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mmu_circSnhg4_1233
Basic information of circular RNA
PanCircBase ID:
mmu_circSnhg4_1233
mm39_Chr. Position ID:
chr18|35710610|35717934|+
Gene name:
Snhg4
Transcript:
ENSMUST00000237592.2
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
10
Exon/intron indexes:
5,6,7,8,9,10,11,12,13,14
Exon/intron offsets:
0,858,1347,1708,3612,4039,4361,5158,6320,6957
Genomic length:
7324
Exon/intron sizes in nt:
6,24,21,13,53,12,61,26,00,00,00,00,000
Flanking exon/introns:
chr18:35690422-35710610|chr18:35717934-35720683
Splice length:
1233
Other database IDs:
circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_136937
Human Ortholog IDs:
Mature spliced Sequence:
GAGTGGAGTCAACATATCAATGGAGCAAGTCACAGTCGTCGATGCCAGCTTCTTCTTGAAATCTACCCAGAATGGAATCCTGACAATGATACTGGACACACAATGGGTGATCCATTCATGCTGCAGCAGTCTACAAACCCAGCACCAGGGATTCTGGGACCGCCGCCTCCTTCATTTCATCTTGGAGGACCAGCAGTTGGACCAAGAGGAAATCTGGGTGCTGGTAATGGAAACCTACAAGGACCAAGACACATGCAAAAAGGCAGAGTGGAAACCAGCCGAGTTGTTCACATTATGGATTTTCAGCGAGGAAAAAACTTGAGATACCAGCTGTTACAACTGGTAGAACCATTTGGAGTCATTTCAAATCATCTGATTTTAAATAAAATTAATGAGGCATTTATTGAAATGGCCACCACAGAAGATGCTCAGGCTGCTGTGGATTATTATACAACTACACCAGCATTAGTGTTTGGCAAGCCAGTGAGAGTTCATTTATCCCAGAAGTATAAGAGAATAAAGAAACCTGAAGGAAAACCAGATCAGAAGTTTGATCAAAAGCAAGAACTTGGTCGTGTGATACATCTCAGCAATTTACCTCATTCTGGCTATTCTGACAGTGCCGTCCTCAAGCTTGCTGAGCCTTATGGGAAAATAAAGAATTATATCTTAATGAGGATGAAAAGTCAGGCTTTTATTGAGATGGAAACCAGAGAAGATGCAATGGCAATGGTTGACCACTGTTTAAAGAAGGCACTTTGGTTTCAGGGGAGATGTGTTAAAGTTGATCTGTCTGAGAAATACAAAAAACTGGTGCTGCGGATTCCTAACAGAGGCATTGACTTACTGAAAAAAGATAAATCCCGGAAAAGATCCTATTCTCCAGATGGAAAAGAATCTCCAAGTGATAAGAAGTCCAAAACTGATGCTCAGAAGACTGAGAGTCCAGCTGAGGGTAAAGAACAAGAAGAGAAGTCGGGTGAGGATGGTGAGAAGGACACCAAGGATGACCAGACAGAACAGGAGCCCAGCATGCTTCTTGAATCTGAAGATGAACTGCTTGTTGATGAGGAAGAAGCTGCAGCACTACTAGAAAGTGGTAGTTCAGTGGGCGATGAGACCGATCTTGCTAATTTAGGGGATGTATCTTCTGATGGGAAAAAGGAGCCTTCAGATAAAGCTGTGAAAAAAGATCCAAGTGCTTCAGCAACATCCAAGAAAAAACTTAAAAAA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TCTGATGGGAAAAAGGAGCCT
59
AGAAGAAGCTGGCATCGACG
60.46
