HsaINT1021917 @ hg38
Intron Retention
Gene
ENSG00000135363 | LMO2
Description
LIM domain only 2 [Source:HGNC Symbol;Acc:HGNC:6642]
Coordinates
chr11:33869346-33869987:-
Coord C1 exon
chr11:33869710-33869987
Coord A exon
chr11:33869587-33869709
Coord C2 exon
chr11:33869346-33869586
Length
123 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
GAAAAAGGAAATGAAACCAGAGACAGAGGGAAGCTGAGCGAAAATAGACCTTCCCGAGAGAGGAGGAAGCCCGGAGAGAGACGCACGGTCCCCTCCCCGCCCCTAGGCCGCCGCCCCCTCTCTGCCCTCGGCGGCGAGCAGCGCGCCGCGACCCGGGCCGAAGGTGCGAGGGGCTCCGGGCGGCCGGGCGGGCGCACACCATCCCCGCGGGCGGCGCGGAGCCGGCGACAGCGCGCGAGAGGGACCGGGCGGTGGCGGCGGCGGGACCGGGATGGAAG
Seq A exon
GTTAAGTCCTGAGCAGCAGCAGCAGCTGCAGCCGCCTGGAGCCAGGCTGCGCGCCCCGGCCCCCGCCTCGGCCGCGGCGCGCCCGCAGCCCGGTGATTCGCTCTCTCTCTTTGGCGTTTGAAG
Seq C2 exon
GGAGCGCGGTGACTGTCCTTGAGCGCGGAGGGGCGAGCTCGCCGGCGGAGCGCCGGAGCAAGCGGAGGCGCAGGAGCGGCGGCGACGGCGGCGGCGGCGGCGGCGCCCGAGCACCCGAGGGGGTCCGAGCCCCGGCAGCCGGCCAGCCCCGCGCCACAAAGGGAGCGCCCCCGCCGCCCGGCACCCCGCCTCCCTCCCCAATGTCCTCGGCCATCGAAAGGAAGAGCCTGGACCCTTCAGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000135363:ENST00000257818:3
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=0.988
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
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:
CCTTCCCGAGAGAGGAGGAAG
R:
GCTCAAGGACAGTCACCGC
Band lengths:
254-377
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains