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mmu_circGtf2h1_1154
Basic information of circular RNA
PanCircBase ID:
mmu_circGtf2h1_1154
mm39_Chr. Position ID:
chr7|46451095|46463628|+
Gene name:
Gtf2h1
Transcript:
ENSMUST00000006774.11
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
9
Exon/intron indexes:
2,3,4,5,6,7,8,9,10
Exon/intron offsets:
0,2145,3289,5064,6865,7128,10760,10990,12444
Genomic length:
12533
Exon/intron sizes in nt:
169,193,163,94,150,80,128,88,89
Flanking exon/introns:
chr7:46445712-46451095|chr7:46463628-46464723
Splice length:
1154
Other database IDs:
CIRCpedia: MMU_CIRCpedia_20965, circAtlas: mmu-Gtf2h1_0016
Human Ortholog IDs:
Mature spliced Sequence:
CACCTTATAGCCATCATGGCGACTTCATCAGAAGAAGTGTTGCTGATTGTGAAGAAGGTTCGTCAGAAGAAGCAGGATGGAGCACTGTACCTCATGGCAGAGAGAATTGCTTGGGCACCTGAAGGCAAAGACAGATTTACAATCAGCCATATGTATGCAGATATTAAATGCCAGAAAATCAGTCCAGAGGGAAAAGCTAAAATACAACTTCAGCTGGTCCTGCATGCAGGGGACACAACAAACTTCCATTTTTCCAACGAAAGCACGGCAGTGAAAGAACGGGATGCAGTGAAGGACCTCCTTCAGCAGCTGCTGCCCAAGTTCAAGCGGAAAGCTAATAAAGAGCTGGAGGAGAAGAACAGAATGCTCCAAGAAGATCCTGTTTTATTCCAACTCTATAAAGACCTTGTTGTGAGCCAAGTGATCAGTGCTGAGGAATTCTGGGCCAATCGTTTAAATGTGAATGCAACAGATAGTTCTACATCCAGTCACAAGCAGGATGTTGGTATTTCTGCAGCATTTCTGGCTGATGTCCGGCCCCAAACGGATGGCTGTAATGGTCTGAGATATAATTTAACTTCTGATATCATTGAATCTATATTTAGGACCTATCCAGCAGTAAAAATGAAATATGCAGAAACTGTACCACACAACATGACAGAAAAGGAGTTCTGGACACGCTTTTTCCAGTCCCATTATTTTCACAGGGACCGACTAAATACAGGATCGAAGGACCTCTTTGCAGAATGTGCCAAAATAGATGAGAAGGGATTAAAAACAATGGTTTCATTAGGAGTGAAAAACCCAATGCTAGATTTGACATCGTTGGAAGATAAGCCATTAGACGAGGGCTATGGCATTTCCTCTGTGCCATCTACTTCCAATTCCAAATCCATAAAGGAGAATAGTAATGCTGCCATCATCAAAAGGTTTAACCACCACAGTGCCATGGTCCTGGCTGCTGGTCTCAGGAAACAACAAGCACAAAATGGACAGAATGGTGAGCCCAGCAGCGTGGATGGGAATTCTGGGGATACAGACTGCTTTCAGCCAGCAGTCAAAAGGGCAAAGTTGCAGGAGTCCATTGAATATGAAGACTTGGGAAACAACAATTCTGTGAAAACGATTGCACTGAATCTCAAGAAGTCAGACAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CAAAGTTGCAGGAGTCCATTGA
59.11
ACAGTGCTCCATCCTGCTTC
60.04
176
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AGTTGCAGGAGTCCATTGAA
57.04
ACAGTGCTCCATCCTGCTTC
60.04
173
PCR template sequence:
CAGTCAAAAGGGCAAAGTTGCAGGAGTCCATTGAATATGAAGACTTGGGAAACAACAATTCTGTGAAAACGATTGCACTGAATCTCAAGAAGTCAGACAGCACCTTATAGCCATCATGGCGACTTCATCAGAAGAAGTGTTGCTGATTGTGAAGAAGGTTCGTCAGAAGAAGCAGGATGGAGCACTGTACCTCATGGCAG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
