HsaINT1021938 @ hg38
Intron Retention
Gene
ENSG00000136944 | LMX1B
Description
LIM homeobox transcription factor 1 beta [Source:HGNC Symbol;Acc:HGNC:6654]
Coordinates
chr9:126693524-126693812:+
Coord C1 exon
chr9:126693524-126693601
Coord A exon
chr9:126693602-126693745
Coord C2 exon
chr9:126693746-126693812
Length
144 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGA
5' ss Score
10.57
3' ss Seq
GAACTGCGCTCTCCCTGCAGATG
3' ss Score
12.35
Exon sequences
Seq C1 exon
GTCCGAGAGACACTGGCAGCTGAGACGGGCCTCAGTGTGCGCGTGGTCCAGGTCTGGTTTCAGAACCAAAGAGCAAAG
Seq A exon
GTAAGAGGCCACCCCCCATCCCCACTGGCCCCGGGTAGGGTGGGACTAGAGGGGGCAGCCAGAAGACTACGGTCCAGGGGGCGTGGGGCTGGCTGTGCCTGGGGGCGAGGGGCAGCACCGGCCTGAACTGCGCTCTCCCTGCAG
Seq C2 exon
ATGAAGAAGCTGGCGCGGCGGCACCAGCAGCAGCAGGAGCAGCAGAACTCCCAGCGGCTGGGCCAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000136944:ENST00000526117:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.192 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0004624=Homeobox=FE(43.9=100)
A:
NA
C2:
PF0004624=Homeobox=PD(3.5=5.9)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTCCGAGAGACACTGGCAGC
R:
CAGCCGCTGGGAGTTCTG
Band lengths:
138-282
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains