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mmu_circSec63_1216
Basic information of circular RNA
PanCircBase ID:
mmu_circSec63_1216
mm39_Chr. Position ID:
chr10|42665295|42686921|+
Gene name:
Sec63
Transcript:
ENSMUST00000019937.5
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
12
Exon/intron indexes:
3,4,5,6,7,8,9,10,11,12,13,14
Exon/intron offsets:
0,1879,5475,6906,8383,9447,12333,12522,14590,15776,17224,21543
Genomic length:
21626
Exon/intron sizes in nt:
115,113,62,59,51,109,95,133,93,155,148,83
Flanking exon/introns:
chr10:42659537-42665295|chr10:42686921-42688431
Splice length:
1216
Other database IDs:
circBase: hsa_circ_0130199, circAtlas: hsa-SEC63_0041, CIRCpedia: HSA_CIRCpedia_68500
Human Ortholog IDs:
Mature spliced Sequence:
GAAAATAGTTCTGCTTGCAGGATGGGCACTGTTCTTATTTCTTGCATACAAAGTTTCCAAAACAGACCGAGAATATCAAGAGTACAATCCTTATGAAGTACTAAATTTGGATCCTGGAGCAACAGTGGCAGAAATTAAGAAACAGTATCGCTTGTTGTCACTTAAATATCATCCAGATAAAGGAGGTGATGAAGTCATGTTCATGAGGATAGCAAAAGCATATGCAGCTTTAACAGATGAAGAGTCTCGGAAAAATTGGGAAGAATTTGGAAATCCAGATGGGCCTCAAGCTACAAGCTTTGGAATTGCTTTGCCAGCTTGGATAGTTGACCAGAAAAATTCAATTCTGGTTTTACTTGTGTATGGATTGGCTTTTATGGTTATTCTTCCTGTTGTGGTGGGCTCTTGGTGGTATCGGTCAATACGATATAGTGGAGACCAGATTCTAATACGTACAACACAGATTTATACATACTTTGTTTATAAAACTCGAAATATGGATATGAAACGTCTCATCATGGTTTTAGCTGGAGCTTCTGAATTTGACCCTCAGTATAATAAAGATTCCACAAGCAGGCCAACAGATAATATTTTAATACCACAGCTAATCAGGGAAATTGGCAGCATAAATTTAAAGAAGAATGAACCTCCACTCACCTGTCCATACAGCCTGAAGGCCAGAGTTCTTTTACTGTCTCATCTTGCTAGAATGAAAATTCCTGAGACACTGGAAGAAGATCAACAGTTCATGCTGAAAAAATGTCCTGCTCTGCTTCAAGAAATGGTTAATGTAATCTGCCAGCTAATAATAATGGCCCGGAGCCGTGAAGAAAGGGAGTTTCGTGCTCCAACTTTGGCATCCTTAGAAAACTGTATGAAGCTTTCCCAGATGGCTGTTCAGGGGCTCCAGCAGTTTAAGTCTCCCCTTCTGCAGCTCCCTCATATTGAAGAGGACAATCTTAGGAGAGTTTCGAATCATAAAAAGTACAAAATTAAAACTATCCAGGATTTGGTTAGTTTAAAAGAATCAGATCGTCATAGTCTGCTACACTTCCTTGAAGATGAAAAGTATGAAGAGGTCATGGCGGTCCTTGGGAGTTTCCCGTATGTGACCATGGACATAAAATCACAGGTCTTGGATGATGAAGATAGCAACAACATCACAGTAGGATCCCTAGTTACAGTGTTGGTTAAGTTGACGAGGCAGACCATGGCT
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TCACAGGTCTTGGATGATGAAGA
59.16
TCTCGGTCTGTTTTGGAAACT
57.45
162
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TCACAGGTCTTGGATGATGAAGA
59.16
TCGGTCTGTTTTGGAAACTTTGT
59.24
160
PCR template sequence:
