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mmu_ciNsd1_1388
Basic information of circular RNA
PanCircBase ID:
mmu_ciNsd1_1388
mm39_Chr. Position ID:
chr13|55458354|55459742|+
Gene name:
Nsd1
Transcript:
ENSMUST00000224973.2
CircRNA type:
Circular intronic (ci)RNA
Exon/Intron count:
1
Exon/intron indexes:
20
Exon/intron offsets:
0
Genomic length:
1388
Exon/intron sizes in nt:
1388
Flanking exon/introns:
chr13:55458354-55459931
Splice length:
1388
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GTTGGTGCTTCAGTCCATTCAGAGCACTCCTCCTCTATCAGGGTTTTCAGAATCTGATGCCTGCCACTTGTGTCACTCAGAAAGCACATGCTGTGTGTAAGCACGTGCCCACATTGAGAGCTCTGCTCCATATTCTTATTTGAGTGAAAATAAAGGCCTAAAATCTCAGCTTATATAGAAACAGAAACTTATTTCCATTTACCTTATTTTACCTTTCCAGCAACCCATAAAGATTCTGTTCTATGTATATCTGTTCATGGGGCAGTTCAAGTGAAGCTTGGGTAAATAAATGACTTGTTGAGAATAGTTCAAAGAGCTACCCTGAAAAACAATGAGGCATCTTAGAGAATTCAGGTTGCAAGAGTCTCCTTCCTTCACTGTAGACTTTTTCTTTGTGAATGAAGTAATTGTGTCAGTTTAACACCAGACAAAGCTGCTCAGGCAGATGAGATATCCAGGACTTTGTGTCTTCTGGGCAGTGACTTGGATCTTAGGATTTTAGCTGTTTGGACATGCTAGCTGTTGTGAAAGACCAAGAACAGATGTGTGTGTGGCTCTTTTAGAGGGAGGTTATTATACATTATACTAATGCCTGCTTCTAAAATGTACAGCGAGCTTTAGTGTAGAAGTCAGGGGAGTGTGTTTATGAGTTGGTTTTCTTTCGGTTTGTATAATCTGACGTCGTGATATAACAGAAAGCAAAGTAAGATGTGGGCAAGGCCATTACACTGAAATGTCAGAACCAGGAAGGAGAAATAGGGATTCACTTAGAGTGTCTCCTGGCACAGGATGTGACTGGCATAGTTCTGATGAGTTCCATCAGTGAAGTCTAGTGTATTCATTTGGAGATGGGAACATTTACATGCTGTTGTTCATGGGGACTAGATGCAAGGTTACGTTAGTTCTAGGTTTTCCCTCTCATTCTACATGGACAATGCAGATAAAGTTCTGTGCTGGTTTCAAGACTTAAAATTCAGCAAAGGTGAGTCGGCTTCCCTTATTATTTTTGCATCTGTATACTATTTCAGTTTAAGACAAAATAAGCAAGTATGTTAAAAGGCTGGAATGTTCCTCTTTGAGTTAACTATTTAAAAGCTGTCGAGCTCGGTATGGTCATACACTGAGAAATGTAGGTGCAGACAACCCTGGCTCCATGGTGAGACCCTGTCTCAAATAACACAAACAAACTAAATTTTTTAAAGCTCTTCTAGGACAAACAGAATTTGCAAACAAATGTGGAAATATTGATAATTGTTTCATCTTTAGAGGAACTTTGGGGTTTGTTTGGTTGGTTTTCTACTGTACAGCCCTTCTTGCTAGAAATAGTCTCTTGCTTGTGTTTAGTTGATACTTAGTTACTCAACCTTGATTCTTTGCTGTTATTTTAT
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
ACTGTACAGCCCTTCTTGCT
58.94
ACAAGTGGCAGGCATCAGAT
59.67
161
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
ACTGTACAGCCCTTCTTGCT
58.94
CACAAGTGGCAGGCATCAGA
60.61
162
PCR template sequence:
TTGGTTTTCTACTGTACAGCCCTTCTTGCTAGAAATAGTCTCTTGCTTGTGTTTAGTTGATACTTAGTTACTCAACCTTGATTCTTTGCTGTTATTTTATGTTGGTGCTTCAGTCCATTCAGAGCACTCCTCCTCTATCAGGGTTTTCAGAATCTGATGCCTGCCACTTGTGTCACTCAGAAAGCACATGCTGTGTGTAA
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-16-5p(1), mmu-miR-382-3p(1), mmu-miR-5101(1), mmu-miR-697(1)
siRNAs for circular RNA silencing
Junction sequence
GCTGTTATTTTATGTTGGTGCTTCAG
siRNA sets
ACCAACATAAAATAACAGC, CACCAACATAAAATAACAG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CINSD1_1388_ORF_5
0.5486
-0.218320009
0.011608341
102
ORF sequence:
ATGTTGGTGCTTCAGTCCATTCAGAGCACTCCTCCTCTATCAGGGTTTTCAGAATCTGATGCCTGCCACTTGTGTCACTCAGAAAGCACATGCTGTGTGTAA
Peptide sequence:
MLVLQSIQSTPPLSGFSESDACHLCHSESTCCV
IRESfinder result
IRESfinder score
0.832360602
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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