, TGAGTAGAATCTGGTGTGT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCGTF2I_801_ORF_1
1.0828
0.318825331
0.996942032
1074
ORF sequence:
ATGGTTGACCAGCTCTTCTGCAAGAAATTTGCCGAGGCCTTGGGAAGCACGGAAGCCAAGGCTGTACCGTACCAAAAATTTGAGGCCCATCCCAATGATCTCTATGTGGAAGGACTTCCAGAAAACATTCCTTTCCGAAGCCCCTCGTGGTATGGAATCCCAAGACTGGAAAAAATCATCCAAGTGGGCAATCGAATTAAATTTGTTATCAAGAGACCAGAGCTGCTCACTCACAGCACAACTGAAGTGACTCAGCCACGGACAAACACACCAGATTCTACTCAACATGTCCCTTCAGAAACCAGTGAGGACCCCGAAGTTGAGGTGACCATTGAAGATGATGACTATTCTCCACCCACCAAGAGGCTAAAGAGCACGGAGCCGCCCCCGCCCCCGCCCGTCCCGGAGCCCGCCAACGCTGGCAAGCGCAAAGTGAGGGAGTTCAACTTTGAGAAATGGAACGCACGCATCACTGACCTACGGAAACAAGTTGAAGAGTTGTTCGAAAGAAAATATGCTCAAGCCATCAAAGCCAAAGGCCCGGTGACGATCCCGTACCCTCTTTTCCAGTCCCATGTTGAAGATCTTTACGTAGAAGGGCTTCCTGAAGGGATTCCTTTTAGAAGGCCGTCGACGTACGGCATTCCTCGCCTTGAGAGGATATTGCTGGCGAAGGAAAGGATCCGCTTCGTGATTAAGAAACATGAGCTTCTGAACTCAACACGAGAAGATTTACAGCTTGATAAACCAGCCTCAGGAGTGAAAGAAGAGTGGTACGCTCGCATCACCAAACTGAGGAAGATGGTTGACCAGCTCTTCTGCAAGAAATTTGCCGAGGCCTTGGGAAGCACGGAAGCCAAGGCTGTACCGTACCAAAAATTTGAGGCCCATCCCAATGATCTCTATGTGGAAGGACTTCCAGAAAACATTCCTTTCCGAAGCCCCTCGTGGTATGGAATCCCAAGACTGGAAAAAATCATCCAAGTGGGCAATCGAATTAAATTTGTTATCAAGAGACCAGAGCTGCTCACTCACAGCACAACTGAAGTGACTCAGCCACGGACAAACACACCA
Peptide sequence:
MVDQLFCKKFAEALGSTEAKAVPYQKFEAHPNDLYVEGLPENIPFRSPSWYGIPRLEKIIQVGNRIKFVIKRPELLTHSTTEVTQPRTNTPDSTQHVPSETSEDPEVEVTIEDDDYSPPTKRLKSTEPPPPPPVPEPANAGKRKVREFNFEKWNARITDLRKQVEELFERKYAQAIKAKGPVTIPYPLFQSHVEDLYVEGLPEGIPFRRPSTYGIPRLERILLAKERIRFVIKKHELLNSTREDLQLDKPASGVKEEWYARITKLRKMVDQLFCKKFAEALGSTEAKAVPYQKFEAHPNDLYVEGLPENIPFRSPSWYGIPRLEKIIQVGNRIKFVIKRPELLTHSTTEVTQPRTNTP
IRESfinder result
IRESfinder score
0.413818202
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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