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TTCTGATGGGAAAAAGGAGCCT
59.62
GAAGAAGCTGGCATCGACGA
60.46
140
PCR template sequence:
TTTAGGGGATGTATCTTCTGATGGGAAAAAGGAGCCTTCAGATAAAGCTGTGAAAAAAGATCCAAGTGCTTCAGCAACATCCAAGAAAAAACTTAAAAAAGAGTGGAGTCAACATATCAATGGAGCAAGTCACAGTCGTCGATGCCAGCTTCTTCTTGAAATCTACCCAGAATGGAATCCTGACAATGATACTGGACACA
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-20b-5p(1), mmu-miR-93-5p(1), mmu-miR-17-5p(1), mmu-miR-138-5p(1), mmu-miR-136-5p(1), mmu-miR-29b-1-5p(1), mmu-miR-183-5p(1), mmu-miR-29b-2-5p(1), mmu-miR-129-5p(1)
siRNAs for circular RNA silencing
Junction sequence
AAAACTTAAAAAAGAGTGGAGTCAAC
siRNA sets
ACTCCACTCTTTTTTAAGT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSNHG4_1233_ORF_1
1.1296
0.126893754
0.99999943
2364
ORF sequence:
ATGGGTGATCCATTCATGCTGCAGCAGTCTACAAACCCAGCACCAGGGATTCTGGGACCGCCGCCTCCTTCATTTCATCTTGGAGGACCAGCAGTTGGACCAAGAGGAAATCTGGGTGCTGGTAATGGAAACCTACAAGGACCAAGACACATGCAAAAAGGCAGAGTGGAAACCAGCCGAGTTGTTCACATTATGGATTTTCAGCGAGGAAAAAACTTGAGATACCAGCTGTTACAACTGGTAGAACCATTTGGAGTCATTTCAAATCATCTGATTTTAAATAAAATTAATGAGGCATTTATTGAAATGGCCACCACAGAAGATGCTCAGGCTGCTGTGGATTATTATACAACTACACCAGCATTAGTGTTTGGCAAGCCAGTGAGAGTTCATTTATCCCAGAAGTATAAGAGAATAAAGAAACCTGAAGGAAAACCAGATCAGAAGTTTGATCAAAAGCAAGAACTTGGTCGTGTGATACATCTCAGCAATTTACCTCATTCTGGCTATTCTGACAGTGCCGTCCTCAAGCTTGCTGAGCCTTATGGGAAAATAAAGAATTATATCTTAATGAGGATGAAAAGTCAGGCTTTTATTGAGATGGAAACCAGAGAAGATGCAATGGCAATGGTTGACCACTGTTTAAAGAAGGCACTTTGGTTTCAGGGGAGATGTGTTAAAGTTGATCTGTCTGAGAAATACAAAAAACTGGTGCTGCGGATTCCTAACAGAGGCATTGACTTACTGAAAAAAGATAAATCCCGGAAAAGATCCTATTCTCCAGATGGAAAAGAATCTCCAAGTGATAAGAAGTCCAAAACTGATGCTCAGAAGACTGAGAGTCCAGCTGAGGGTAAAGAACAAGAAGAGAAGTCGGGTGAGGATGGTGAGAAGGACACCAAGGATGACCAGACAGAACAGGAGCCCAGCATGCTTCTTGAATCTGAAGATGAACTGCTTGTTGATGAGGAAGAAGCTGCAGCACTACTAGAAAGTGGTAGTTCAGTGGGCGATGAGACCGATCTTGCTAATTTAGGGGATGTATCTTCTGATGGGAAAAAGGAGCCTTCAGATAAAGCTGTGAAAAAAGATCCAAGTGCTTCAGCAACATCCAAGAAAAAACTTAAAAAAGAGTGGAGTCAACATATCAATGGAGCAAGTCACAGTCGTCGATGCCAGCTTCTTCTTGAAATCTACCCAGAATGGAATCCTGACAATGATACTGGACACACAATGGGTGATCCATTCATGCTGCAGCAGTCTACAAACCCAGCACCAGGGATTCTGGGACCGCCGCCTCCTTCATTTCATCTTGGAGGACCAGCAGTTGGACCAAGAGGAAATCTGGGTGCTGGTAATGGAAACCTACAAGGACCAAGACACATGCAAAAAGGCAGAGTGGAAACCAGCCGAGTTGTTCACATTATGGATTTTCAGCGAGGAAAAAACTTGAGATACCAGCTGTTACAACTGGTAGAACCATTTGGAGTCATTTCAAATCATCTGATTTTAAATAAAATTAATGAGGCATTTATTGAAATGGCCACCACAGAAGATGCTCAGGCTGCTGTGGATTATTATACAACTACACCAGCATTAGTGTTTGGCAAGCCAGTGAGAGTTCATTTATCCCAGAAGTATAAGAGAATAAAGAAACCTGAAGGAAAACCAGATCAGAAGTTTGATCAAAAGCAAGAACTTGGTCGTGTGATACATCTCAGCAATTTACCTCATTCTGGCTATTCTGACAGTGCCGTCCTCAAGCTTGCTGAGCCTTATGGGAAAATAAAGAATTATATCTTAATGAGGATGAAAAGTCAGGCTTTTATTGAGATGGAAACCAGAGAAGATGCAATGGCAATGGTTGACCACTGTTTAAAGAAGGCACTTTGGTTTCAGGGGAGATGTGTTAAAGTTGATCTGTCTGAGAAATACAAAAAACTGGTGCTGCGGATTCCTAACAGAGGCATTGACTTACTGAAAAAAGATAAATCCCGGAAAAGATCCTATTCTCCAGATGGAAAAGAATCTCCAAGTGATAAGAAGTCCAAAACTGATGCTCAGAAGACTGAGAGTCCAGCTGAGGGTAAAGAACAAGAAGAGAAGTCGGGTGAGGATGGTGAGAAGGACACCAAGGATGACCAGACAGAACAGGAGCCCAGCATGCTTCTTGAATCTGAAGATGAACTGCTTGTTGATGAGGAAGAAGCTGCAGCACTACTAGAAAGTGGTAGTTCAGTGGGCGATGAGACCGATCTTGCTAATTTAGGGGATGTATCTTCTGATGGGAAAAAGGAGCCTTCAGATAAAGCTGTGAAAAAAGATCCAAGTGCTTCAGCAACATCCAAGAAAAAACTTAAAAAA
Peptide sequence:
MGDPFMLQQSTNPAPGILGPPPPSFHLGGPAVGPRGNLGAGNGNLQGPRHMQKGRVETSRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNKINEAFIEMATTEDAQAAVDYYTTTPALVFGKPVRVHLSQKYKRIKKPEGKPDQKFDQKQELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRMKSQAFIEMETREDAMAMVDHCLKKALWFQGRCVKVDLSEKYKKLVLRIPNRGIDLLKKDKSRKRSYSPDGKESPSDKKSKTDAQKTESPAEGKEQEEKSGEDGEKDTKDDQTEQEPSMLLESEDELLVDEEEAAALLESGSSVGDETDLANLGDVSSDGKKEPSDKAVKKDPSASATSKKKLKKEWSQHINGASHSRRCQLLLEIYPEWNPDNDTGHTMGDPFMLQQSTNPAPGILGPPPPSFHLGGPAVGPRGNLGAGNGNLQGPRHMQKGRVETSRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNKINEAFIEMATTEDAQAAVDYYTTTPALVFGKPVRVHLSQKYKRIKKPEGKPDQKFDQKQELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRMKSQAFIEMETREDAMAMVDHCLKKALWFQGRCVKVDLSEKYKKLVLRIPNRGIDLLKKDKSRKRSYSPDGKESPSDKKSKTDAQKTESPAEGKEQEEKSGEDGEKDTKDDQTEQEPSMLLESEDELLVDEEEAAALLESGSSVGDETDLANLGDVSSDGKKEPSDKAVKKDPSASATSKKKLKK
IRESfinder result
IRESfinder score
0.578159762
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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