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mmu_circGramd3_675
Basic information of circular RNA
PanCircBase ID:
mmu_circGramd3_675
mm39_Chr. Position ID:
chr18|56618283|56630485|+
Gene name:
Gramd3
Transcript:
ENSMUST00000237355.2
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
7
Exon/intron indexes:
8,9,10,11,12,13,14
Exon/intron offsets:
0,164,3539,4403,5459,6683,12108
Genomic length:
12202
Exon/intron sizes in nt:
72,81,112,123,88,105,94
Flanking exon/introns:
chr18:56615788-56618283|chr18:56630485-56635659
Splice length:
675
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
TACATATTCGTTTCCTTGCTGTCCAGAGACTCAACCTACAAACTGATAAAATCTGTGTGCGGACACTTAGAGAACACAAGTGTTGGTAACAGTCCCAACCCATCTTCTGCTGAAAACAGTTTCCGGGCAGATCGCCCTTCGTCTCTGCCTCTGGATTTCAATGATGAATTCTCAGACCTGGACGGAGTGGTTCGACAACGAAGGCAAGACTTGGAAGGATACAGCAGCTCAGGATCCCAGACTCCGGAATCTGAGAACTCCCGAGACTTCCACGTGACCGAATCTCAGACAGTTCTGAATGTCACAAAGGGAGAAACAAAACCACCTCGGACAGATGCCCACGGGAGCAGAGCACCTGATGGAAAAGCCAAGATCCTGCCTGCCCATGGTCAATCAGAAACTATTGGAATTTTACATAAAATGGAGTCTCGGAAGTGCCCGACTCTCCATCACATCCTGATAGTCTATGCAATTATTGTCTGTGCCCTGATCATCTCCACCTTCTACATGAGATACAGGATTAACACTCTGGAGGAGCGCCTGGGGACCCTGACGTCCATCATGGATCCCCACAGTACTGAGCAGACAGCCCCATCCGGCCTGGGATCACAAATGCAGTTAAATGTGGAGGTCCTCTGCCAAGAACTTACAGCTAACATAGTGAAATTGGAAAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GCCTGGGATCACAAATGCAG
59.54
TGTGTTCTCTAAGTGTCCGCA
59.32
155
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GGAGGTCCTCTGCCAAGAAC
60.04
TGGGACTGTTACCAACACTTGT
59.76
146
PCR template sequence:
TACTGAGCAGACAGCCCCATCCGGCCTGGGATCACAAATGCAGTTAAATGTGGAGGTCCTCTGCCAAGAACTTACAGCTAACATAGTGAAATTGGAAAAGTACATATTCGTTTCCTTGCTGTCCAGAGACTCAACCTACAAACTGATAAAATCTGTGTGCGGACACTTAGAGAACACAAGTGTTGGTAACAGTCCCAACC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
8
Interacting miRNAs (#binding sites)
mmu-miR-181a-5p(1), mmu-miR-211-5p(1), mmu-miR-204-5p(1), mmu-miR-709(1), mmu-miR-181b-5p(1), mmu-miR-136-5p(1), mmu-miR-680(1), mmu-miR-181d-5p(1)
siRNAs for circular RNA silencing
Junction sequence
GAAATTGGAAAAGTACATATTCGTTT
siRNA sets
AAACGAATATGTACTTTTC, TATGTACTTTTCCAATTTC, ACGAATATGTACTTTTCCA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCGRAMD3_675_ORF_1
0.8451
0.245738596
0.98223855
930
ORF sequence:
ATGGAGTCTCGGAAGTGCCCGACTCTCCATCACATCCTGATAGTCTATGCAATTATTGTCTGTGCCCTGATCATCTCCACCTTCTACATGAGATACAGGATTAACACTCTGGAGGAGCGCCTGGGGACCCTGACGTCCATCATGGATCCCCACAGTACTGAGCAGACAGCCCCATCCGGCCTGGGATCACAAATGCAGTTAAATGTGGAGGTCCTCTGCCAAGAACTTACAGCTAACATAGTGAAATTGGAAAAGTACATATTCGTTTCCTTGCTGTCCAGAGACTCAACCTACAAACTGATAAAATCTGTGTGCGGACACTTAGAGAACACAAGTGTTGGTAACAGTCCCAACCCATCTTCTGCTGAAAACAGTTTCCGGGCAGATCGCCCTTCGTCTCTGCCTCTGGATTTCAATGATGAATTCTCAGACCTGGACGGAGTGGTTCGACAACGAAGGCAAGACTTGGAAGGATACAGCAGCTCAGGATCCCAGACTCCGGAATCTGAGAACTCCCGAGACTTCCACGTGACCGAATCTCAGACAGTTCTGAATGTCACAAAGGGAGAAACAAAACCACCTCGGACAGATGCCCACGGGAGCAGAGCACCTGATGGAAAAGCCAAGATCCTGCCTGCCCATGGTCAATCAGAAACTATTGGAATTTTACATAAAATGGAGTCTCGGAAGTGCCCGACTCTCCATCACATCCTGATAGTCTATGCAATTATTGTCTGTGCCCTGATCATCTCCACCTTCTACATGAGATACAGGATTAACACTCTGGAGGAGCGCCTGGGGACCCTGACGTCCATCATGGATCCCCACAGTACTGAGCAGACAGCCCCATCCGGCCTGGGATCACAAATGCAGTTAAATGTGGAGGTCCTCTGCCAAGAACTTACAGCTAACATAGTGAAATTGGAAAAG
Peptide sequence:
MESRKCPTLHHILIVYAIIVCALIISTFYMRYRINTLEERLGTLTSIMDPHSTEQTAPSGLGSQMQLNVEVLCQELTANIVKLEKYIFVSLLSRDSTYKLIKSVCGHLENTSVGNSPNPSSAENSFRADRPSSLPLDFNDEFSDLDGVVRQRRQDLEGYSSSGSQTPESENSRDFHVTESQTVLNVTKGETKPPRTDAHGSRAPDGKAKILPAHGQSETIGILHKMESRKCPTLHHILIVYAIIVCALIISTFYMRYRINTLEERLGTLTSIMDPHSTEQTAPSGLGSQMQLNVEVLCQELTANIVKLEK
IRESfinder result
IRESfinder score
0.542172919
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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