HsaINT0091728 @ hg19
Intron Retention
Gene
ENSG00000121454 | LHX4
Description
LIM homeobox 4 [Source:HGNC Symbol;Acc:21734]
Coordinates
chr1:180240515-180241141:+
Coord C1 exon
chr1:180240515-180240669
Coord A exon
chr1:180240670-180240969
Coord C2 exon
chr1:180240970-180241141
Length
300 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGA
5' ss Score
9.22
3' ss Seq
CCCTTGTGCTTGTGTGGCAGGTT
3' ss Score
9.65
Exon sequences
Seq C1 exon
ATGACTCAGAGGCTGGAGCTAAGCGGCCCCGGACCACCATCACAGCCAAGCAGCTGGAGACATTAAAGAATGCATACAAGAACTCCCCCAAGCCTGCCCGGCACGTGAGGGAGCAGCTGTCCTCAGAGACAGGCCTGGACATGAGGGTCGTACAG
Seq A exon
GTGAGATGCCAGCACTCCTGTGCCCTCCGGGGATCCCAGGCCCGGGACAGGGGTGGAAGGTATCCTGAGTGACATCAGCTCACGGGTGGTTGGGCTCAGGGCTTGACCCCAGGGCTTTTGCCAGAACTGAAGACAGAGTTCTGAGGCCCACCTGGGGAGAGGGGGTGGGGCGCATCGCACTCCCAGACCTGTGCTCCATTCAGGCTTCAGTCTGCTTCCAGCCGCCCGCCTAGGGGGTCCTGGGGGCTTTGGGTTTGTGGTGGACGCCCCCTGAGTATGTCCCTTGTGCTTGTGTGGCAG
Seq C2 exon
GTTTGGTTTCAGAACAGAAGGGCCAAAGAGAAACGCCTGAAGAAGGATGCAGGGCGGCACCGCTGGGGGCAGTTCTATAAGAGCGTCAAGAGGAGCCGGGGCAGCAGCAAGCAGGAGAAGGAGAGCTCTGCAGAGGACTGTGGGGTTAGTGACAGTGAGCTGAGCTTCCGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000121454-LHX4:NM_033343:4
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.712 A=NA C2=0.483
Domain overlap (PFAM):
C1:
PF0004624=Homeobox=PU(77.2=84.6)
A:
NA
C2:
PF0004624=Homeobox=PD(19.3=19.0)
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:
TGACTCAGAGGCTGGAGCTAA
R:
CTCGGAAGCTCAGCTCACTGT
Band lengths:
326-626
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)