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mmu_circTdrd7_910
Basic information of circular RNA
PanCircBase ID:
mmu_circTdrd7_910
mm39_Chr. Position ID:
chr4|46020804|46029807|+
Gene name:
Tdrd7
Transcript:
ENSMUST00000107777.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
13,14,15,16
Exon/intron offsets:
0,2590,4852,8842
Genomic length:
9003
Exon/intron sizes in nt:
135,111,503,161
Flanking exon/introns:
chr4:46018616-46020804|chr4:46029807-46034295
Splice length:
910
Other database IDs:
CIRCpedia: MMU_CIRCpedia_217803, circAtlas: mmu-Tdrd7_0002
circBase: hsa_circ_0137477, circAtlas: hsa-TDRD7_0004, CIRCpedia: HSA_CIRCpedia_61965
Human Ortholog IDs:
Mature spliced Sequence:
ATCACTAATGTTCATAGCAGCCGTGCACTCGACGTTCAGTTCCTGGACTCTGGCAATTCGACATCCGTGAAAGTGTCAGAACTCAGAGAAATCCCACCGCGGTTCCTGCAGGAAATGCTTGCCATACCCCCTCAGGCTATAAAGTGCTGCTTGGCTGATCTTCCACAGTCCATTGGCATGTGGACACCAGATGCTGTTCTGTGGTTAAGAGATTCTGTTTTGAATTGCTCGGACTGTAGTATTAAGGTTACAAAAATGGATGAGACCAAGGGGGTTGCCTATGTGTACTTATTCACTCCCAATAACTTCCCGGATCCCCATCGCAGTATTAACCGGCAGATCACAAACGCAGACCTGTGGAAACATCAGAAGGATGTGTTTCTGAGCGCGGTGTCTACTGCGGCCAGTTCCCCTGGCAACAGGAATGGTGGCACACCTGCTCCGGGCAGCCCTGCAGAGAGTCTCAGAAAGAGCCACCCAGAGGTTATCAAGAAGTCTGTCCTGGACCATACCAGCTCTTTCTCCTTGGAGGAACTGCCCCCTCCTGTCCACCTGTCAAGGTCAGGGGAACACATGGATGTGTATGTGCCTGTGGCCTGTCACCCAGGCCATTTTGTCATCCAGCCCTGGCAGGAGATCCATAAGCTAGAAGTGCTGATGGAAGAGATGATCCTGTACTACAGCGTGTCCGAGGAGCGCCACATAGCGGTGGAGCGAGACCAAGTGTACGCAGCCAAAGTGGAGAATAAGTGGTACAGGGTACTTTTAAAAGGAATCCTGACCAATGGGCTGGTGTCTGTGTACGAGCTGGACTACGGCAAGCATGAGCTCGTCAACATAAGGAAAGTGCAGCCCCTAGTGGACGTGTTCCGAAAGCTGCCCTTCCAGGCGGTCACCGCTCAACTGGCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AAGGAAAGTGCAGCCCCTAG
59.67
TCACGGATGTCGAATTGCCA
60.04
141
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AAGGAAAGTGCAGCCCCTAG
59.67
GCGGTGGGATTTCTCTGAGT
59.75
171
PCR template sequence:
GACTACGGCAAGCATGAGCTCGTCAACATAAGGAAAGTGCAGCCCCTAGTGGACGTGTTCCGAAAGCTGCCCTTCCAGGCGGTCACCGCTCAACTGGCAGATCACTAATGTTCATAGCAGCCGTGCACTCGACGTTCAGTTCCTGGACTCTGGCAATTCGACATCCGTGAAAGTGTCAGAACTCAGAGAAATCCCACCGC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
10
Interacting miRNAs (#binding sites)
mmu-miR-16-5p(1), mmu-miR-15a-5p(1), mmu-miR-429-3p(1), mmu-miR-200b-3p(1), mmu-miR-322-5p(1), mmu-miR-15b-5p(1), mmu-miR-10b-5p(1), mmu-miR-382-5p(1), mmu-miR-1198-5p(1), mmu-miR-193b-3p(1)
siRNAs for circular RNA silencing
Junction sequence
GCTCAACTGGCAGATCACTAATGTTC
siRNA sets
TTAGTGATCTGCCAGTTGA, TAGTGATCTGCCAGTTGAG, AACATTAGTGATCTGCCAG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCTDRD7_910_ORF_1
1.1822
0.297897275
0.98078632
804
ORF sequence:
ATGCTTGCCATACCCCCTCAGGCTATAAAGTGCTGCTTGGCTGATCTTCCACAGTCCATTGGCATGTGGACACCAGATGCTGTTCTGTGGTTAAGAGATTCTGTTTTGAATTGCTCGGACTGTAGTATTAAGGTTACAAAAATGGATGAGACCAAGGGGGTTGCCTATGTGTACTTATTCACTCCCAATAACTTCCCGGATCCCCATCGCAGTATTAACCGGCAGATCACAAACGCAGACCTGTGGAAACATCAGAAGGATGTGTTTCTGAGCGCGGTGTCTACTGCGGCCAGTTCCCCTGGCAACAGGAATGGTGGCACACCTGCTCCGGGCAGCCCTGCAGAGAGTCTCAGAAAGAGCCACCCAGAGGTTATCAAGAAGTCTGTCCTGGACCATACCAGCTCTTTCTCCTTGGAGGAACTGCCCCCTCCTGTCCACCTGTCAAGGTCAGGGGAACACATGGATGTGTATGTGCCTGTGGCCTGTCACCCAGGCCATTTTGTCATCCAGCCCTGGCAGGAGATCCATAAGCTAGAAGTGCTGATGGAAGAGATGATCCTGTACTACAGCGTGTCCGAGGAGCGCCACATAGCGGTGGAGCGAGACCAAGTGTACGCAGCCAAAGTGGAGAATAAGTGGTACAGGGTACTTTTAAAAGGAATCCTGACCAATGGGCTGGTGTCTGTGTACGAGCTGGACTACGGCAAGCATGAGCTCGTCAACATAAGGAAAGTGCAGCCCCTAGTGGACGTGTTCCGAAAGCTGCCCTTCCAGGCGGTCACCGCTCAACTGGCAGATCACTAA
Peptide sequence:
MLAIPPQAIKCCLADLPQSIGMWTPDAVLWLRDSVLNCSDCSIKVTKMDETKGVAYVYLFTPNNFPDPHRSINRQITNADLWKHQKDVFLSAVSTAASSPGNRNGGTPAPGSPAESLRKSHPEVIKKSVLDHTSSFSLEELPPPVHLSRSGEHMDVYVPVACHPGHFVIQPWQEIHKLEVLMEEMILYYSVSEERHIAVERDQVYAAKVENKWYRVLLKGILTNGLVSVYELDYGKHELVNIRKVQPLVDVFRKLPFQAVTAQLADH
IRESfinder result
IRESfinder score
0.461428849
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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