HsaINT0091721 @ hg19
Intron Retention
Gene
ENSG00000107187 | LHX3
Description
LIM homeobox 3 [Source:HGNC Symbol;Acc:6595]
Coordinates
chr9:139090754-139091726:-
Coord C1 exon
chr9:139091524-139091726
Coord A exon
chr9:139090906-139091523
Coord C2 exon
chr9:139090754-139090905
Length
618 bp
Sequences
Splice sites
5' ss Seq
GAGGTCAGC
5' ss Score
5.66
3' ss Seq
ACCGCTCGCCCGCCGCGCAGAGG
3' ss Score
6.35
Exon sequences
Seq C1 exon
GCGCTTCGGGACCAAGTGCGCCGCGTGCCAGCTGGGCATCCCGCCCACGCAGGTGGTGCGCCGCGCCCAGGACTTCGTGTACCACCTGCACTGCTTTGCCTGCGTCGTGTGCAAGCGGCAGCTGGCCACGGGCGACGAGTTCTACCTCATGGAGGACAGCCGGCTCGTGTGCAAGGCGGACTACGAAACCGCCAAGCAGCGAG
Seq A exon
GTCAGCCGAGGGGACGACGCTCCCACCTTTCCTGGTCTGAAAAAAATGGGGCTGAGGCCACGCCCAGGGGGGCGTCCGGGGAAATTCTCTCCCCAAGCGCTCACTAAGGGGGCCTGGGCTAGGGCGGTGTAGGCAGCAGGAAGCCGAGGCCGGGAACGGCGGAGTCACGGACAGACCCGCGTCCCGAACCGCTTCGTTCGGTCCGAAGTGTGCGGCTTTTCGCCCCTGGTCGGAATTATCGCCCTAAATTCTTGGCCGCGAAGGCTGGGCCATACCCACACCCTTAGAATAAAGGGGAGCCCGCGGGGAAATCAGGGTGCTTGGAGAAGGGAGCCAAGGCTGAAGGCGGGGGCGCCGTGGAGGTGCGATTTTAGGGAAGGCGCCGCCCCCGCCCCCGCGGCAGAACCCGCCCTCCGCCGGCGCCCCCTCCACCCCAGCCCGGGTGCTGCCCGTTTTTGCCAATCGCTCCCAGCGCCCGCGCCTTCCGAGAAGCCTGTGGGGCGGGATGGGGGTGGGCACCTGAGGCCCCGACGTCCCCGCGCCGGCCGGGGTGGGAGGGCTGGGGGTCCGGCCGGGGCCGGAGGGGCTGCCGCGCCTCACCGCTCGCCCGCCGCGCAG
Seq C2 exon
AGGCCGAGGCCACGGCCAAGCGGCCGCGCACGACCATCACCGCCAAGCAGCTGGAGACGCTGAAGAGCGCTTACAACACCTCGCCCAAGCCGGCGCGCCACGTGCGCGAGCAGCTCTCGTCCGAGACGGGCCTGGACATGCGCGTGGTGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000107187-LHX3:NM_014564:3
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
No protein impact description available
No structure available
Features
Disorder rate (Iupred):
C1=0.019 A=NA C2=0.693
Domain overlap (PFAM):
C1:
PF0041217=LIM=PD(3.6=2.9),PF0041217=LIM=WD(100=87.0)
A:
NA
C2:
PF0004624=Homeobox=PU(77.2=86.3)
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:
GCGCTTCGGGACCAAGTG
R:
ATGTCCAGGCCCGTCTCG
Band lengths:
342-960
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)