HsaINT0091734 @ hg38
Intron Retention
Gene
ENSG00000106852 | LHX6
Description
LIM homeobox 6 [Source:HGNC Symbol;Acc:HGNC:21735]
Coordinates
chr9:122227409-122228845:-
Coord C1 exon
chr9:122228657-122228845
Coord A exon
chr9:122227481-122228656
Coord C2 exon
chr9:122227409-122227480
Length
1176 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGC
5' ss Score
9.6
3' ss Seq
TCCCTCCCCCCCTCCCCCAGGTG
3' ss Score
12.77
Exon sequences
Seq C1 exon
CTCTCCTCCTGCTCCTGCAGCAGCCTCTGCTCCCACTGCGGCTGTGGTCCCCCTCGGCGCAGCTCTCCGCGCTGCGCGCCCGCTGAGCCCGAGGTTCCCCGGCCCATGTACTGGAAGCATGAGAACGCCGCCCCGGCGTTGCCCGAGGGCTGCCGGCTGCCGGCCGAGGGCGGCCCCGCCACCGACCAG
Seq A exon
GTGAGCCGGCGAACGACTGGGTGAGCGGCCCGGGCCGGGGTCGGGCAGGGTCCGGGACCCAGCCGGGCCGAGCAGGGTGGCGGGCGGTTGCAGGAAGGAGGGGTACGAGGGTGCGCCTGTGAGTGTGTGCTTGTGAGTGTGGGAGCGCGCGCGCGAGCGGGGGGGGGGGGTCGCGGAAAGCGGGAACACATTATGCAAATGTTGGAGGAATTTCTCAAAAAGCGATTTAGTAAAGACACAGGCGAATCAAGAGGAGGCGAGGCCGGTATTGTCCGTCTGAATAGGCGCTGATAGCGCCGATGCGCCGGGGGTTGTGCCGGCGCAGCGCTGAGAATCCCGACGCGGGGCCGGTACCCGGCGCGCCGAGGGGCTGGAGGGTGCTTTTTCCTCCCCTTGAGCGCCTCTCTTTTCTCTTTTTGGTCCCGTTTCGCCCCGATCTCGCTCTCTTTTTGCTCCGGGTTTCCCTCCGACTGGCCCTCGAAAGGCGCCTGAATCCGTGTCAATATAGCTGCTTCAATTTCGCCGCGCGTGTCAGGCGGGCGGGCGGGCGGGTGCTCACCGCGCTCGGGGTTTTCTTTTCTTCAACCACCCTCCGCCCCTCACCCATCTCTTTTTTATTTTCTTTCTTTCTCTCTTTTCTCCTTTTTGCATTTTGTGCCGAGAGGAGAAGGGAGCGAGGAAGGGGAGTGGGGTGGGGGGGCGGGTGGAGAGAGAAAAAATTCGATTTTTAATTACTACCATTAAAAAATCAAATTTGCAATTCTTTGGGCGGCCTGATGGATCTCACTGATTGACAGTTGGAATTGACACTCTGGCTACCTCTTATCTTGGGCATTCACGACAATTTCTAATTGCAGGTAGTTTGTGTGTGTGTGCGCGTGTTTTTCTTCCCCCCTCAGAGGCTTGGATTGCAAGGGAACTAAGCGATTACTTCAAGAGCCACGGGTTAAGTGCAGGGAGAGGGGGAGAGAGAGGGAAAAAATCCAATCCAAATTCAAATTGCTTCATTAGAGAGACACCGCTTTTGTGGGGAAGGGCTTTAAATGCCCACTACAAAGTTAGGACTCATTGTTCGGCGCCGGTTTATATAACAGGCGCGGGGAGGCGCTGGGCTCAGGCTGTGCGGAGCCAGTTCAGCAGCCGCCGCCGCCTGCGTTCCCTCCCCCCCTCCCCCAG
Seq C2 exon
GTGATGGCCCAGCCAGGGTCCGGCTGCAAAGCGACCACCCGCTGTCTTGAAGGGACCGCGCCGCCCGCCATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000106852:ENST00000394319:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.546 A=NA C2=0.246
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Associated events
Other assemblies
Conservation
Mouse
(mm9)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTCTCCTCCTGCTCCTGC
R:
GCGGTCCCTTCAAGACAGC
Band lengths:
248-1424
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