RnoINT0038653 @ rn6
Intron Retention
Gene
ENSRNOG00000005286 | Coch
Description
cochlin [Source:RGD Symbol;Acc:1308536]
Coordinates
chr6:72360109-72362144:+
Coord C1 exon
chr6:72360109-72360162
Coord A exon
chr6:72360163-72361987
Coord C2 exon
chr6:72361988-72362144
Length
1825 bp
Sequences
Splice sites
5' ss Seq
CCGGTGAGT
5' ss Score
10.9
3' ss Seq
CACGTGCCCTTTCTCTTCAGTGC
3' ss Score
10.18
Exon sequences
Seq C1 exon
GTGCGTGGCTGCTGCTGCTGCTGCTGCCTCGGCTCGCGCGCGCGGAGGGAGCCG
Seq A exon
GTGAGTTAGGTGCGGGCGGAGGAAGGAGGACAGGGTCAGTCCACGCAGGCTGAGGATCTGCGGAGGGATGCGGGGCTGGAGAGGCGGAGGCCCGCCCGCACCCATTTCCAACGCACCCCTCGGGCTTACCTGTTTTTCCACGCCAGTGTCCCCGGGGTTGGTCCGTGCCTCCTTCCCGGGCGCACACCACGTAGCCCCGGGACCATTCGTCCGGAGTTACTGGGGACAACTGTTTGGTCCCAGCCCACAGAGGAGGGCTGCTCAGGTCATGGTCCCACCTAGTCCGATCACCTTACCGTTGCTTGTAACCTCTATGGAGAACAACGTCGGCGGTTCCTATCGCTCACTGGGAGCCTCAAAAGAGTTTGTTCCACGTAGAAGTCCGAGTGTGGTTCGGTGTCTTTTCTGCGGTGTAAGAGGCAGTTTCGTTTCTAAAAATCTTAGGTTTGCCTTTCTTCAAAGTAGAAAGGGTAAGTACCTTTTGCCCAACGAAGCAAGTGTTAGCAGCTCCAGACAGTCTGGGTCCAAGGATTTCAGGGCCATCGCCGCCGCCCCACTCCCACCCCCATCCCCATCACTGAAAACGGAAAAGATTGGGGTTATTTGATAGAGGTGCTAGACTCCTATCTGAAGTTAGGATTTTAATCGAGCCTGAGAAATTGATATAGCACCTTGCGTCTTCCCCTTACTTCCGCGGTCCGGGTAGCAGCCTAGACAAGGGTCCTTGGCAGAGACAAGTTACTCAACTTGCAAAACCATCCCCTATCTTGCCCGATGAGGGAGACTTTTTTTTTTTTTTTAAAGTCTGTCTTGGATAACTTCAATTCCCTGTGTTCGGAAAGTCGTATTTAATAACCTTAATCTCTATTTACTCATCAGTAAATTGACAGACCACCATTTTGCTGTTTGTTGTAATCTGACAAATTAACACCTTTGGTAGTAACTTTCTTGCTTGTTTGCATTTTTGAAGGGTGTCGTTGTGGCGCAGGCTGAGCCCACTGTGTAACCCGCTCTAGCCTCAGACTCAAGGCAATCTTCCCACCTCAGTTTCCTGAGTGCTGGGCTGGCTTTGTGAGCTACTCTGGGTCCAAAACTGCATATATTATTGGTCTGACTGATTGTAAGATTTAAGCATATTAGCAGTGCTTTCTATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATATCCCTTTGGACAGATCTGGGAGAGATTCAGTCAGAAGCAAATAGAAGACTAACTTCCTTGTGTCCTATCCTTTGGGAGTTGTGGAGTACTCCATAGGCTGGCTAACTCTATGACTTTCATTTCCTCATTTGTAAAATGTGGGAGTAAATCCCATTCTGCCGATCCAGGCACCAGTTAACTGGTTGGTTTGTGTGAATGTGGGACTGTGAGGCCCAGAATGTATCAGGTAACCCGGCTAAACAGCCCCCTGGGAAGGACAGCTTGAAGACTAAGGCTCAATATAGACTTACCGTCATCATAAATAACTATGGACAGTTTCGTCACAATTAGGACTTTTTATGTCTAGATCAAAGACTAACGTTATTTTCTCATTCTGATGTACTCTCAGTTACATTTTCCAAGTTGATGAAGAACTGGGAACAATGTCACATTAGATGTCTGTAGCAACCGGGCCCTAGATTAAATTGGAAACCCCTTTGGATTGCTAATATTTAAAATGGTGTCCACGTTTAAGTCGGTGTTTTGGTAGCAGTATAGAAATCGGGGGAATAAACACAGCCCCACACCTCACGTCCCCTGCAATGCCCTCCAGGAGTTCTTACACACGTGCCCTTTCTCTTCAG
Seq C2 exon
TGCCCATCCCCATCACCTGCTTTACCAGAGGCCTGGATATCCGGAAAGAAAAAGCGGATGTTCTCTGCCCAGGAGGCTGCTCTCTGGAGGAATTTTCTGTGTTTGGGAACATAGTGTATGCCTCGGTGTCCAGCATCTGCGGGGCTGCTGTCCACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000005286:ENSRNOT00000007365:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0381514=LCCL=PU(53.3=90.6)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Mouse
(mm9)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]