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mmu_circDctn4_610
Basic information of circular RNA
PanCircBase ID:
mmu_circDctn4_610
mm39_Chr. Position ID:
chr18|60667664|60679405|+
Gene name:
Dctn4
Transcript:
ENSMUST00000223984.2
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
7
Exon/intron indexes:
2,3,4,5,6,7,8
Exon/intron offsets:
0,3671,6979,9446,10764,11155,11628
Genomic length:
11741
Exon/intron sizes in nt:
71,17,94,41,08,21,74,100
Flanking exon/introns:
chr18:60659437-60667664|chr18:60679405-60679838
Splice length:
610
Other database IDs:
circAtlas: mmu-Dctn4_0007
Human Ortholog IDs:
Mature spliced Sequence:
GTGGACTCACATTATTGTCCCAGCTGCTTAGAAAACATGCCGTCAGCTGAAGCCAAATTAAAAAAGAATAGATGTGCCAACTGCTTTGACTGTCCTGGATGCATGCACACCCTTTCTACCCGTGCAACAAGCATCTCCACACAGCTTCCCGATGACCCAGCCAAAACCACCATGAAGAAAGCCTATTACTTGGCCTGTGGATTTTGTCGATGGACATCTAGAGATGTGGGCATGGCAGACAAATCTGTCGCTAGTGGTGGTTGGCAAGAACCAGAAAACCCTCACACACAACGGATGAACAAGTTGATTGAGTATTACCAGCAGCTTGCTCAGAAGGAAAAGGTCGAACGAGATCGCAAGAAGCTGGCACGGCGAAGAAATTACATGCCTTTGGCTTTTTCGCAACACACTATTCATGTAGTGGACAAGTACAGTCTTGGGACCAGGCTTCAGCGACCACGAGCTGGTGCATCCATCAGTACACTTGCTGGACTTTCCCTTAGAGAAGGAGAAGATCAGAAAGAGGTGAAGATTGAGCCGGCTCAGGCTGTCGCTGAAGTGGAGCCTCTGCCTGAAGACTATTACACGCGGCCAGTGAACCTAACAGAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TCAGGCTGTCGCTGAAGTG
60.01
GGACAGTCAAAGCAGTTGGC
59.69
163
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CTCAGGCTGTCGCTGAAGTG
61.01
GGACAGTCAAAGCAGTTGGC
59.69
164
PCR template sequence:
GAAGATCAGAAAGAGGTGAAGATTGAGCCGGCTCAGGCTGTCGCTGAAGTGGAGCCTCTGCCTGAAGACTATTACACGCGGCCAGTGAACCTAACAGAAGGTGGACTCACATTATTGTCCCAGCTGCTTAGAAAACATGCCGTCAGCTGAAGCCAAATTAAAAAAGAATAGATGTGCCAACTGCTTTGACTGTCCTGGAT
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-96-5p(1), mmu-miR-29b-2-5p(1), mmu-miR-207(1)
siRNAs for circular RNA silencing
Junction sequence
AACCTAACAGAAGGTGGACTCACATT
siRNA sets
ATGTGAGTCCACCTTCTGT, AATGTGAGTCCACCTTCTG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCDCTN4_610_ORF_1
0.8415
0.179650172
0.822115408
624
ORF sequence:
ATGCCGTCAGCTGAAGCCAAATTAAAAAAGAATAGATGTGCCAACTGCTTTGACTGTCCTGGATGCATGCACACCCTTTCTACCCGTGCAACAAGCATCTCCACACAGCTTCCCGATGACCCAGCCAAAACCACCATGAAGAAAGCCTATTACTTGGCCTGTGGATTTTGTCGATGGACATCTAGAGATGTGGGCATGGCAGACAAATCTGTCGCTAGTGGTGGTTGGCAAGAACCAGAAAACCCTCACACACAACGGATGAACAAGTTGATTGAGTATTACCAGCAGCTTGCTCAGAAGGAAAAGGTCGAACGAGATCGCAAGAAGCTGGCACGGCGAAGAAATTACATGCCTTTGGCTTTTTCGCAACACACTATTCATGTAGTGGACAAGTACAGTCTTGGGACCAGGCTTCAGCGACCACGAGCTGGTGCATCCATCAGTACACTTGCTGGACTTTCCCTTAGAGAAGGAGAAGATCAGAAAGAGGTGAAGATTGAGCCGGCTCAGGCTGTCGCTGAAGTGGAGCCTCTGCCTGAAGACTATTACACGCGGCCAGTGAACCTAACAGAAGGTGGACTCACATTATTGTCCCAGCTGCTTAGAAAACATGCCGTCAGCTGA
Peptide sequence:
MPSAEAKLKKNRCANCFDCPGCMHTLSTRATSISTQLPDDPAKTTMKKAYYLACGFCRWTSRDVGMADKSVASGGWQEPENPHTQRMNKLIEYYQQLAQKEKVERDRKKLARRRNYMPLAFSQHTIHVVDKYSLGTRLQRPRAGASISTLAGLSLREGEDQKEVKIEPAQAVAEVEPLPEDYYTRPVNLTEGGLTLLSQLLRKHAVS
IRESfinder result
IRESfinder score
0.38632649
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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