GGACATAAAATCACAGGTCTTGGATGATGAAGATAGCAACAACATCACAGTAGGATCCCTAGTTACAGTGTTGGTTAAGTTGACGAGGCAGACCATGGCTGAAAATAGTTCTGCTTGCAGGATGGGCACTGTTCTTATTTCTTGCATACAAAGTTTCCAAAACAGACCGAGAATATCAAGAGTACAATCCTTATGAAGTA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
9
Interacting miRNAs (#binding sites)
mmu-miR-200a-3p(1), mmu-miR-141-3p(1), mmu-miR-199a-5p(1), mmu-miR-7b-5p(1), mmu-miR-335-5p(1), mmu-miR-709(1), mmu-miR-351-5p(1), mmu-miR-335-3p(1), mmu-miR-670-5p(1)
siRNAs for circular RNA silencing
Junction sequence
GCAGACCATGGCTGAAAATAGTTCTG
siRNA sets
TATTTTCAGCCATGGTCTG, GAACTATTTTCAGCCATGG, CTATTTTCAGCCATGGTCT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSEC63_1216_ORF_1
0.8937
-0.001704993
0.987972608
1116
ORF sequence:
ATGTTCATGAGGATAGCAAAAGCATATGCAGCTTTAACAGATGAAGAGTCTCGGAAAAATTGGGAAGAATTTGGAAATCCAGATGGGCCTCAAGCTACAAGCTTTGGAATTGCTTTGCCAGCTTGGATAGTTGACCAGAAAAATTCAATTCTGGTTTTACTTGTGTATGGATTGGCTTTTATGGTTATTCTTCCTGTTGTGGTGGGCTCTTGGTGGTATCGGTCAATACGATATAGTGGAGACCAGATTCTAATACGTACAACACAGATTTATACATACTTTGTTTATAAAACTCGAAATATGGATATGAAACGTCTCATCATGGTTTTAGCTGGAGCTTCTGAATTTGACCCTCAGTATAATAAAGATTCCACAAGCAGGCCAACAGATAATATTTTAATACCACAGCTAATCAGGGAAATTGGCAGCATAAATTTAAAGAAGAATGAACCTCCACTCACCTGTCCATACAGCCTGAAGGCCAGAGTTCTTTTACTGTCTCATCTTGCTAGAATGAAAATTCCTGAGACACTGGAAGAAGATCAACAGTTCATGCTGAAAAAATGTCCTGCTCTGCTTCAAGAAATGGTTAATGTAATCTGCCAGCTAATAATAATGGCCCGGAGCCGTGAAGAAAGGGAGTTTCGTGCTCCAACTTTGGCATCCTTAGAAAACTGTATGAAGCTTTCCCAGATGGCTGTTCAGGGGCTCCAGCAGTTTAAGTCTCCCCTTCTGCAGCTCCCTCATATTGAAGAGGACAATCTTAGGAGAGTTTCGAATCATAAAAAGTACAAAATTAAAACTATCCAGGATTTGGTTAGTTTAAAAGAATCAGATCGTCATAGTCTGCTACACTTCCTTGAAGATGAAAAGTATGAAGAGGTCATGGCGGTCCTTGGGAGTTTCCCGTATGTGACCATGGACATAAAATCACAGGTCTTGGATGATGAAGATAGCAACAACATCACAGTAGGATCCCTAGTTACAGTGTTGGTTAAGTTGACGAGGCAGACCATGGCTGAAAATAGTTCTGCTTGCAGGATGGGCACTGTTCTTATTTCTTGCATACAAAGTTTCCAAAACAGACCGAGAATATCAAGAGTACAATCCTTATGA
Peptide sequence:
MFMRIAKAYAALTDEESRKNWEEFGNPDGPQATSFGIALPAWIVDQKNSILVLLVYGLAFMVILPVVVGSWWYRSIRYSGDQILIRTTQIYTYFVYKTRNMDMKRLIMVLAGASEFDPQYNKDSTSRPTDNILIPQLIREIGSINLKKNEPPLTCPYSLKARVLLLSHLARMKIPETLEEDQQFMLKKCPALLQEMVNVICQLIIMARSREEREFRAPTLASLENCMKLSQMAVQGLQQFKSPLLQLPHIEEDNLRRVSNHKKYKIKTIQDLVSLKESDRHSLLHFLEDEKYEEVMAVLGSFPYVTMDIKSQVLDDEDSNNITVGSLVTVLVKLTRQTMAENSSACRMGTVLISCIQSFQNRPRISRVQSL
IRESfinder result
IRESfinder score
0.713617391
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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