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mmu_circGapvd1_1256
Basic information of circular RNA
PanCircBase ID:
mmu_circGapvd1_1256
mm39_Chr. Position ID:
chr2|34615054|34619186|-
Gene name:
Gapvd1
Transcript:
ENSMUST00000102800.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
7,6,5,4
Exon/intron offsets:
0,336,2173,3288
Genomic length:
4132
Exon/intron sizes in nt:
19,01,35,87,844
Flanking exon/introns:
chr2:34610740-34615054|chr2:34619186-34620474
Splice length:
1256
Other database IDs:
circAtlas: mmu-Gapvd1_0010
circAtlas: hsa-GAPVD1_0014, CIRCpedia: HSA_CIRCpedia_160408
Human Ortholog IDs:
Mature spliced Sequence:
TGCTGAAGCTTCCCCTGCTGAGTGTTGCCAGCATGCCAAGATTTTGGAAGATACACAGTTTGTTGATGGATATAAGCAACTGGGATTTCAGGAAACAGCTTATGGAGAATTCCTGAGTCGGTTAAGAGAAAATCCACGACTTATTGCCTCCTCTTTGGTTGCTGGAGAAAAACTCAATCAGGAGAACACACAAAGTGTTATCTACACTGTTTTTACCTCCTTGTATGGCAACTGTATTATGCAAGAAGATGAAAGCTACCTCCTTCAGGTTTTACGATACTTGATTGAATTTGAACTTAAAGAAAGTGACAACCCCAGGCGCCTTTTGAGGAGAGGAACTTGTGCCTTCAGCATCTTATTTAAACTTTTTTCTGAAGGACTGTTTTCTGCCAAACTTTTCCTTACGGCTACTTTGCATGAGCCAATCATGCAGCTCCTCGTAGAGGATGAAGACCACCTGGAAACAGATCCAAACAAGCTGATAGAGAGATTCTCTCCAGCTCAGCAAGAAAAACTCTTTGGAGAGAAAGGCTCAGATAGATTTAGGCAAAAGGTTCAAGAAATGGTAGATTCCAATGAGGCTAAACTAGTGGCTTTGGTGAACAAATTTATTGGTTATCTTAAACAGAATACATACTGCTTTCCACATAGTTTGAGGTGGATTGTGTCACAGATGTACAAAACTCTTTCTTGTGTAGACAGATTGGAGGTTGGGGAAGTCAGAGCAATGTGTACCGATCTTCTGCTGGCTTGCTTCATTTGTCCTGCAGTTGTCAATCCAGAGCAGTATGGGATAATATCTGATGCTCCTATTAATGAGGTGGCAAGATTTAACCTGATGCAGGTTGGCCGCCTTTTGCAGCAGCTAGCAATGACTGGCACTGAAGAAGGAGATCCCCGGACCAAAAATAGCCTTGGAAAATTTGACAAAGGCTGTGTCGCTGCTTTCCTTGATGTTGTAATTGGGGGCCGTGCAGTGGAGACTCCGCCAATGTCCTCTGTTAATCTTCTGGAAGGCTTGAGCAGAACTGTGGTGTATATAAGTTACAGTCAGCTTATTACTCTGGTAAATTTTATGAAGAGTGTGATGTCTGGAGATCAACTGAAAGAAGATAGAATGGCTCTTGACAATTTGTTGGCAAACCTGCCCCAGGCTAAGCCAGGGAAGAGCAGCAGTCTGGACATGACTCCCTATAGCACTCCTCAGATGTCTCCAGCAACCACTCCAGCCAACAAGAAGAATCGATTACCTATAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CAGGGAAGAGCAGCAGTCTG
60.39
CAAAATCTTGGCATGCTGGC
58.63
142
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GGAAGAGCAGCAGTCTGGAC
60.39
CCAAAATCTTGGCATGCTGGC
61.01
140
PCR template sequence:
