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mmu_circNdst4_683
Basic information of circular RNA
PanCircBase ID:
mmu_circNdst4_683
mm39_Chr. Position ID:
chr3|125501730|125515851|+
Gene name:
Ndst4
Transcript:
ENSMUST00000173932.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
9,10,11,12,13
Exon/intron offsets:
0,1967,5222,6468,14018
Genomic length:
14121
Exon/intron sizes in nt:
12,41,75,17,11,10,103
Flanking exon/introns:
chr3:125491650-125501730|chr3:125515851-125518299
Splice length:
683
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GAACAACTGCACTTTATTTATTTCTTCTAATGCACCCCTCCATCATCAGCAATCTTCCTAGCCCCAAAACCTTTGAAGAAGTTCAATTTTTTAATGGCAACAACTATCACAAGGGAATTGAGTGGTATATGGACTTTTTCCCCACTCCTTCCAACATTACCAGTGATTTCCTATTTGAAAAGAGTGCTAACTACTTCCACTCAGAAGAGGCTCCCAAGAGGGCTGCATCTCTTGTTCCCAAAGCCAAGATCATTACTATCCTCATAGACCCCTCGGACAGGGCATATTCTTGGTACCAGCACCAACGATCTCATGAAGATCCAGCTGCCCTGAGGTTCAATTTCTATGAAGTTATCACAACAGGACATTGGGCCCCTCCTGATTTAAAAACATTGCAGAGGAGATGTCTGGTGCCTGGGTGGTATGCAGTGCACATAGAAAGATGGCTGGCCTACTTTTCTACTTCCCAGTTGCTAATTATTGATGGACAACAGCTGAGATCTGACCCAGCTACTGTGATGGATGAAGTCCAGAAGTTTCTAGGAGTTACACCTCATTATAATTACTCGGAAGCACTAACGTTTGATCCCCAGAAAGGCTTTTGGTGTCAGCTACTAGAAGGAGGAAAAACCAAATGCCTTGGGAAAAGCAAAGGCCGAAAATACCCGCCCATGGATTCAGAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TCCCCAGAAAGGCTTTTGGT
59.44
TTGCTGATGATGGAGGGGTG
59.74
149
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CCCCAGAAAGGCTTTTGGTG
59.32
TTGCTGATGATGGAGGGGTG
59.74
148
PCR template sequence:
TGATCCCCAGAAAGGCTTTTGGTGTCAGCTACTAGAAGGAGGAAAAACCAAATGCCTTGGGAAAAGCAAAGGCCGAAAATACCCGCCCATGGATTCAGAGGAACAACTGCACTTTATTTATTTCTTCTAATGCACCCCTCCATCATCAGCAATCTTCCTAGCCCCAAAACCTTTGAAGAAGTTCAATTTTTTAATGGCAA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
3
Interacting miRNAs (#binding sites)
mmu-miR-27b-3p(1), mmu-miR-27a-3p(1), mmu-miR-93-5p(1)
siRNAs for circular RNA silencing
Junction sequence
CATGGATTCAGAGGAACAACTGCACT
siRNA sets
CAGTTGTTCCTCTGAATCC, AGTGCAGTTGTTCCTCTGA, AGTTGTTCCTCTGAATCCA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCNDST4_683_ORF_1
0.73
0.040396519
0.822006036
732
ORF sequence:
ATGCCTTGGGAAAAGCAAAGGCCGAAAATACCCGCCCATGGATTCAGAGGAACAACTGCACTTTATTTATTTCTTCTAATGCACCCCTCCATCATCAGCAATCTTCCTAGCCCCAAAACCTTTGAAGAAGTTCAATTTTTTAATGGCAACAACTATCACAAGGGAATTGAGTGGTATATGGACTTTTTCCCCACTCCTTCCAACATTACCAGTGATTTCCTATTTGAAAAGAGTGCTAACTACTTCCACTCAGAAGAGGCTCCCAAGAGGGCTGCATCTCTTGTTCCCAAAGCCAAGATCATTACTATCCTCATAGACCCCTCGGACAGGGCATATTCTTGGTACCAGCACCAACGATCTCATGAAGATCCAGCTGCCCTGAGGTTCAATTTCTATGAAGTTATCACAACAGGACATTGGGCCCCTCCTGATTTAAAAACATTGCAGAGGAGATGTCTGGTGCCTGGGTGGTATGCAGTGCACATAGAAAGATGGCTGGCCTACTTTTCTACTTCCCAGTTGCTAATTATTGATGGACAACAGCTGAGATCTGACCCAGCTACTGTGATGGATGAAGTCCAGAAGTTTCTAGGAGTTACACCTCATTATAATTACTCGGAAGCACTAACGTTTGATCCCCAGAAAGGCTTTTGGTGTCAGCTACTAGAAGGAGGAAAAACCAAATGCCTTGGGAAAAGCAAAGGCCGAAAATACCCGCCCATGGATTCAGAG
Peptide sequence:
MPWEKQRPKIPAHGFRGTTALYLFLLMHPSIISNLPSPKTFEEVQFFNGNNYHKGIEWYMDFFPTPSNITSDFLFEKSANYFHSEEAPKRAASLVPKAKIITILIDPSDRAYSWYQHQRSHEDPAALRFNFYEVITTGHWAPPDLKTLQRRCLVPGWYAVHIERWLAYFSTSQLLIIDGQQLRSDPATVMDEVQKFLGVTPHYNYSEALTFDPQKGFWCQLLEGGKTKCLGKSKGRKYPPMDSE
IRESfinder result
IRESfinder score
0.719641547
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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