top of page
mmu_circCtdspl2_923
Basic information of circular RNA
PanCircBase ID:
mmu_circCtdspl2_923
mm39_Chr. Position ID:
chr2|121807811|121834628|+
Gene name:
Ctdspl2
Transcript:
ENSMUST00000036647.13
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
8
Exon/intron indexes:
3,4,5,6,7,8,9,10
Exon/intron offsets:
0,1561,3821,9618,11459,16015,26570,26737
Genomic length:
26817
Exon/intron sizes in nt:
139,150,213,79,112,87,63,80
Flanking exon/introns:
chr2:121799760-121807811|chr2:121834628-121837343
Splice length:
923
Other database IDs:
circAtlas: mmu-Ctdspl2_0017
circAtlas: hsa-CTDSPL2_0087, CIRCpedia: HSA_CIRCpedia_368508
Human Ortholog IDs:
Mature spliced Sequence:
GAAGAGAGAGAAAATCCTTCGAAGCGGAGTAGAATTGAACGTGATATAGATAATAATTTAATCACATCAACACCAAGAACCGGAGAAAAGCCTGACAAACAGTTGTCTCGAGTAAGACGGAAAAGTCCAGTCAATGGAGAAGCTGGTAGTTATGAAATGACAAATCAACATATAAAGCAAAATGGAAAATTAGAAGATAACCCTTGCTCTGGTAGTCCTCCGAGGACTACATTGTTGGGGACCATATTTTCGCCTGTCTTCAACTTTTTTTCACCAGCAAATAAAAATGGAACGTCAGGCTCAGATTCCCCAGGACAGGCTGTGGAAGCTGAGGAGATAGTGAAACAACTTGACATGGAACAGGTGGATGAAATTACTACCAGCACCACGTCAGCTAATGGAGCGGCTTACTCAAATCAAGCAGTTCAAGTGAGGCCATCACTAAATAATGGTTTAGAAGAAGCAGAAGAAACAGTTACCCGGGATATCCCACCCCTTACAGCACCAGTAACTCCAGAGAGTGGGTACTCGTCAGCCCATGCAGAGGCCACCTATGAAGAAGACTGGGAAGTATTTGACCCCTATTATTTCATCAAACATGTTCCGCCTCTGACAGAAGAACAGCTAAATAGGAAACCTGCTCTTCCTTTGAAAACAAGAAGCACACCAGAGTTCTCCCTGGTCTTAGATCTGGATGAGACACTAGTGCACTGCAGTCTGAATGAGCTAGAAGATGCAGCGCTCACTTTTCCAGTCCTTTTCCAAGATGTCATTTATCAGGTTTATGTGAGATTAAGACCATTCTTCAGGGAATTCCTGGAACGAATGTCTCAGATGTATGAGATCATTCTTTTTACTGCTTCTAAGAAGGTGTATGCAGACAAGTTACTGAACATACTAGACCCTAAAAAGCAACTGGTCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
ACTGCTTCTAAGAAGGTGTATGCA
60.02
TGTCAGGCTTTTCTCCGGTT
59.53
165
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
ACTGCTTCTAAGAAGGTGTATGCA
60.02
TTGTCAGGCTTTTCTCCGGT
59.53
166
PCR template sequence:
GAATGTCTCAGATGTATGAGATCATTCTTTTTACTGCTTCTAAGAAGGTGTATGCAGACAAGTTACTGAACATACTAGACCCTAAAAAGCAACTGGTCAGGAAGAGAGAGAAAATCCTTCGAAGCGGAGTAGAATTGAACGTGATATAGATAATAATTTAATCACATCAACACCAAGAACCGGAGAAAAGCCTGACAAAC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
6
Interacting miRNAs (#binding sites)
mmu-miR-1904(2), mmu-miR-148a-3p(1), mmu-miR-139-5p(1), mmu-miR-136-5p(1), mmu-miR-483-5p(1), mmu-miR-207(1)
siRNAs for circular RNA silencing
Junction sequence
AGCAACTGGTCAGGAAGAGAGAGAAA
siRNA sets
TTTCTCTCTCTTCCTGACC,TTCTCTCTCTTCCTGACCA,TCTCTCTCTTCCTGACCAG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCCTDSPL2_923_ORF_1
0.9495
0.095476017
0.940383722
816
ORF sequence:
ATGACAAATCAACATATAAAGCAAAATGGAAAATTAGAAGATAACCCTTGCTCTGGTAGTCCTCCGAGGACTACATTGTTGGGGACCATATTTTCGCCTGTCTTCAACTTTTTTTCACCAGCAAATAAAAATGGAACGTCAGGCTCAGATTCCCCAGGACAGGCTGTGGAAGCTGAGGAGATAGTGAAACAACTTGACATGGAACAGGTGGATGAAATTACTACCAGCACCACGTCAGCTAATGGAGCGGCTTACTCAAATCAAGCAGTTCAAGTGAGGCCATCACTAAATAATGGTTTAGAAGAAGCAGAAGAAACAGTTACCCGGGATATCCCACCCCTTACAGCACCAGTAACTCCAGAGAGTGGGTACTCGTCAGCCCATGCAGAGGCCACCTATGAAGAAGACTGGGAAGTATTTGACCCCTATTATTTCATCAAACATGTTCCGCCTCTGACAGAAGAACAGCTAAATAGGAAACCTGCTCTTCCTTTGAAAACAAGAAGCACACCAGAGTTCTCCCTGGTCTTAGATCTGGATGAGACACTAGTGCACTGCAGTCTGAATGAGCTAGAAGATGCAGCGCTCACTTTTCCAGTCCTTTTCCAAGATGTCATTTATCAGGTTTATGTGAGATTAAGACCATTCTTCAGGGAATTCCTGGAACGAATGTCTCAGATGTATGAGATCATTCTTTTTACTGCTTCTAAGAAGGTGTATGCAGACAAGTTACTGAACATACTAGACCCTAAAAAGCAACTGGTCAGGAAGAGAGAGAAAATCCTTCGAAGCGGAGTAGAATTGAACGTGATATAG
Peptide sequence:
MTNQHIKQNGKLEDNPCSGSPPRTTLLGTIFSPVFNFFSPANKNGTSGSDSPGQAVEAEEIVKQLDMEQVDEITTSTTSANGAAYSNQAVQVRPSLNNGLEEAEETVTRDIPPLTAPVTPESGYSSAHAEATYEEDWEVFDPYYFIKHVPPLTEEQLNRKPALPLKTRSTPEFSLVLDLDETLVHCSLNELEDAALTFPVLFQDVIYQVYVRLRPFFREFLERMSQMYEIILFTASKKVYADKLLNILDPKKQLVRKREKILRSGVELNVI
IRESfinder result
IRESfinder score
0.648180015
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
bottom of page