HsaINT0091720 @ hg19
Intron Retention
Gene
ENSG00000107187 | LHX3
Description
LIM homeobox 3 [Source:HGNC Symbol;Acc:6595]
Coordinates
chr9:139091524-139092599:-
Coord C1 exon
chr9:139092428-139092599
Coord A exon
chr9:139091727-139092427
Coord C2 exon
chr9:139091524-139091726
Length
701 bp
Sequences
Splice sites
5' ss Seq
CAAGTGAGC
5' ss Score
6.39
3' ss Seq
CGGCCCTGTGCGTCCCGCAGGCG
3' ss Score
9.64
Exon sequences
Seq C1 exon
AGATCCCGCTGTGCGCTGGCTGTGACCAGCACATCCTGGACCGCTTCATCCTCAAGGCTCTGGACCGCCACTGGCACAGCAAGTGTCTCAAGTGCAGCGACTGCCACACGCCACTGGCCGAGCGCTGCTTCAGCCGAGGGGAGAGCGTTTACTGCAAGGACGACTTTTTCAA
Seq A exon
GTGAGCCCCGAAACCTCACCTCAGTGTGGGAGCGGAGGGCACGCCTGCCCCAGGGACTCCTCCCCTCACAATCACCAAGGCCAGGCCCTCGAAGCCTGCGTCTCTCGCAATCCCAGCCCACTCCTGTCACCCAGGCAGGGCACCCTGTGGCCTGGCCAAATTAAGGGTGGGGCCTCTCCATGGGTGCTCCCTGGGTGGCTGGGCCTGGCTGGGACATCAGCAAGTATTATTTGGAAAAAAAAGCAATTTATTACCTAAATCACAGAAGCAGTCATTAGAGAAGATACACCCCTATTTGTAGGATTCTACTGGACTTAGTTCCTCCGAAATTGGTGATGTTTTAGTTCCTAATGCTGGCACCCAGCGGCTCTGGCCCAGTGGCCTTCATGGCTCCAGCTGTGGGGTGTGAGGGACTGGCCCCAGATGGGTCCTCTCCCTCCGGATTCACCTTCCCAGATCCAGCATGGGTCCTGCAGGCAATGGCGGCTGGGCTCCCCGAGGTCTTTCTGAGATTGAGGTTCCCTTCTCAGTGGGAGTGGGCAGCTCTGCCCCGGCGGCCAGGCTGGCGACCACCCTGCAGGGCCGGACAGAGCCTTCCTCCGGGGCCGCCTTCCCAGGCAGCCGCTTGCCTCTCTCCAACCCGCTCGGGGCGAAATGAGCCTCGCGCTTCCGCGCTGAGCCCGGCCCTGTGCGTCCCGCAG
Seq C2 exon
GCGCTTCGGGACCAAGTGCGCCGCGTGCCAGCTGGGCATCCCGCCCACGCAGGTGGTGCGCCGCGCCCAGGACTTCGTGTACCACCTGCACTGCTTTGCCTGCGTCGTGTGCAAGCGGCAGCTGGCCACGGGCGACGAGTTCTACCTCATGGAGGACAGCCGGCTCGTGTGCAAGGCGGACTACGAAACCGCCAAGCAGCGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000107187-LHX3:NM_014564:2
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
No protein impact description available
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.019
Domain overlap (PFAM):
C1:
PF0041217=LIM=PU(94.6=91.4)
A:
NA
C2:
PF0041217=LIM=PD(3.6=2.9),PF0041217=LIM=WD(100=87.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CACATCCTGGACCGCTTCATC
R:
CTGCTTGGCGGTTTCGTAGTC
Band lengths:
342-1043
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
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)