HsaINT0091724 @ hg19
Intron Retention
Gene
ENSG00000107187 | LHX3
Description
LIM homeobox 3 [Source:HGNC Symbol;Acc:6595]
Coordinates
chr9:139092428-139096955:-
Coord C1 exon
chr9:139096780-139096955
Coord A exon
chr9:139092600-139096779
Coord C2 exon
chr9:139092428-139092599
Length
4180 bp
Sequences
Splice sites
5' ss Seq
GGGGTAAGC
5' ss Score
7.79
3' ss Seq
GAACTTCCTCGTGCCCACAGAGA
3' ss Score
9.17
Exon sequences
Seq C1 exon
GCCCCGCACGACGCGGCGGGACTTGGGAGCCCCGAACCCTCCAGGGGACGCTGACCTAGGAGGAGCGCGTCTCGCGCCACTCGGCCTGGTGGCCGCGATGCTGCTGGAAACGGGGCTCGAGCGCGACCGAGCGAGGCCCGGGGCCGCCGCCGTCTGCACCTTGGGCGGGACTCGGG
Seq A exon
GTAAGCCCCAGCAGGACACTGAGGACAGAAACGGCAAGGGCGGCAGAGGCGCGAGGAAGGGGGTGCGTGCAGGGCCAGCGGCCAGGCAAAGAAAGTCCCGCCGCTCTGCAGGCGGGACACAGAGATGGAAACTGCAGAGAGTGAGTTTCCAGATCCCAGGGTGGCGGGGAGGGCCTGACGCTGGCCTGCAAGAGTGCGGGACAGCGGTTGGAGTGGAGGCCCCTAGAAAAAAAGGGGGCATCGCAGGCACAGCTGGGGGGCGATGGGGCCGACCAAGGGGTGCTAGGTTCCCCCGGTGACCAGTGCCCGTCAGCTCTTGCACACAGCCCGGCCCAGGTCTCTGGACCCCACAGCAGGGGACCCAAGCCTGTGTCTCCCGCCTGAACCACCCTCCCCAAGGGCCATTCCATCACCACGGACGCTGGGAAATAATGGAGGCATTGTTGGAGGGCTGGCCAGATGCCAGCAGGGTGGGCCGCCTCCTTAACCTGCCGCCGCCCCTTCCCCAGTCCTGCCACACACGACCCCTGATCGCTTCGGCAGCAGCTGACACTCAGCCACCTGCACCCAGCACAGCCCGCACACACTCGGCTTTGCACCCGCGTGTCCTTGCCCTGGCCCTTCTTGGGTAACAAGTGCTGTGCAAAGTGAAGGGGCAGAAAGCTGGCTGCATGGGCCACTGCTCAAAACGGACACATCGGACCTGCTGGGAGCTAGGAGGGAGGGACTGTGGTTTCTTGTGCCCATCCTTCTGGGCCTGGGCCCTTAAAGCTCACAGTCCAGAAGCCATAGGCAGAGTGGACAGAGTATTGCTGTGAGACCCACAGGGAGAGGGACCTGCAGGATGGCATCAGCCCCTGGTCCCCCAACCCTTCCTGTGTGTTTCTGCGCACTGCCAGGGCACCCCTGCCTTTGCCAAGTCCTGTGCTGCCGAGGGCCACCCACTGCTGTGTTCTTCCCCGGGTGGCTGCCCAGGGCTGGTGCTGGCCCAGGGCCCTCTGGGCAGGGGTGGGTGCGTCCCTCTGCCTGCAAGGACAGGTGGGTTCTGGAGAGCTCACCTGTGTGGACTGGGGCAAGAGGCTGAAATATCAGGTAAGGGACCGTGTTCCAATGGAGCCGGAGTGCTGGGGGCTGGAAATGGAAGGTGTGCCCTGGGGCTTCCCCAGCTCGGCCCCTCACGACCCGAGGTCTTGGCTGCGTGTCCAGGACACAGAGCCTGTTCTCTCTCAAGGATTGCCCTTCCTCCCTGAGCCGTCCGGGGCCGCAGTTCCAGGGGTGGAGCCCAGAAGCCTGTTAGCATCTGGGATCGGTCCGGCACCTTGCGGTTCCGGTACGCAGCCCTCGGCGCCACACTCACCCCTTCTGCGTTTCGGGTTGAGCTCCCGCCGACCATCTGCTGCTCCCGAGGCCAAACCTCAGCGGCGGGAGGACCCTGCTGCCTTCTCGACCCCTCTCCCGGGAACCTTAGCCCTCCTGGCGTGTGCTCCAGCTCAGGCCTCTGCCTCTGGGCCGCTCCGGCGCAGGAAGCTGCGGGGCCGGGACGAACGCTGGCGGGAAGCCCTGACCTGGGCCCTCCCTTACCGGTGCCCGCCCTCGGGCCGGGCACGCGGGGCGGCCTCTGGGCACCGCAGGTCCCGGCGCAAAGGCGCTCAGAGTCCGCAGTGGCCCGGGCTGGTCTCCGCGACCCCCGGCCCCGCCCCGCCCCGCGGCCCCGCCCCCCGGCCGCTCCGCCCTCCGCTCGGCCAGAGGCTCCGGGCCCCAGGGCGGCCCGCGGGCGCAGCGCCCAGCAGCACCCGGAGTCGCTTGGACGCCGGTTCGGGGCTATTGCGGGGTGGCGTCGCTGGGCCCGGGAAAGTTCGGGACTGGAGAGTGGCGACGCCGGGCGGCGGGACCCATGGAGGCGCGCGGGGAGCTGGGCCCGGCCCGGGAGTCGGCGGGAGGCGACCTGCTGCTAGCACTGCTGGCGCGGAGGGCGGACCTGCGCCGAGGTGGGTGCCCGGGCCGAGTGGCTGCACCGGGGAGACCAGGAGATCCTCAGGCCTTTCCGGGCCTGGCCGCGGAGGCTGGCAGGAGCTAGAGGATCTGGGCGGGAGTGGGCGCGAGGACCCCGGAACGTCCGCGCCTGGGCGCCTCAGCCTGTATTTGTTGCAGGGCCCCTGGCCTGGGTTGTCAGGGAGTGAGTGAGGTTGTGGCACTGCGCTGCTCCGGCCAGGGAGCTCTCGGGGGTCCAGGGTGGGCTTAGGAGACCTCTGCAGCCCGGAGCCAGCTCCCTGGGCTGGAGGAGGCGCAGGGAGCAGTGGCGGGGCAGTGACCACGGGACAGGAGGGTCCCCAAGAAGGCCGCCCCAGCCGGACTCTTTCCACGTTCCAGCGGAACAGAGTCAGATGCAGGGGCCAAGGTCGAGCTGAACTCCGACCGTCGGTCTCCCCGAAGTCAGGTTTCAGCGTCTGCGCCCACAGACACCCGCTCGGTTTATCCCCGCTCAGGGCCCGTCTGTAGGAAAAAGCCTCTCTTCTCCAGGCCCCCCAGCTTCCTGGTGGCACCACTCTAGCTCCCAGCACTTTGGTTCTTAGGGAACCTGGGCAGTTCTCCTCGACTCCCGGGCCAGCTGGAGCCGCAGGATGGGGAAGGAGGCCCCGGAGCCAGTGGGGAGTGAGAGGGACCGGCCGGCGGGAAGGGGGTTACATCCAGGCTGTGGGGGCTCGCGGTTCCCTACTTATTTATTTATTTTTCGACGGTTCCTGGGAGGGGTTGGCCGCGGGGGCTGGGGGGCGGAGAGAGGGAGGGAGGAAGGAGGACTGCGCGCCCGCGCTCGGGAGAGCTGGCCGGAGCGGGCGGGCTGGCGTCCAGGCTCCGCCGACCCCGCCATCCCTGACACAGGAGCCCCCGCCAGGGCTGGAGTCGCCATGCAGCGTAAGGCTGGGGTCGCGGGCGCGGCGCGGGGTGGGCTGGGGCGGCTTTTGCCCGACGCGGGCGCCGGCGGCGAGCTGCGGCCGAGGCGCTGTCCGGTCCGCGGTGCTGAATCCGCGCTGTGTCGGCCTGTCGGGCCGCCCCGCTCCGAGCCGGGTCCTCGCCTGCGATCGCTGCCCACGATGGGGACCCCGGGCGCGCAGCGGGTCCTCGACGCTCCGCACCCGGAGCTGCGGTTTTGCCGGATGCGGGGCGCATTCATCGCCGGTTTCCCGCCACTGCGTGGGGAGGCGCAGCCCAGTTTTTTCCGCCGGAGGTCGAGGGAGCCCCTTCCTGGTGTCTCTCACCCACTGGGAGATGGGCTGGAGCCGGCGGGGTCCACAGCCAGGGAGGCGGGTGCAATATGTCAGTAAATCCCGGTCCCTTCAGCGGGCACTCCTCTCTTCCAGAGACTTTTTCTAAGTGAAGAGGGAGTCCTCAGCCCTTGACACCTGGAAAACCCGCTCACAGACTCGAGGCTCCCACAGGGCACCCTTGGACCTCCCCAGTGTGGTTCCTCCAGGGGGCCTGCAGTACCGAAGTGGGGTGTGGGGGGCAGAAGCAGCGGGAAGCCAGACGTTTGAGTAACTCTGACGGTGTTGGGGGCACCCACGCCTGACACAAAGGCAGTGGATCGGCTTGTCCAGTCCACTCATAAGTAATTTTGCGGCTGCCCAATGATGGGGAAGGCATTGATATTTACCCCGGAGGCCTGCAGACAGGGCCACCAGGCAGGGCAGCCACATTTGCGAGGAGTCCCTAGAAAGAGTGGCCATGACGCTTAACATGAAGGAGACCCGATGGGGTGCCCCAGCTCCAGGTGATGGTGAAGACCCGTTTCCCTATGTTTCCTGCCGGGCTTCAGAGAGCAGATCCCCCTGGGGTGGGGTTTTCATTTGAGCTCCACATGCACCCTTCTTGGCACTGGCAACATTTTGTAATTGAGTATTCAGCCTCGTGAAATGGCCTGGGCTGCTTTCTTGCTCACACACATTTTTAGACCGATGTCAGTTTCCCCTTAGCTCCTGACATAGGATGCGGTGCCTGCACACTCCCGGAACTTGCGGGGCCACTTAAGCTGGCTGGGGAAGAGGGTGTGTAGGGAAAGGAGGACCCCTCGGCAGCCCTGAGTCCTGTGGGCCGGAGGGGAGACTGGCTCGCGTTGGGGTGGGAAGGTGGCTTCACTGCCTCCTGGTCTACGAGGTGACCCAGAACTTCCTCGTGCCCACAG
Seq C2 exon
AGATCCCGCTGTGCGCTGGCTGTGACCAGCACATCCTGGACCGCTTCATCCTCAAGGCTCTGGACCGCCACTGGCACAGCAAGTGTCTCAAGTGCAGCGACTGCCACACGCCACTGGCCGAGCGCTGCTTCAGCCGAGGGGAGAGCGTTTACTGCAAGGACGACTTTTTCAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000107187-LHX3:NM_178138:1
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
No protein impact description available
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0041217=LIM=PU(94.6=91.4)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
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)