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mmu_circDennd4c_1163
Basic information of circular RNA
PanCircBase ID:
mmu_circDennd4c_1163
mm39_Chr. Position ID:
chr4|86743154|86744317|+
Gene name:
Dennd4c
Transcript:
ENSMUST00000045512.15
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
1
Exon/intron indexes:
23
Exon/intron offsets:
0
Genomic length:
1163
Exon/intron sizes in nt:
1163
Flanking exon/introns:
chr4:86739707-86743154|chr4:86744317-86746204
Splice length:
1163
Other database IDs:
CIRCpedia: MMU_CIRCpedia_32635, circAtlas: mmu-Dennd4c_0031
Human Ortholog IDs:
Mature spliced Sequence:
GTAGTACTTCAACTGTGCTATTTTCTACTCAAGCTCCAGTCGAGGATGCAGTCTTCAGTGAGGTTACTAATTTCAAGAAGAATGGTGATAGAGGAGAGAAAAAACAGAAGCATTTCCCTGAGAGGAGCTGTAGCTTTAGTTCTGAAAGTCGAGCGGGGATGCTGCTTAAGAAGAGCAGTTTGGACCTGAATTCAAGCGAAATGGCCATCATGATGGGAGCAGATGCCAAGATCCTCACAGCAGCACTGACATGTCCTAAGACTTCCCCGCCTCATGTCACAAGAACTCACAGCTTTGAGAATGTTAACTGTCATCTAGCTGACAGTAGGACTCGCATGTCAGAAGGCACCCGGGATTCTGAGCACAGATCATCTCCTGTGCTAGAGATGCTGGAGGAAAGCCAGGAGCTCCTGGAGCCTGTGGTTGGTGATAATGTGGCAGAGACTGCGGCAGAGATGACGTGTAACAGTCTACAAAGTAACAGTCACAGTGACCAGTCCAGAGACACACAAGCTGGAGCCCAAGATCCAGTGAACAAGAGGAGCAGTTCATATGCTACTAGGAAAGCCATTGAGAGGGAGGATGTGGAGACGGGACTAGATCCGTTGTCTCTTTTAGCCACTGAATGTGTAGAAAAAACGTCTGATTCTGAAGATAAGTTATTTTCTCCAGTAATTTCACGTAATCTGGCTGATGAAATTGAAAGTTACATGAACCTAAAAAGCCCACTAGGCAGTAAATCTTGTAGTATGGAATTGCATGGAGAGGGGAACCAGGAGCCTGGCTCTCCTGCTGTGTTTGCTCACCCTTTAGAAAGGAGCTCGAGTCTGCCTTCAGACCGTGGCCCGCCAGCACGAGACAGCACCGAGACTGAGAAGAGCTCCCCTGCTGTGTCCAGCTCTAAAACTCTGACTGGGCGTTTCAAGCCACAGAGTCCTTACCGCGCTTACAAAGACCGGTCCACTTCCTTATCAGCATTAGTACGTTCTTCACCAAACAGCTCTCTGGGTTCTGTAGTCAATTCTCTATCGGGGCTAAAGTTGGACAATATACTCTCAGGGCCCAAGATAGATGTCCTAAAATCTAGTATGAAACAAGCAGCAACGGTGGCCAGTAAGATGTGGGTGGCTGTAGCATCTGCCTATAGCTACTCAGATGACGAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TGAAACAAGCAGCAACGGTG
59.9
AGTAACCTCACTGAAGACTGCA
59.03
142
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TGAAACAAGCAGCAACGGTG
59.9
TAACCTCACTGAAGACTGCATCC
60.06
140
PCR template sequence:
CAAGATAGATGTCCTAAAATCTAGTATGAAACAAGCAGCAACGGTGGCCAGTAAGATGTGGGTGGCTGTAGCATCTGCCTATAGCTACTCAGATGACGAGGTAGTACTTCAACTGTGCTATTTTCTACTCAAGCTCCAGTCGAGGATGCAGTCTTCAGTGAGGTTACTAATTTCAAGAAGAATGGTGATAGAGGAGAGAA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
14
Interacting miRNAs (#binding sites)
