HsaINT0092597 @ hg19
Intron Retention
Gene
ENSG00000136944 | LMX1B
Description
LIM homeobox transcription factor 1, beta [Source:HGNC Symbol;Acc:6654]
Coordinates
chr9:129455421-129455880:+
Coord C1 exon
chr9:129455421-129455602
Coord A exon
chr9:129455603-129455802
Coord C2 exon
chr9:129455803-129455880
Length
200 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGG
5' ss Score
9.16
3' ss Seq
TTCCCCTCTCTCTGAGCCAGGTC
3' ss Score
5.72
Exon sequences
Seq C1 exon
TGAAGAGCGAGGATGAAGATGGGGACATGAAGCCGGCCAAGGGGCAGGGCAGTCAGAGCAAGGGCAGCGGGGATGACGGGAAGGACCCGCGGAGGCCCAAGCGACCCCGGACCATCCTCACCACGCAGCAGCGAAGAGCCTTCAAGGCCTCCTTCGAGGTCTCGTCGAAGCCTTGCCGAAAG
Seq A exon
GTGAGGGGCGGCCGGGGGGCGGGGCTCAGGCTGATGCCCGCACACCCACTGCCTTTCTGGAGACCACCCCCTGCTCCTGCTGGGGGTAGGGACATCCCTCCATCCTCCATCTCTCCGCACATCCCATCATACCCCTAAACCCACCATCTCCCCGTTGCTGCCCCTGGAGGGCCTGACCTGTTCCCCTCTCTCTGAGCCAG
Seq C2 exon
GTCCGAGAGACACTGGCAGCTGAGACGGGCCTCAGTGTGCGCGTGGTCCAGGTCTGGTTTCAGAACCAAAGAGCAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000136944-LMX1B:NM_001174146:4
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.765 A=NA C2=0.192
Domain overlap (PFAM):
C1:
PF0004624=Homeobox=PU(47.4=44.3)
A:
NA
C2:
PF0004624=Homeobox=FE(43.9=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AAGAGCGAGGATGAAGATGGG
R:
GACCACGCGCACACTGAG
Band lengths:
228-428
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains
- Pre-implantation embryo development
Other AS DBs:
FasterDB (Includes CLIP-seq data)
AS-ALPS (AS-induced ALteration of Protein Structure, links to PINs)
APPRIS (Selection of principal isoform)
DEU primates (Only for human)