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mmu_circGramd3_960
Basic information of circular RNA
PanCircBase ID:
mmu_circGramd3_960
mm39_Chr. Position ID:
chr18|56607090|56625071|+
Gene name:
Gramd3
Transcript:
ENSMUST00000237355.2
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
10
Exon/intron indexes:
4,5,6,7,8,9,10,11,12,13
Exon/intron offsets:
0,2584,4830,8602,11193,11357,14732,15596,16652,17876
Genomic length:
17981
Exon/intron sizes in nt:
11,26,71,04,96,72,81,10,00,00,00,000
Flanking exon/introns:
chr18:56602724-56607090|chr18:56625071-56630391
Splice length:
960
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GTCAAAATCCAGTTTTGATGGTTCCAGTTTGTTGAGTGATAAGAATGACTGTAAAACTGAAAGCAAGACTGACTCTAAGACCGAAAGAAAAAAGTCTTCATCGTCTAGTCAGTACAAGGCGAACATGCACTTTCACAAGTTATTCCTGGATGTCCCAACTGAGGAGCCACTGAGGCAAAGCTTTACCTGTGCTCTTCAGAAAGAAATTCTGTACCAAGGAAAGCTCTTTGTGTCGGAAAACTGGATTTGTTTTCATTCCAAGGTCTTTGGAAAAGACACTAAGATCTCCATTCCAGCTTTCTCGGTAACCTTGATCAAGAAAACCAAAACTGCCCTTCTGGTGCCAAACGCCCTGATCATCGCGACGGTCACAGACAGGTACATATTCGTTTCCTTGCTGTCCAGAGACTCAACCTACAAACTGATAAAATCTGTGTGCGGACACTTAGAGAACACAAGTGTTGGTAACAGTCCCAACCCATCTTCTGCTGAAAACAGTTTCCGGGCAGATCGCCCTTCGTCTCTGCCTCTGGATTTCAATGATGAATTCTCAGACCTGGACGGAGTGGTTCGACAACGAAGGCAAGACTTGGAAGGATACAGCAGCTCAGGATCCCAGACTCCGGAATCTGAGAACTCCCGAGACTTCCACGTGACCGAATCTCAGACAGTTCTGAATGTCACAAAGGGAGAAACAAAACCACCTCGGACAGATGCCCACGGGAGCAGAGCACCTGATGGAAAAGCCAAGATCCTGCCTGCCCATGGTCAATCAGAAACTATTGGAATTTTACATAAAATGGAGTCTCGGAAGTGCCCGACTCTCCATCACATCCTGATAGTCTATGCAATTATTGTCTGTGCCCTGATCATCTCCACCTTCTACATGAGATACAGGATTAACACTCTGGAGGAGCGCCTGGGGACCCTGACGTCCATCATGGATCCCCACAGTACTGA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TTAACACTCTGGAGGAGCGC
59.75
TCGGTCTTAGAGTCAGTCTTGC
59.51
145
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TTAACACTCTGGAGGAGCGC
59.75
CGGTCTTAGAGTCAGTCTTGCT
59.51
144
PCR template sequence:
GTGCCCTGATCATCTCCACCTTCTACATGAGATACAGGATTAACACTCTGGAGGAGCGCCTGGGGACCCTGACGTCCATCATGGATCCCCACAGTACTGAGTCAAAATCCAGTTTTGATGGTTCCAGTTTGTTGAGTGATAAGAATGACTGTAAAACTGAAAGCAAGACTGACTCTAAGACCGAAAGAAAAAAGTCTTCA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
13
Interacting miRNAs (#binding sites)
mmu-miR-93-5p(1), mmu-miR-181a-5p(1), mmu-miR-211-5p(1), mmu-miR-204-5p(1), mmu-miR-709(1), mmu-miR-320-3p(1), mmu-miR-181b-5p(1), mmu-miR-495-3p(1), mmu-miR-136-5p(1), mmu-miR-96-5p(1), mmu-miR-680(1), mmu-miR-181d-5p(1), mmu-miR-7a-1-3p(1)
siRNAs for circular RNA silencing
Junction sequence
CCCACAGTACTGAGTCAAAATCCAGT
siRNA sets
GATTTTGACTCAGTACTGT, ATTTTGACTCAGTACTGTG, TTTTGACTCAGTACTGTGG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCGRAMD3_960_ORF_1