mmu-miR-155-5p(1), mmu-miR-135a-5p(1), mmu-miR-322-5p(1), mmu-miR-217-5p(1), mmu-miR-125b-5p(1), mmu-miR-181b-5p(1), mmu-miR-214-3p(1), mmu-miR-434-5p(1), mmu-miR-433-3p(1), mmu-miR-680(1), mmu-miR-669d-5p(1), mmu-miR-484(1), mmu-miR-452-3p(1), mmu-miR-670-5p(1)
siRNAs for circular RNA silencing
Junction sequence
CTCAGATGACGAGGTAGTACTTCAAC
siRNA sets
TTGAAGTACTACCTCGTCA, GTTGAAGTACTACCTCGTC, AAGTACTACCTCGTCATCT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCDENND4C_1163_ORF_1
0.8334
0.105696547
0.995037096
1194
ORF sequence:
ATGCTGCTTAAGAAGAGCAGTTTGGACCTGAATTCAAGCGAAATGGCCATCATGATGGGAGCAGATGCCAAGATCCTCACAGCAGCACTGACATGTCCTAAGACTTCCCCGCCTCATGTCACAAGAACTCACAGCTTTGAGAATGTTAACTGTCATCTAGCTGACAGTAGGACTCGCATGTCAGAAGGCACCCGGGATTCTGAGCACAGATCATCTCCTGTGCTAGAGATGCTGGAGGAAAGCCAGGAGCTCCTGGAGCCTGTGGTTGGTGATAATGTGGCAGAGACTGCGGCAGAGATGACGTGTAACAGTCTACAAAGTAACAGTCACAGTGACCAGTCCAGAGACACACAAGCTGGAGCCCAAGATCCAGTGAACAAGAGGAGCAGTTCATATGCTACTAGGAAAGCCATTGAGAGGGAGGATGTGGAGACGGGACTAGATCCGTTGTCTCTTTTAGCCACTGAATGTGTAGAAAAAACGTCTGATTCTGAAGATAAGTTATTTTCTCCAGTAATTTCACGTAATCTGGCTGATGAAATTGAAAGTTACATGAACCTAAAAAGCCCACTAGGCAGTAAATCTTGTAGTATGGAATTGCATGGAGAGGGGAACCAGGAGCCTGGCTCTCCTGCTGTGTTTGCTCACCCTTTAGAAAGGAGCTCGAGTCTGCCTTCAGACCGTGGCCCGCCAGCACGAGACAGCACCGAGACTGAGAAGAGCTCCCCTGCTGTGTCCAGCTCTAAAACTCTGACTGGGCGTTTCAAGCCACAGAGTCCTTACCGCGCTTACAAAGACCGGTCCACTTCCTTATCAGCATTAGTACGTTCTTCACCAAACAGCTCTCTGGGTTCTGTAGTCAATTCTCTATCGGGGCTAAAGTTGGACAATATACTCTCAGGGCCCAAGATAGATGTCCTAAAATCTAGTATGAAACAAGCAGCAACGGTGGCCAGTAAGATGTGGGTGGCTGTAGCATCTGCCTATAGCTACTCAGATGACGAGGTAGTACTTCAACTGTGCTATTTTCTACTCAAGCTCCAGTCGAGGATGCAGTCTTCAGTGAGGTTACTAATTTCAAGAAGAATGGTGATAGAGGAGAGAAAAAACAGAAGCATTTCCCTGAGAGGAGCTGTAGCTTTAGTTCTGAAAGTCGAGCGGGGATGCTGCTTAAGAAGAGCAGTTTGGACCTGA
Peptide sequence:
MLLKKSSLDLNSSEMAIMMGADAKILTAALTCPKTSPPHVTRTHSFENVNCHLADSRTRMSEGTRDSEHRSSPVLEMLEESQELLEPVVGDNVAETAAEMTCNSLQSNSHSDQSRDTQAGAQDPVNKRSSSYATRKAIEREDVETGLDPLSLLATECVEKTSDSEDKLFSPVISRNLADEIESYMNLKSPLGSKSCSMELHGEGNQEPGSPAVFAHPLERSSSLPSDRGPPARDSTETEKSSPAVSSSKTLTGRFKPQSPYRAYKDRSTSLSALVRSSPNSSLGSVVNSLSGLKLDNILSGPKIDVLKSSMKQAATVASKMWVAVASAYSYSDDEVVLQLCYFLLKLQSRMQSSVRLLISRRMVIEERKNRSISLRGAVALVLKVERGCCLRRAVWT
IRESfinder result
IRESfinder score
0.538326544
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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