HsaINT0092594 @ hg19
Intron Retention
Gene
ENSG00000136944 | LMX1B
Description
LIM homeobox transcription factor 1, beta [Source:HGNC Symbol;Acc:6654]
Coordinates
chr9:129376722-129377848:+
Coord C1 exon
chr9:129376722-129376867
Coord A exon
chr9:129376868-129377661
Coord C2 exon
chr9:129377662-129377848
Length
794 bp
Sequences
Splice sites
5' ss Seq
TGGGTGAGT
5' ss Score
8.73
3' ss Seq
TTTCGCCCTGTGCGCTACAGGCT
3' ss Score
7.91
Exon sequences
Seq C1 exon
GCGTCCCATGGATATAGCAACAGGTCCCGAGTCGCTGGAGAGGTGCTTCCCTCGCGGGCAGACGGACTGCGCCAAGATGTTGGACGGCATCAAGATGGAGGAGCACGCCCTGCGCCCCGGGCCCGCCACTCTGGGGGTGCTGCTGG
Seq A exon
GTGAGTGCGGGGTCGGAACGCCCGAGTGGTCTCGGGCGTGGGATGGGGCGTCGTCCGGCTGTGGACACGGGCGTTGGGGCCAACGGATAAAGGAAATGGGTTTGCAGGACATGGGGAGGAGGCAGAGACAGGACTCCTGGAGTGATCGCCAGAGGGCCGCAAGTACGCCTCCGGCAGGCGTCCTGAGGGGACAGGACAGCTCCAGTCGCCACCCACCATCCTTTCCAGGCTTAGGTTCTAGAGCTGCCACTCCGATGTGGTAGGTGGCGGGTGGCAGGGGTGATGGAGGACCTAGCAATCACCTTGGCGAGCTTGGGAGAGGCGCAAGGTCACCTGGGGTGGGGGAGATTCTAAGAGAAAAACGTCTCCCTGGTCACTCAAACCACAGATTTTGGGGAGATCGGGGATAGAAGACCACGAACGCCACCGTGGGGCGTGTCAGCCAGCGAGCGCCCCAGCCTCACCTCGCCTGTCTTGGTCCCAGCCGGCCACCCTGCGCCGTGCTCGTTGTCATTTGTCTTAACACGGAGCGCGGATTCTCCGGAGAAGGGGAGAGCACAGCGCCGAGCCAAGGCTCGAGGCCCGCGGCCTCTCCACGCCGGAGCCCGAGGACTGGGACGGACTAGCCGGGGCCGCCCGGCCCCTGGCGCGGCGGTCCGGGGAGCGCAGGCGGCAGGCGGTGATCCCGGGCGGCCCGAGCCCTCGGGGCCGAGGGCTGTGGGCCCGGTGCGACCGGGACGCCGGGGCTGGGCCGGGCGGCGCTGACGGCCGGGCTTTCGCCCTGTGCGCTACAG
Seq C2 exon
GCTCCGACTGCCCGCATCCCGCCGTCTGCGAGGGCTGCCAGCGGCCCATCTCCGACCGCTTCCTGATGCGAGTCAACGAGTCGTCCTGGCACGAGGAGTGTTTGCAGTGCGCGGCGTGTCAGCAAGCCCTCACCACCAGCTGCTACTTCCGGGATCGGAAACTGTACTGCAAACAAGACTACCAACA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000136944-LMX1B:NM_001174146:1
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.032 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0041217=LIM=PU(94.6=84.1)
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:
GCGTCCCATGGATATAGCAACA
R:
TGTTGGTAGTCTTGTTTGCAGT
Band lengths:
333-1127
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)