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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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