HsaINT0092596 @ hg38
Intron Retention
Gene
ENSG00000136944 | LMX1B
Description
LIM homeobox transcription factor 1 beta [Source:HGNC Symbol;Acc:HGNC:6654]
Coordinates
chr9:126690836-126693323:+
Coord C1 exon
chr9:126690836-126691068
Coord A exon
chr9:126691069-126693141
Coord C2 exon
chr9:126693142-126693323
Length
2073 bp
Sequences
Splice sites
5' ss Seq
CCGGTGAGG
5' ss Score
9.35
3' ss Seq
CCGGGTTGTGTCCCCCACAGTGA
3' ss Score
7.91
Exon sequences
Seq C1 exon
GCTCTTCGCGGCCAAGTGCAGCGGCTGCATGGAGAAGATCGCCCCCACCGAGTTCGTGATGCGGGCGCTGGAGTGCGTGTACCACCTGGGCTGCTTCTGCTGCTGCGTGTGTGAACGGCAGCTACGCAAGGGCGACGAATTCGTGCTCAAGGAGGGCCAGCTGCTGTGCAAGGGTGACTACGAGAAGGAGAAGGACCTGCTCAGCTCCGTGAGCCCCGACGAGTCCGACTCCG
Seq A exon
GTGAGGCCTGGCCTGAGCTGGGGGCAGGCCTCAGGGACGGGGGTTGCTGGGGTGTCCTGGAGGGGAGTCCCGGCTGGAGAAGCCACCTCCTGCTTCCAGGACCTGAGCTGCACACAGATGGTACATGCATATCCAGATGCACACGCGCACTGACGTGTCCACCTGTGTGCACATGATACGAACATGCATCCCCCCAGGCACACTACCCCTGAGACCTACGCATCCATACATATAAACATATGTGTGATCACATGTGTGCACACAAGCACATAAAATGCATGCAGGAATACCCCTACCCTGAGTATGGATACATGTACATGTATGTGGAGATATGTGTTCACATACCCGGGAATTCAAAAGCCACACCCAGGTCCACACACACAAGTGTACACACTTAAGCATACATACACATACACACATGACACAGCACACTTGTGCACTAAACACCGGTCCACATGGCTGCACATATATGTTTGTCCACATGCTCACATGTACTGTGGATTGTGCTTGTGTGCACACACACACCTCTTGTTCTCTGGCCCACCCCCCTTACCCTCTCTGCCTTGATGGCCCCCCACCAACCCGCAGCCCAGCTCCACAGGGGTCTTCACCAGCACCCAGTCCACAGGCTGGGGATGCCTGAGAGGCAGGGAGATGATGTGCCTTCCCCTTCTCAGCCCCCTGGAGCCTTCAGCAGTGAGAAGCAAACAGCCTCGAGCCAGCCTCTGTTTCCCAGCCGAAGGGAGGGGGCTGGGCCCTCTGTGCTGGAGGGAAAGACCCCATTTCCCAGGGTGAAGGACCCTCCCTCCTCTGCTCTAGCCCCCAAAAGGACGAGGCCAATTTGAAGGCCTCCTGGCAGACAGGGCAAGCCCAGCCAGGAGTGAGCCTTAAGGAGGGAAAGCCCAGGAGGTGGCTTTGGTCCTTGTTCTTCCTGGGAACAGTGGGGAAGGACTGGAGCAGGAGGCATGGAGAGGAGGTGTCCCGGTCTGCCAGGCCCCATGGGTAACCTGGAGCCCTCCGGCAACAGGATCTGCCACATGGGAAGGGTTTTCCATGGCCAGGGCCTGCGTGGAGGCAGTGAGCCCACCACCATCTGTCCCTACCCATCCCTGGGCAGGGCACTGCTGCAGCCAGCTCCATGGCTTCCAGCTGCCTGGACTCCTGAGGAAGAGCAGAGGCTGGCCAGCCCCAGCAGAGGGGGTCTCAGTGGGAGGAGATCACCCGCCTCATACTCCAAGAACAGGATTGAAGAAAGGAGACCAGCCTGGGGGGCAGCGGGAGGCCCAGTGGTGGCTGGGGAGGCTTGGCCATCCATCTGGGGCTGCTGGCATTTCTGAGACCCAAACCTGGGGCGGGGAAGTGCCATGTGTGCATGGTGGGTGTGGCTGTAGCACTGGGAGAATGCACATGCTTCCGCACGCTGTGTGTGTCTGTCCAGATGCATGCATGCCTGTACGTTCCTGCCCGTGAGCATGGGCCCATGTGTGTGAATACGCCTGTGAGTTGCACGCGTGAGGGCCTTTGTGAGCCCACGTGTATGTGGCAGCAGGTGAGTGTGCATCTTACGAGTGTGTGCGTGCATACGCTGTGGTCAGAAGCACTCTTGTGTGAATATCTGTGGTGTGTGTCTTTGCTTGCACACTTTCGTGTATGTCCACACAGCCATGTGCACAACCGTGCGTGCACCTGTCTGCCTGTTCCCCGAGTGGGCCTGCCTTCCTGAAAGTGTGTGCAGCCACATGTACGTGTGTGCATGCCTGTGCTGTGGTTGTCCGAGGCGCACCTGTGTGAGTTCCTGTGCAGGTGTGCCCTGCGGCCCAGGATGAGGGAGTGAGGCGTGTGTGCCGGGGAAGGGACTCGCAGGGTACAGCAGGCAGGAGACCAGGGCCCAGATGAGGTAGGGCCTGTGGGCCACGGGAGGGAAGGAGATCTTATCCTGGGCCACTGGGGAGCCACGGCAGGTGTCAACAGAGGGGACAGGCTCCCATCGGGCAGCAGGTTGCCGAAGGGGACAAGGCTGAGGCCTGGGCTGCCCCCGCCCCTTCATCACAGGCCGGGTTGTGTCCCCCACAG
Seq C2 exon
TGAAGAGCGAGGATGAAGATGGGGACATGAAGCCGGCCAAGGGGCAGGGCAGTCAGAGCAAGGGCAGCGGGGATGACGGGAAGGACCCGCGGAGGCCCAAGCGACCCCGGACCATCCTCACCACGCAGCAGCGAAGAGCCTTCAAGGCCTCCTTCGAGGTCTCGTCGAAGCCTTGCCGAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000136944:ENST00000526117:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.114 A=NA C2=0.766
Domain overlap (PFAM):
C1:
PF0041217=LIM=PD(3.6=2.5),PF0041217=LIM=WD(100=74.7)
A:
NA
C2:
PF0004624=Homeobox=PU(47.4=44.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
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