0.943
0.221325913
0.999966923
1794
ORF sequence:
ATGCACTTTCACAAGTTATTCCTGGATGTCCCAACTGAGGAGCCACTGAGGCAAAGCTTTACCTGTGCTCTTCAGAAAGAAATTCTGTACCAAGGAAAGCTCTTTGTGTCGGAAAACTGGATTTGTTTTCATTCCAAGGTCTTTGGAAAAGACACTAAGATCTCCATTCCAGCTTTCTCGGTAACCTTGATCAAGAAAACCAAAACTGCCCTTCTGGTGCCAAACGCCCTGATCATCGCGACGGTCACAGACAGGTACATATTCGTTTCCTTGCTGTCCAGAGACTCAACCTACAAACTGATAAAATCTGTGTGCGGACACTTAGAGAACACAAGTGTTGGTAACAGTCCCAACCCATCTTCTGCTGAAAACAGTTTCCGGGCAGATCGCCCTTCGTCTCTGCCTCTGGATTTCAATGATGAATTCTCAGACCTGGACGGAGTGGTTCGACAACGAAGGCAAGACTTGGAAGGATACAGCAGCTCAGGATCCCAGACTCCGGAATCTGAGAACTCCCGAGACTTCCACGTGACCGAATCTCAGACAGTTCTGAATGTCACAAAGGGAGAAACAAAACCACCTCGGACAGATGCCCACGGGAGCAGAGCACCTGATGGAAAAGCCAAGATCCTGCCTGCCCATGGTCAATCAGAAACTATTGGAATTTTACATAAAATGGAGTCTCGGAAGTGCCCGACTCTCCATCACATCCTGATAGTCTATGCAATTATTGTCTGTGCCCTGATCATCTCCACCTTCTACATGAGATACAGGATTAACACTCTGGAGGAGCGCCTGGGGACCCTGACGTCCATCATGGATCCCCACAGTACTGAGTCAAAATCCAGTTTTGATGGTTCCAGTTTGTTGAGTGATAAGAATGACTGTAAAACTGAAAGCAAGACTGACTCTAAGACCGAAAGAAAAAAGTCTTCATCGTCTAGTCAGTACAAGGCGAACATGCACTTTCACAAGTTATTCCTGGATGTCCCAACTGAGGAGCCACTGAGGCAAAGCTTTACCTGTGCTCTTCAGAAAGAAATTCTGTACCAAGGAAAGCTCTTTGTGTCGGAAAACTGGATTTGTTTTCATTCCAAGGTCTTTGGAAAAGACACTAAGATCTCCATTCCAGCTTTCTCGGTAACCTTGATCAAGAAAACCAAAACTGCCCTTCTGGTGCCAAACGCCCTGATCATCGCGACGGTCACAGACAGGTACATATTCGTTTCCTTGCTGTCCAGAGACTCAACCTACAAACTGATAAAATCTGTGTGCGGACACTTAGAGAACACAAGTGTTGGTAACAGTCCCAACCCATCTTCTGCTGAAAACAGTTTCCGGGCAGATCGCCCTTCGTCTCTGCCTCTGGATTTCAATGATGAATTCTCAGACCTGGACGGAGTGGTTCGACAACGAAGGCAAGACTTGGAAGGATACAGCAGCTCAGGATCCCAGACTCCGGAATCTGAGAACTCCCGAGACTTCCACGTGACCGAATCTCAGACAGTTCTGAATGTCACAAAGGGAGAAACAAAACCACCTCGGACAGATGCCCACGGGAGCAGAGCACCTGATGGAAAAGCCAAGATCCTGCCTGCCCATGGTCAATCAGAAACTATTGGAATTTTACATAAAATGGAGTCTCGGAAGTGCCCGACTCTCCATCACATCCTGATAGTCTATGCAATTATTGTCTGTGCCCTGATCATCTCCACCTTCTACATGAGATACAGGATTAACACTCTGGAGGAGCGCCTGGGGACCCTGACGTCCATCATGGATCCCCACAGTACT
Peptide sequence:
MHFHKLFLDVPTEEPLRQSFTCALQKEILYQGKLFVSENWICFHSKVFGKDTKISIPAFSVTLIKKTKTALLVPNALIIATVTDRYIFVSLLSRDSTYKLIKSVCGHLENTSVGNSPNPSSAENSFRADRPSSLPLDFNDEFSDLDGVVRQRRQDLEGYSSSGSQTPESENSRDFHVTESQTVLNVTKGETKPPRTDAHGSRAPDGKAKILPAHGQSETIGILHKMESRKCPTLHHILIVYAIIVCALIISTFYMRYRINTLEERLGTLTSIMDPHSTESKSSFDGSSLLSDKNDCKTESKTDSKTERKKSSSSSQYKANMHFHKLFLDVPTEEPLRQSFTCALQKEILYQGKLFVSENWICFHSKVFGKDTKISIPAFSVTLIKKTKTALLVPNALIIATVTDRYIFVSLLSRDSTYKLIKSVCGHLENTSVGNSPNPSSAENSFRADRPSSLPLDFNDEFSDLDGVVRQRRQDLEGYSSSGSQTPESENSRDFHVTESQTVLNVTKGETKPPRTDAHGSRAPDGKAKILPAHGQSETIGILHKMESRKCPTLHHILIVYAIIVCALIISTFYMRYRINTLEERLGTLTSIMDPHST
IRESfinder result
IRESfinder score
0.563849104
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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