12
Interacting miRNAs (#binding sites)
mmu-miR-183-5p(2), mmu-miR-134-5p(1), mmu-miR-135a-5p(1), mmu-miR-130a-3p(1), mmu-miR-148b-3p(1), mmu-miR-217-5p(1), mmu-miR-301b-3p(1), mmu-miR-218-5p(1), mmu-miR-301a-3p(1), mmu-miR-207(1), mmu-miR-335-3p(1), mmu-miR-697(1)
siRNAs for circular RNA silencing
Junction sequence
AGAAGTCAGACAGCACCTTATAGCCA
siRNA sets
TATAAGGTGCTGTCTGACT, CTATAAGGTGCTGTCTGAC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCGTF2H1_1154_ORF_1
0.9758
0.193849527
0.99632205
1149
ORF sequence:
ATGGCGACTTCATCAGAAGAAGTGTTGCTGATTGTGAAGAAGGTTCGTCAGAAGAAGCAGGATGGAGCACTGTACCTCATGGCAGAGAGAATTGCTTGGGCACCTGAAGGCAAAGACAGATTTACAATCAGCCATATGTATGCAGATATTAAATGCCAGAAAATCAGTCCAGAGGGAAAAGCTAAAATACAACTTCAGCTGGTCCTGCATGCAGGGGACACAACAAACTTCCATTTTTCCAACGAAAGCACGGCAGTGAAAGAACGGGATGCAGTGAAGGACCTCCTTCAGCAGCTGCTGCCCAAGTTCAAGCGGAAAGCTAATAAAGAGCTGGAGGAGAAGAACAGAATGCTCCAAGAAGATCCTGTTTTATTCCAACTCTATAAAGACCTTGTTGTGAGCCAAGTGATCAGTGCTGAGGAATTCTGGGCCAATCGTTTAAATGTGAATGCAACAGATAGTTCTACATCCAGTCACAAGCAGGATGTTGGTATTTCTGCAGCATTTCTGGCTGATGTCCGGCCCCAAACGGATGGCTGTAATGGTCTGAGATATAATTTAACTTCTGATATCATTGAATCTATATTTAGGACCTATCCAGCAGTAAAAATGAAATATGCAGAAACTGTACCACACAACATGACAGAAAAGGAGTTCTGGACACGCTTTTTCCAGTCCCATTATTTTCACAGGGACCGACTAAATACAGGATCGAAGGACCTCTTTGCAGAATGTGCCAAAATAGATGAGAAGGGATTAAAAACAATGGTTTCATTAGGAGTGAAAAACCCAATGCTAGATTTGACATCGTTGGAAGATAAGCCATTAGACGAGGGCTATGGCATTTCCTCTGTGCCATCTACTTCCAATTCCAAATCCATAAAGGAGAATAGTAATGCTGCCATCATCAAAAGGTTTAACCACCACAGTGCCATGGTCCTGGCTGCTGGTCTCAGGAAACAACAAGCACAAAATGGACAGAATGGTGAGCCCAGCAGCGTGGATGGGAATTCTGGGGATACAGACTGCTTTCAGCCAGCAGTCAAAAGGGCAAAGTTGCAGGAGTCCATTGAATATGAAGACTTGGGAAACAACAATTCTGTGAAAACGATTGCACTGAATCTCAAGAAGTCAGACAGCACCTTATAG
Peptide sequence:
MATSSEEVLLIVKKVRQKKQDGALYLMAERIAWAPEGKDRFTISHMYADIKCQKISPEGKAKIQLQLVLHAGDTTNFHFSNESTAVKERDAVKDLLQQLLPKFKRKANKELEEKNRMLQEDPVLFQLYKDLVVSQVISAEEFWANRLNVNATDSSTSSHKQDVGISAAFLADVRPQTDGCNGLRYNLTSDIIESIFRTYPAVKMKYAETVPHNMTEKEFWTRFFQSHYFHRDRLNTGSKDLFAECAKIDEKGLKTMVSLGVKNPMLDLTSLEDKPLDEGYGISSVPSTSNSKSIKENSNAAIIKRFNHHSAMVLAAGLRKQQAQNGQNGEPSSVDGNSGDTDCFQPAVKRAKLQESIEYEDLGNNNSVKTIALNLKKSDSTL
IRESfinder result
IRESfinder score
0.527764901
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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