RnoINT0038657 @ rn6
Intron Retention
Gene
ENSRNOG00000005286 | Coch
Description
cochlin [Source:RGD Symbol;Acc:1308536]
Coordinates
chr6:72364634-72364905:+
Coord C1 exon
chr6:72364634-72364678
Coord A exon
chr6:72364679-72364757
Coord C2 exon
chr6:72364758-72364905
Length
79 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGC
5' ss Score
10.22
3' ss Seq
CCTTCTTTGGCTCTCTGTAGACT
3' ss Score
9.53
Exon sequences
Seq C1 exon
GTAAAAGACTGAAGAAAACACCGGAGAAGAAGACTGGCAATAAAG
Seq A exon
GTAAGCTAAGTGTTCAGGGAAATGGTGTTTCCTTCTGCTGCTCCGGAGACTAACAAAGCCCTTCTTTGGCTCTCTGTAG
Seq C2 exon
ACTGCAAGGCAGACATTGCATTTCTCATCGATGGAAGCTTTAATATAGGGCAGCGCCGATTTAATTTGCAGAAGAATTTTGTTGGGAAGGTGGCACTAATGTTGGGAGTTGGAACCGAAGGACCACACGTGGGCCTCGTTCAAGCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000005286:ENSRNOT00000007365:7
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.750 A=NA C2=0.020
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0009223=VWA=PU(27.8=90.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ACCGGAGAAGAAGACTGGCAA
R:
CTTGAACGAGGCCCACGTG
Band lengths:
170-249
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]