HsaINT1018197 @ hg38
Intron Retention
Gene
ENSG00000107187 | LHX3
Description
LIM homeobox 3 [Source:HGNC Symbol;Acc:HGNC:6595]
Coordinates
chr9:136200582-136205109:-
Coord C1 exon
chr9:136204934-136205109
Coord A exon
chr9:136200754-136204933
Coord C2 exon
chr9:136200582-136200753
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:ENST00000371748:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 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]
SPECIAL DATASETS
- Autistic and control brains