HsaINT0091738 @ hg19
Intron Retention
Gene
ENSG00000106852 | LHX6
Description
LIM homeobox 6 [Source:HGNC Symbol;Acc:21735]
Coordinates
chr9:124976562-124979567:-
Coord C1 exon
chr9:124979347-124979567
Coord A exon
chr9:124976663-124979346
Coord C2 exon
chr9:124976562-124976662
Length
2684 bp
Sequences
Splice sites
5' ss Seq
ACGGTACCC
5' ss Score
6.32
3' ss Seq
GCTGCTTCTATCGCCCCCAGGGA
3' ss Score
8.92
Exon sequences
Seq C1 exon
CCGATTCGGGACCAAGTGTGCCCGGTGCGGCCGACAGATCTACGCCAGCGACTGGGTGCGGAGAGCTCGCGGCAACGCCTACCACCTGGCCTGCTTCGCCTGCTTCTCGTGCAAGCGCCAGCTGTCCACTGGTGAGGAGTTCGGCCTGGTCGAGGAGAAGGTGCTCTGCCGCATCCACTACGACACCATGATTGAGAACCTCAAGAGGGCCGCCGAGAACG
Seq A exon
GTACCCAACCTGCTCCGCCTGGCACCTCTGCCCCCAGCCCTTTCCCACCCCACCCCACCCCAGCACCCCAGGAACCACCCACACTCCTCTACCGATTGGGCCCTCCCGGTATAGTCCCGCAGGCAGCGTAGGGGTGGGGCGGCGAACAGATCTTGCACTTCCGGGTCGATCTTTTGCTTAGGAGTCAGAAGTCACTGCCCTCCTTTGTAACTATGTTTCCTTATCAGTAAAATGGCGTTAACAACAGAACACCTTCCCAAAGATAGATGAGCTAGCTGATGTGTTGTAAAGCCAGGAGGCACTCAGTGAACCCTAGAGATGGTTCTCATAATCGGGCAGCCTACTCCACCTTTGGACAGCTCTCATTGGCCTGGGGGCTCATCCCCTCCGGTTGCCTGGGACCAGGCTTGGGCCAGTCCTGGAGAGATGACTTGGCTCCCATTCTCCCATTTCCTATCCTAGCAGCTCCAAGCCAGAGGTTTGAGGAAGGGTTTTCATCCTGGACCAGGGTCTCTAACTATAAGGGGAAAGGACCAGGTTTCTGAGTCTGGAGACCAGGCTCTCCCATACTGTGTTGACATATGAGGTTTCCTTTTCTCTCTGGGCCTCAGTCCCTACATCTGTGCAAGACAGATACTGGACTAGAATGATCCCTAAATCTCTTCTGGCTCTGACATTGTGATTCCCCAGATTGCCCAGGAACAAGATCCAGGTCTTCCACGGATCCTGGGGACAGGGTCACAGATGGGATGGAGCTGGGAAAGGGCAGTGCTTGGCTGTGGGCAGAGGCAGGGACTCTTTCTCTAATTTCCCTGTTAGGGTCTGTGAAAGCTGCTAACTTCTCTGTAACAGGGATTATTTTATGTAATCCTTACAACAGCCCTAGGAAGTAGGTGGCACGGCCCCATTTTACAGAAGAAGAAACAGGATTTGCCAAAAATTACATACTAGTAGATTTGCCTAGCTCCAAAGCCCAGCCTCTTAACTACCATACCATACCATATCATACCATACCACACCACCTTGGCCCTAAGCTCTAGGGCACCTTAATCAGATCTCATAAAGCCAAGGAGGCTTCTGGGATGTAGCTGCCTCTGTTTTAGTTTCCCATCTAAAAAACCAACACACCAATCCTTGCCCTGCCTGCTTTCCTAGGGGACATTAATACCACAGAGTGTCTGCCCAACCCCCAGTTTTTCTGGGGAGGAGTATGAACCACCCTGCCTCAACTTCTAGGTCCCAGCCTGGAGACTAGTCAGGGACCGCAAGAGTGTTCCTGGCCATGGGCATACCAGGGCCATCATTTTCTCCTGCCAGGATCAGGACTAAGTGGGTCTAAGGGGGCATCTAGTGAACTTGGGTTTCACTTGCTGCCTGCTTATCTGCAGTGATGGGCAATGAAATTATCTGCAGTGGTCAGCAAGTCAGCAGTAGAGCTGGGATGGAAACCCAGGAGTCAGAGCTTTCCCACACTGTGGTCCATCAGCGACCACAGGCTCCTTCCACACATGGTCCAACCAGGACCACCTGTAGTTACAACCTTGCCAATTACATCCTAGCTCTCACAGCCACACCTGTCCACAGACTTAACATGCTGAGGAACTTGAAAGCTGGGGCCTCCGATCTCTCTTACTGATCAGCCCTCAGTATTGGCTACTGTTTCACTTTTTAAACATAACACACACACAGATACACACACGTTCATTGTAGAAAAATTAGAAAAGACGGTAAGCAAAAAGAAGAAAATAACGATTGCTCCAAATGCTGCCTTCTTCATATTTTAATGTGTATCTTCTCAGATTTTTTTCCATGTATGTTACAATGTTTGCTTTTTTCCTTCAACATAATTTTTTCCTAATTAAAAAGTTACAATAAATTGTGAACAATGGTTATTTCTGAGTGCTGGAATTACTGGTGATTTTTATTTTCTTCTTTGTGCTTATGGAAATTTTCTGAGATTTTGAGGATATTCAGAACAATGAAGTATTAAAAATAAAATGGGAATATGGTTAGTGTTTTAGTATGACTGTAAAAGTAATATGAGTGGAAAGAGAATATCTAACATATACGCCGGTTAACAAAATTAAACCTTACAGAAGTAAGGCAACATATGATTGTTTTTAAATACCTCAAAAGTTACAGGAATACTGAAAGTAAAAAGTTTCCATAATCACATTCCTGGGAAGTAAACCACTGCCAACACCTTGTTGTATATTCTTACAACCTTTTTTCCTTCCGCTTATTTTTATAAAATTAGGAGCATAGTTCCGTTACTTGCTTGCTTCCTATCTCCTCTAGCCTTTGGTGTCCCCCAGTTTCGCCAGCAGGGAGCCCAGTTTGGGACATTAGGGTCAGCTAGCTTTCGGATTCTAGTTGAAAGGGCCAGGGCAGGGGCTTTCCTTCTCTCTGAGCCTCAGTTTCCTCCCATGTATAATGAGGTAACGCCACCTCTCCTTAGGGCTGTAAGACGTGGTCCAGTCGTGTAAGAAGTGTCCAGTACTAAGCGGACGCTCAGAAACCCCTTCCCCAAAGACTGAGCTCAGGGACTAGGACCCTGGGATCCCTGCTCCCAGCCAACTCCCGCTCCTGACCCTTCCAGGGACAAGCTCCCCCCACCCCCGTCCTTTCCAGGCTGCCACTAGAAGAGATGGGGACGCGTGGTCAGCTGCTTCTATCGCCCCCAG
Seq C2 exon
GGAACGGCCTCACGTTGGAGGGGGCAGTGCCCTCGGAACAGGACAGTCAACCCAAGCCGGCCAAGCGCGCGCGGACGTCCTTCACCGCGGAACAGCTGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000106852-LHX6:NM_014368:5
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.824
Domain overlap (PFAM):
C1:
PF0041217=LIM=PD(3.4=2.7),PF0041217=LIM=WD(100=77.3)
A:
NA
C2:
PF0004624=Homeobox=PU(21.1=35.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
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]
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)