HsaINT0091729 @ hg19
Intron Retention
Gene
ENSG00000121454 | LHX4
Description
LIM homeobox 4 [Source:HGNC Symbol;Acc:21734]
Coordinates
chr1:180240970-180244188:+
Coord C1 exon
chr1:180240970-180241141
Coord A exon
chr1:180241142-180243319
Coord C2 exon
chr1:180243320-180244188
Length
2178 bp
Sequences
Splice sites
5' ss Seq
GAGGTGAGC
5' ss Score
8.7
3' ss Seq
CTCCGTTCTTTTGTCCACAGAGG
3' ss Score
10.55
Exon sequences
Seq C1 exon
GTTTGGTTTCAGAACAGAAGGGCCAAAGAGAAACGCCTGAAGAAGGATGCAGGGCGGCACCGCTGGGGGCAGTTCTATAAGAGCGTCAAGAGGAGCCGGGGCAGCAGCAAGCAGGAGAAGGAGAGCTCTGCAGAGGACTGTGGGGTTAGTGACAGTGAGCTGAGCTTCCGAG
Seq A exon
GTGAGCAGGGCTGGAGGGGCCAGGCCGAGGCCTTAGGAAAGTCCCCTGGGAATCTGTAATCCCTGGCACTCAGGAGGGATCTTTCTTGAGGCCTTGGCAACTCCCTCCTGAACACAGGCTTTTCCTTAAGACTTGCAGTGAAGGGTGGGGGAAATGGTAGTGGCCCTTTACCATGGGACAGGAGTAGGAAACAAGATTGCTGAGGTCTGGAAGCTGGGATGGGCCAGGCCCCGTCCTGTGGCCCCAAGGTCTCCCCTCCCCTCCTGCTGACTGGGGCCTCCCTCATCAGCCCACACAGCTATGAACAGATGACTGGGTTCCAGCCTTGTGCCCCTAGCCCCTCTCCCATCTTTGTCCCCTTTGCTGGGACACTGGCCTACTCCCATAGTCCCCTAGAGCCACCCCTTCCTCCAGTCCTGGTGGTGGGGAGGTCATGCTCCACAGGTTTTTTCCTGGGAAATCAGTACTGTGAGTGCATGTGAGATGGGGAACTGGCTTCACTTCCGAAATCCCTTTCCCCACCACTCACTTCATTCTGTCCCCTGCACACAAGCTTTGCAGCATGCACTATATTCAAATTCATGCATCAGCAAAATTGTAAATTACTGCATGTTATGAATCCTCAGGTTGTTTGCAAAGAATCATAACTGTTCTCAGGTACTGAGTTCTCAAATGTGGAAGGTCTTCTGCGGAGGGGGAAAGGGAAGAGTACTCAACTGGCGATCAGAGACCTGGTTTCCAGTGCAGCTCTGTCAAATCGATTCACTTCTCTTGAGCCCCAGTATTCCCAAGAGGAATACCATATCTTTGCCCATCTCACTGCGTTGTGGGGATCAATGAACACAACCAACTGTGGATGTGCTTGGGGAAAGCCTGGCACATTTGTATACCTGGAAGGCATGATCGTTCCCACAGGGAGCGTGTGGCTCCCGCAGAGGGCCCTGGTCATTTGGGATGACAGGTATAGGGAAAAGGCTAACTCATGGCCATTTGACAATGGAGTGGAGCCTTCATCTTCCTGCTCCCTTTAAAGAGCATGAGCTCCCCCCACCATGTTTTTTCATAAGGGGAATGGGGGGCAGGCCTCAGAAGGGATGGGGTGTTGAAGTCTAGTCTGGGGAGGCCTTATTTAGGGATTGGTGCAGAGGCCCAGGTGGAAATAGAAAAGGAAGTTTGTGGGACAGAGGATGGAACAAGTTGCCTGCCAGGACAACGATGCCCTGGGAGGACTCTAGTTCAGCCCAGAGGTCAGCTGAGCCCTAGAGGGCAGCCTCCTCTGAGAACACAGGGCCCGTGAGGCCTTGGGGACAGCTCATGGGACTAATACTCACCTTTTAGGCTTCTTGGCAGGATTGGGAAAGTCAATCTCATCTGGGCTGTTGAAGTCAACACCTAGAACATACTGGATTGTTAAGCTCATTTCTGTTGGGTGCAGGTGGGTCCCTGGGCTGACCTATCATTGGTTTCTCTGGGAATAATTTCTCAAAGACTAAAACTGCTCACCTCTGTTGGAGAGAGAAATTCTTTCAAGTGGCAAAGATTCCATTAGATCCCCTTAATGAAATTCTTTAAGAAAAAAGAAGGTTCATTTGCCTTAATCAAGTCAATTCTTTGTCCCCAGTGAAGAGCTTATTGAATACAGACAGAAACCAAGTCCTTTGATATTGAACCTCTCTTCCAGATAGACCAGAAGGATTTTGTACAGATGTCTAAGAGTGGTCCTCAGCTTCCCTGACCATATGGGCCTGCTTGCTTCCCAATCAACTAAACCAAGCCCTTTCTCAGCTTGAAAGCTTTCAGGGTAAATGTTGTCAGCATGTAGTTTCCATTTGTGATGTGGAGACATCTGACCCACCCAGCCTTAGGCATTCATCCTCCTCAGTGTAGCCAGAGTATTAGTACACGAGCCACAAGGGACCAACGAGCTCACCAAACATTTGTCCATCCTTCTGGGACCTGGGAATTTAGTCTTTGCAGGTGTTTCTTGTTTTTCTCCTTGGCCTGGGTTGGCCTCTGGATATCAGGCTGCCATATTGGTGTGTCTGACCCATGCTTGGCTGCAAGGCAGCTGCCATCCTTGGGCATCTTTCCTGGTCATGTGTGTTCCTAGGTTGTGAAGAGCAGGGGACCATCAGAGTCCTGGCAGCTGACAATAAATCTCCGTTCTTTTGTCCACAG
Seq C2 exon
AGGATCAAATTCTCTCAGAACTTGGCCACACCAATAGGATTTATGGCAACGTGGGGGACGTTACAGGCGGACAGTTAATGAATGGGAGCTTCTCCATGGACGGGACAGGACAATCCTATCAGGACTTGAGGGATGGGAGCCCCTATGGAATCCCCCAGTCTCCATCCTCCATATCGTCCCTGCCATCCCACGCTCCTTTGCTCAATGGGCTGGATTACACGGTGGACAGTAATTTGGGCATCATTGCGCATGCAGGGCAGGGAGTAAGCCAGACGCTGAGAGCCATGGCTGGGGGACCCACCTCTGACATCTCCACAGGAAGCAGTGTAGGCTATCCCGACTTTCCAACTAGCCCAGGCTCTTGGCTCGATGAAATGGATCATCCTCCTTTTTAAACTTCTCTCCTCCCCACCCTACCTGCCCCCCTGGCTTGAGAGAATATCTTCAAGGATCAAAAGAGACTTGCCTTTTAAGGATCGAAAGTACGCCAATGTGAATTTCCATTATTTTCAATGGAAGTCCTCCGCTGATTCCTAGAAGGCTGTGAGACCACACTAGGGCATTGTTTCCCTGGGGAAGCAGTGGGAGAGCAGACTCATCTCAGAACACAGCACAGGGGGTAATGGCCTAGAGCTCTAGGGACACTGGCTTGTTGGGTCTCTCCCCTGCTGTTCTGCTTAGGGGCTTGGCTGCTCAGTGCTTTGGTAGCACAAGGTGACTGTGATAGGCCCCCTTGGCCTTTGGGAACTTTGCTCCAACTGGTGTGTCTCACACAATGCCTCCCAAAACACTGCTCTCACCAGAACTGAGACTCCTAAGGTAGAGGCCTCACAGCCCTTGAGTAAAATAAAAGTGATTTCTGGACCATC
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000121454-LHX4:NM_033343:5
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.483 A=NA C2=0.634
Domain overlap (PFAM):
C1:
PF0004624=Homeobox=PD(19.3=19.0)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping 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
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)