AAGCCAGGGAAGAGCAGCAGTCTGGACATGACTCCCTATAGCACTCCTCAGATGTCTCCAGCAACCACTCCAGCCAACAAGAAGAATCGATTACCTATAGTGCTGAAGCTTCCCCTGCTGAGTGTTGCCAGCATGCCAAGATTTTGGAAGATACACAGTTTGTTGATGGATATAAGCAACTGGGATTTCAGGAAACAGCT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
4
Interacting miRNAs (#binding sites)
mmu-miR-196a-5p(2), mmu-miR-495-3p(1), mmu-miR-503-5p(1), mmu-miR-369-3p(1)
siRNAs for circular RNA silencing
Junction sequence
CGATTACCTATAGTGCTGAAGCTTCC
siRNA sets
TCAGCACTATAGGTAATCG,GAAGCTTCAGCACTATAGG,AAGCTTCAGCACTATAGGT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCGAPVD1_1256_ORF_1
0.9737
0.072098354
0.993220285
1134
ORF sequence:
ATGCAAGAAGATGAAAGCTACCTCCTTCAGGTTTTACGATACTTGATTGAATTTGAACTTAAAGAAAGTGACAACCCCAGGCGCCTTTTGAGGAGAGGAACTTGTGCCTTCAGCATCTTATTTAAACTTTTTTCTGAAGGACTGTTTTCTGCCAAACTTTTCCTTACGGCTACTTTGCATGAGCCAATCATGCAGCTCCTCGTAGAGGATGAAGACCACCTGGAAACAGATCCAAACAAGCTGATAGAGAGATTCTCTCCAGCTCAGCAAGAAAAACTCTTTGGAGAGAAAGGCTCAGATAGATTTAGGCAAAAGGTTCAAGAAATGGTAGATTCCAATGAGGCTAAACTAGTGGCTTTGGTGAACAAATTTATTGGTTATCTTAAACAGAATACATACTGCTTTCCACATAGTTTGAGGTGGATTGTGTCACAGATGTACAAAACTCTTTCTTGTGTAGACAGATTGGAGGTTGGGGAAGTCAGAGCAATGTGTACCGATCTTCTGCTGGCTTGCTTCATTTGTCCTGCAGTTGTCAATCCAGAGCAGTATGGGATAATATCTGATGCTCCTATTAATGAGGTGGCAAGATTTAACCTGATGCAGGTTGGCCGCCTTTTGCAGCAGCTAGCAATGACTGGCACTGAAGAAGGAGATCCCCGGACCAAAAATAGCCTTGGAAAATTTGACAAAGGCTGTGTCGCTGCTTTCCTTGATGTTGTAATTGGGGGCCGTGCAGTGGAGACTCCGCCAATGTCCTCTGTTAATCTTCTGGAAGGCTTGAGCAGAACTGTGGTGTATATAAGTTACAGTCAGCTTATTACTCTGGTAAATTTTATGAAGAGTGTGATGTCTGGAGATCAACTGAAAGAAGATAGAATGGCTCTTGACAATTTGTTGGCAAACCTGCCCCAGGCTAAGCCAGGGAAGAGCAGCAGTCTGGACATGACTCCCTATAGCACTCCTCAGATGTCTCCAGCAACCACTCCAGCCAACAAGAAGAATCGATTACCTATAGTGCTGAAGCTTCCCCTGCTGAGTGTTGCCAGCATGCCAAGATTTTGGAAGATACACAGTTTGTTGATGGATATAAGCAACTGGGATTTCAGGAAACAGCTTATGGAGAATTCCTGA
Peptide sequence:
MQEDESYLLQVLRYLIEFELKESDNPRRLLRRGTCAFSILFKLFSEGLFSAKLFLTATLHEPIMQLLVEDEDHLETDPNKLIERFSPAQQEKLFGEKGSDRFRQKVQEMVDSNEAKLVALVNKFIGYLKQNTYCFPHSLRWIVSQMYKTLSCVDRLEVGEVRAMCTDLLLACFICPAVVNPEQYGIISDAPINEVARFNLMQVGRLLQQLAMTGTEEGDPRTKNSLGKFDKGCVAAFLDVVIGGRAVETPPMSSVNLLEGLSRTVVYISYSQLITLVNFMKSVMSGDQLKEDRMALDNLLANLPQAKPGKSSSLDMTPYSTPQMSPATTPANKKNRLPIVLKLPLLSVASMPRFWKIHSLLMDISNWDFRKQLMENS
IRESfinder result
IRESfinder score
0.646321713
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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