top of page
mmu_circSnap23_301
Basic information of circular RNA
PanCircBase ID:
mmu_circSnap23_301
mm39_Chr. Position ID:
chr2|120425281|120427268|+
Gene name:
Snap23
Transcript:
ENSMUST00000110711.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
2
Exon/intron indexes:
6,7
Exon/intron offsets:
0,1842
Genomic length:
1987
Exon/intron sizes in nt:
1,56,145
Flanking exon/introns:
chr2:120416757-120425281|chr2:120427268-120429756
Splice length:
301
Other database IDs:
circAtlas: mmu-Sp23_0001
circBase: hsa_circ_0034826, circAtlas: hsa-SP23_0001, CIRCpedia: HSA_CIRCpedia_14320
Human Ortholog IDs:
Mature spliced Sequence:
GACAAAGAACTTTGAGTCTGGAAAGAACTATAAGGCAACATGGGGAGATGGTGGCGACAACTCACCTAGCAATGTAGTATCTAAGCAACCGAGCCGGATTACAAATGGTCAGCCTCAGCAAACTACAGGAGCAGCCAGTGGTGGATACATTAAACGTATAACTAATGATGCCAGAGAAGATGAGATGGAAGAGAACCTGACTCAAGTGGGCAGCATCCTAGGCAACCTAAAGAACATGGCTCTGGATATGGGCAATGAAATTGATGCTCAAAACCAGCAAATACAGAAGATCACAGAAAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CAAGTGGGCAGCATCCTAGG
60.47
CCATCTCCCCATGTTGCCTT
60.03
150
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CAAGTGGGCAGCATCCTAGG
60.47
TGAGTTGTCGCCACCATCTC
60.04
163
PCR template sequence:
TCAAGTGGGCAGCATCCTAGGCAACCTAAAGAACATGGCTCTGGATATGGGCAATGAAATTGATGCTCAAAACCAGCAAATACAGAAGATCACAGAAAAGGACAAAGAACTTTGAGTCTGGAAAGAACTATAAGGCAACATGGGGAGATGGTGGCGACAACTCACCTAGCAATGTAGTATCTAAGCAACCGAGCCGGATT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
1
Interacting miRNAs (#binding sites)
mmu-miR-221-3p(1)
siRNAs for circular RNA silencing
Junction sequence
GATCACAGAAAAGGACAAAGAACTTT
siRNA sets
AAGTTCTTTGTCCTTTTCT,TTCTTTGTCCTTTTCTGTG,AAAGTTCTTTGTCCTTTTC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSNAP23_301_ORF_1
0.9243
0.225443404
0.473696779
348
ORF sequence:
ATGAAATTGATGCTCAAAACCAGCAAATACAGAAGATCACAGAAAAGGACAAAGAACTTTGAGTCTGGAAAGAACTATAAGGCAACATGGGGAGATGGTGGCGACAACTCACCTAGCAATGTAGTATCTAAGCAACCGAGCCGGATTACAAATGGTCAGCCTCAGCAAACTACAGGAGCAGCCAGTGGTGGATACATTAAACGTATAACTAATGATGCCAGAGAAGATGAGATGGAAGAGAACCTGACTCAAGTGGGCAGCATCCTAGGCAACCTAAAGAACATGGCTCTGGATATGGGCAATGAAATTGATGCTCAAAACCAGCAAATACAGAAGATCACAGAAAAG
Peptide sequence:
MKLMLKTSKYRRSQKRTKNFESGKNYKATWGDGGDNSPSNVVSKQPSRITNGQPQQTTGAASGGYIKRITNDAREDEMEENLTQVGSILGNLKNMALDMGNEIDAQNQQIQKITEK
IRESfinder result
IRESfinder score
0.288934858
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
bottom of page