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mmu_circCdh19_968
Basic information of circular RNA
PanCircBase ID:
mmu_circCdh19_968
mm39_Chr. Position ID:
chr1|110835788|110859995|-
Gene name:
Cdh19
Transcript:
ENSMUST00000094626.5
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
6
Exon/intron indexes:
9,8,7,6,5,4
Exon/intron offsets:
0,11489,16937,17697,21775,24087
Genomic length:
24207
Exon/intron sizes in nt:
1,22,12,22,54,18,51,65,000
Flanking exon/introns:
chr1:110823230-110835788|chr1:110859995-110876853
Splice length:
968
Other database IDs:
CIRCpedia: MMU_CIRCpedia_225254, circAtlas: mmu-Cdh19_0001
circAtlas: hsa-CDH19_0001, CIRCpedia: HSA_CIRCpedia_372571
Human Ortholog IDs:
Mature spliced Sequence:
GAACATTTGTCATCAAGGTGACAGCCAATGACGCAGATGATCCTTCAACTGGCTATCATGCTCGCATCCTATACAACTTAGAACGAGGTCAACCATACTTTTCTGTTGAGCCAACAACAGGAGTCATAAGGATATCTTCTAAGATGGATAGAGAGTTGCAAGATACATACTGTGTAATTATTCAAGCCAAGGACATGCTCGGTCAGCCTGGAGCCTTGTCTGGAACAACAACCGTATCAATTAAGCTGTCAGATATTAATGACAACAAGCCAATATTCAAAGAAAGTTTCTACCGCTTCACTATATCTGAATCTGCACCCATTGGAACATCAATAGGGAAAATTATGGCATATGATGATGACATAGGGGAGAATGCAGAGATGGAGTACAGCATTGAAGATGATGATTCAAAAATATTTGACATAATCATTGACAATGACACCCAAGAAGGGATAGTTATACTTAAAAAGAAAGTTGATTTTGAGCAGCAGAGCTATTATGGCATTAGAGCTAAGGTTAAAAACTGCCATGTGGATGAAGAGCTTGCACCTGCCCATGTTAACGCTTCCACAACCTACATTAAAGTTCAAGTAGAAGATGAAGATGAACCTCCTGTTTTCCTCTTACCATATTACATACTTGAAATTCCTGAAGGAAAACCATATGGAACAATTGTGGGGACGGTTTCTGCCACAGACCCAGATCGAAGACAATCTCCTATGAGATATTATCTCACTGGAAGCAAAATGTTTGATATCAATGACAATGGAACAATAATCACCACTAACATGCTTGACAGAGAGGTCAGTGCTTGGTACAACTTGACTGTCACAGCTACTGAAACATACAATGTACAACAGATCTCTTCAGCCCATGTTTATGTACAAGTCTTTAACATTAACGACAATGCTCCAGAGTTCTCTCAATTCTATGAGACTTATGTTTGTGAAAATGCTGAATCTGGTGAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AACGACAATGCTCCAGAGTTCT
59.96
TAGGATGCGAGCATGATAGCC
59.79
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TAACGACAATGCTCCAGAGTTCT
59.74
AGGATGCGAGCATGATAGCC
60.04
140
PCR template sequence:
AGCCCATGTTTATGTACAAGTCTTTAACATTAACGACAATGCTCCAGAGTTCTCTCAATTCTATGAGACTTATGTTTGTGAAAATGCTGAATCTGGTGAGGAACATTTGTCATCAAGGTGACAGCCAATGACGCAGATGATCCTTCAACTGGCTATCATGCTCGCATCCTATACAACTTAGAACGAGGTCAACCATACTT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
2
Interacting miRNAs (#binding sites)
mmu-miR-33-5p(1), mmu-miR-363-3p(1)
siRNAs for circular RNA silencing
Junction sequence
TGAATCTGGTGAGGAACATTTGTCAT
siRNA sets
ATGACAAATGTTCCTCACC, AATGTTCCTCACCAGATTC, AAATGTTCCTCACCAGATT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCCDH19_968_ORF_1
1.0554
0.113750855
0.96247169
846
ORF sequence:
ATGGATAGAGAGTTGCAAGATACATACTGTGTAATTATTCAAGCCAAGGACATGCTCGGTCAGCCTGGAGCCTTGTCTGGAACAACAACCGTATCAATTAAGCTGTCAGATATTAATGACAACAAGCCAATATTCAAAGAAAGTTTCTACCGCTTCACTATATCTGAATCTGCACCCATTGGAACATCAATAGGGAAAATTATGGCATATGATGATGACATAGGGGAGAATGCAGAGATGGAGTACAGCATTGAAGATGATGATTCAAAAATATTTGACATAATCATTGACAATGACACCCAAGAAGGGATAGTTATACTTAAAAAGAAAGTTGATTTTGAGCAGCAGAGCTATTATGGCATTAGAGCTAAGGTTAAAAACTGCCATGTGGATGAAGAGCTTGCACCTGCCCATGTTAACGCTTCCACAACCTACATTAAAGTTCAAGTAGAAGATGAAGATGAACCTCCTGTTTTCCTCTTACCATATTACATACTTGAAATTCCTGAAGGAAAACCATATGGAACAATTGTGGGGACGGTTTCTGCCACAGACCCAGATCGAAGACAATCTCCTATGAGATATTATCTCACTGGAAGCAAAATGTTTGATATCAATGACAATGGAACAATAATCACCACTAACATGCTTGACAGAGAGGTCAGTGCTTGGTACAACTTGACTGTCACAGCTACTGAAACATACAATGTACAACAGATCTCTTCAGCCCATGTTTATGTACAAGTCTTTAACATTAACGACAATGCTCCAGAGTTCTCTCAATTCTATGAGACTTATGTTTGTGAAAATGCTGAATCTGGTGAGGAACATTTGTCATCAAGGTGA
Peptide sequence:
MDRELQDTYCVIIQAKDMLGQPGALSGTTTVSIKLSDINDNKPIFKESFYRFTISESAPIGTSIGKIMAYDDDIGENAEMEYSIEDDDSKIFDIIIDNDTQEGIVILKKKVDFEQQSYYGIRAKVKNCHVDEELAPAHVNASTTYIKVQVEDEDEPPVFLLPYYILEIPEGKPYGTIVGTVSATDPDRRQSPMRYYLTGSKMFDINDNGTIITTNMLDREVSAWYNLTVTATETYNVQQISSAHVYVQVFNINDNAPEFSQFYETYVCENAESGEEHLSSR
IRESfinder result
IRESfinder score
0.633987142
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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