RnoINT0085823 @ rn6
Intron Retention
Gene
ENSRNOG00000009401 | Lmo2
Description
LIM domain only 2 [Source:RGD Symbol;Acc:1307101]
Coordinates
chr3:93920447-93921021:+
Coord C1 exon
chr3:93920447-93920674
Coord A exon
chr3:93920675-93920801
Coord C2 exon
chr3:93920802-93921021
Length
127 bp
Sequences
Splice sites
5' ss Seq
AAGGTTAAG
5' ss Score
3.39
3' ss Seq
TCTCTCTTTGGCGTTTGAAGGGA
3' ss Score
7.3
Exon sequences
Seq C1 exon
GGGAAGCTGAGCGAAAATAGACCTTCGCGAGAGAGGAGGGAGCCCCGGGAGAGCCGCGCGGTCCGCTCCCCGCCCCCAGGCCGCCGCCCCCTCTCTGCCCTCGGCGCCCCGACCCCAGCGAAGGTGCGAGGGGTTCGGGGCGGCCGGGCGGAGCCGGCGACTGCGCGCGATCGGGACCGGGCGGCGGCGGCGGCGGCTGTGGTGACGGCAGCGGGACCGGGATGGAAG
Seq A exon
GTTAAGTCTTGAGCAGCGGCAGCTGTCGCAGCCGCCGGAGGGAGGCCGGGCTGCTCCCCGGCCCCCTGCCTCGGCCGCCGCGCGCGGGGCAGCTGGGTGATTCGCTCTCTCTCTTTGGCGTTTGAAG
Seq C2 exon
GGAGCGCGGTGACTGTCCTTGAGCGTGGAGGGGCGAGCTCGCCGGCCGAGCGACCGAGCAAGAGGAGGCGCAGGAGCGGCGGCGCCCGAGCACCCGAGGGGGTCCGAGTCCAGGCAGCTAGCCAGCCACGCGCCACAAAGGGAGCGCCCCCGCCGCCCGGCACGCCTCCCCCCTCCCCAATGTCCTCGGCCATCGAAAGGAAGAGCCTGGACCCGTCTGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000009401:ENSRNOT00000012625:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=0.690
Domain overlap (PFAM):
C1:
PF124483=Milton=PU(2.4=66.7)
A:
NA
C2:
PF124483=Milton=FE(88.0=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ATAGACCTTCGCGAGAGAGGA
R:
CTCCACGCTCAAGGACAGTCA
Band lengths:
242-369
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]