HsaINT0091727 @ hg19
Intron Retention
Gene
ENSG00000121454 | LHX4
Description
LIM homeobox 4 [Source:HGNC Symbol;Acc:21734]
Coordinates
chr1:180235527-180240669:+
Coord C1 exon
chr1:180235527-180235729
Coord A exon
chr1:180235730-180240514
Coord C2 exon
chr1:180240515-180240669
Length
4785 bp
Sequences
Splice sites
5' ss Seq
ACGGTAAGC
5' ss Score
9.89
3' ss Seq
GCAGTGGTTTTTCCTTGCAGATG
3' ss Score
10.03
Exon sequences
Seq C1 exon
GCGCTTCGGCACAAAATGCACGGCCTGCCAGCAGGGTATCCCCCCAACCCAGGTGGTCCGCAAGGCCCAGGACTTTGTCTACCACCTGCACTGCTTTGCTTGCATCATCTGCAACCGGCAGCTGGCCACGGGGGACGAATTCTACCTCATGGAGGACGGGCGGCTGGTGTGCAAGGAAGACTACGAGACAGCCAAGCAGAACG
Seq A exon
GTAAGCAGCATGGCCCCGCATGGTCCCCTCTCCAGGCCTTTGTTTGGGCCACGCCCTCTGCCTGAGGTGCCCTTCTCATGGCGTCCCACCTGCCCATCCCTCAGAGCCCTACTCATGCACCGCCACCTCTGAGAAGCGTCCCAGATCTCCACACTGAGAGTAAATGCTGAACACCTCCCCGGCCGTTAGCACTCGCCGGCTTCATGGAAGTGTTCATCCAGCCATGGTTCCTGAGAGCCTGCCTGTCTCCATGGTAGGCTCAGAAGCAGCCAAGAACCTGGTTGTTACCATGGTGGTGGCCTCCTTCCCTGGGTGGAGGCTGGGGTGCTGAGGGGTGGCTGGGAGCTTGGTCTGTATTGGACACGTGGGGCTGCCGCTTAGTTTTGCACATCAGGGTGCACATGGACCTCTCAGCAGCCCCTGCCTCAAAGGCCGTCGGTGAGAGCCCAGCACTGGCCTCTGCACACTTCATACATCTGTCTGTTAATTGTGTTCTGTTCGCCTCGCAGACTGTGGGCTCCTCTAGGGCAGGGCCTCCTGGAGTTTCTGCAAGTGCCCAGTGAGTGCTAAAAGAAGAGGCAGGACACATGCCAGATTCAGGGAGGCTCCGTCTCAGCAATATAGCTCCCTCCACCCACTTCAATATAGCTGCCCCCACCCCCTTCACCACAACCACTGCAGGGCCACTGCCCACGGTGGCAGCAGGAGCTCTGCATGGTGGAGGCCGAAGTCAGGTCCCGCATTTAGCAGCCACGCCTGGAAAGGCCTAGCTTGGCCTGGCGGCAGCGGCTCTCGCCCTACATGCCATGCGCTTGGGCAGCCCGGGGACTTTCCAGCGTAGAGCCCAGAACAACACATTCCCCATGCTCCCCTCGCAAAGCCAAGGTGGACACTTTTATTCCTGCAGCCCTACCTCTGGCTTCTCACTCCCAGATGCACCCACATGGTCGTGGGGTCAGGCCCTGGCTCTGAATTTGGGATTTGGCCAAACCCAACATGATAACCTCAGAGGTGTGAACGCACAAAACATCAAGTTCCTTGGCCTTTGACTAGAATTTTGATCAACTCAGGGTGTTACTGTGCAAAAACGGCTCTTGTTGACAGCTCTGGGCTTGATGAGAAAAAAAATTAACAACAATTTTATGTATCTCCTTCTAGATCTTTTCTGGGCCCACACACATATTATACAGATCTCATCAATAATGGAGAAACTGGTTTTTTGTTCATTGAACACAGTATAAAATAAGGGGATTGTGGTGGTGAGGAAGCAGAGGGGATTCATAAGGGCCCTTTAGGTGAGCCAGCTGGAGCTGGGTTTGGCTTTGGTCCATGGCAGGAGTGGGCAGGGCTTCCTGTCTCTTTGAGGACCTTCCCTCCCACCACCCCCACAGCTCTGGCCTTTCAGGGTGGACAGAGGCCTTTGACCTCCTTCCTCCAGAGACCTGGGGCCTCTGCAAACCCATCCCAAGGCTCTTTGCCTGCAATGTACTAATCTGCTCTGGTTTCTTAAAACTCACTCCATGCTATTGCCTTGAAGTCAATTGTGATGTCATGGGAGATTAGGGCAACTTGTCAGGGATGAACCATCACAGCAGATGGACTCAGAGATACCAAGACACCTTTGGAAGTCTAGTGCCGTTCATCAGAGATACTAAGATGGCACGACCTCCCCGGCCTGCAGCTGGTTCTCATCAGAGGCCTCATTTGGACTCTGAGCACTCTCAGCTCAGCATCTCCTGATGTTGTGGGTGGTTCAAGAGACAAGAGAAACAGATGTAGATTGGTCAGAATCTGGCTGGGGAGGTGGGAATGACATTGTGGTGCTCACAGTTTTATCGAGGAATATTTGCACCACAGCAGACCTCTGCAGGATGATGGAAGATGCCGGACTTGCTGTCAGAAGCTGGCTGGGCATCCCCCCACACAGGGAGATCTCCTGGCAAGTTGTAGAACTGGCTGACCCTCGGCTTCTCAGCTGTCTATGGAGGATCATAGCATCTGCCACGTAGGGCTGTTTTCCTGAGGTTTAAATAGGATGAGGCTTGTGAAATGGGATGTGAAATAAGAGACTGACGTGGAGGAGAAGTGCAAACAGGGAGGTGAGGTGTGCTTGAGGTTTTAAAGCAGCGGAATGTTACACAGTATTTCTGGCCTGTTCCCCGGGTCCTTTCCTGACCCCACCCTGGCTGTGAGCAAGGCAGGGCTCCTCTGTCCTGGGCAATCGGTGATCCTTGGAGCAGCGGGGAGTTCTGTCCACTGCAGAATGCCTGGCTGTCTTTTCAGGTTGTTTTAATTCCTCCTTGCTACTCTCAGCCCTCCTGCAGGCTTACAGTTCCCTCCCATTAGCTAAACAAAGGATCTCAGAGCAGTTACTTGCACCTTAGTGTGAATGATTTTGTTCACTTGTTCCGTCTCCCTGGATATTTGCATTTTCAATATAATGAGGTTGCGTTTTATGCCAGGGACAAGTTCTAGGAGACCCTGCATCATTCAAAACTAACATATTTTAAGACTAATTTTCCTGTAGGAATTAATGTAGAGTGTGTGGGGGGGGGGGTGGTATATTCTGAGAGCACATAAATCCATAACCAGTGAAGTGTATCTTTGCCTTAATGCTACTTTTTATTTTCTCAGCATTATCTTGAATACCTTGCAGAACGCTCTCTCCTAAATTAACAGCCCAGGGTATCATGGGCTCCCTTGGCCTTCCTCATAGCGTTTTGTCACATTTAACTTCCGTACCAAAGTTATTGATTTTTGGGTACATTTTTCAGCACGAGCACTGCCACTGCTACTTAATGAATACTTGGATGACATTGTTATGGGATATAAAAAAGATTTTAAATTATAATAACAGTGAATGTTAAAATAACAGCATATTAGTCCCCATCATTGCAAGAAGAAAATCCTGTGTGTGTAGCAGTGCCGAACCAGCGGGCCACCAACCAGGATGACGGGTCTATCCCAGTGGCGCTACCATCTGGCTGTGGTGAAAAGAATTTATAATTCCGTAGGCCAAGCTATTTTGAAATTAAGTGATTCTCGAGAAATTAAAACATTTTTGGTGATTGCATTATTTCACATTTTTTAATATAAAGATTGTACACAAGTGCACTATTTCCCATTTGCATAATTCAAAGTTGCATCAGACACTCCCGTGTAGACTATAAATATGCACAGAAGGGACAGACTCCTCAGAATGAAAAGGAAGGCATTTTGGAGGTTCCCCTTTGTCTTTTGGAATGACTCTCTAAGTAGTGTAGTCTCTGTGGCAGGGGCTCCGGAATCCCTACCCTTCGGGTTCAGGGCTTCAGGGAGGGAGTTGGGCCACAGTAGTTCCGGGATGACAGTGGCCACGTGAGAGAAGAAAACAGCCCGAGGAGAAGGGAAGGCACGGGTGTGTCCCCCCTCACTGTGTACACACATGTCCTGGCTGCACAGCTGCTTCATTCCTCTAGTGCCTCCCAAGATCAGGGCAGGCCGTGTTGCCCTCTGGACTTCCAAGGGGGAAGTGAGTTACTGGCCCAAGTCACTCACTCATCAAGAACACTGAAGCCAGGTCTGCTGACTCCAGGGAGAGCCTTGTAGATTGTGAGGACCGAATGCATATAAAGTCCTTAGTCAACACCAGCACATGGTAGGTGCTAACACATGTTGGCTACTATTGTTTCTAAGAGAGGGTTTTCTTGAATGGAAAGAAAGGAGAAAAGACAGAGAGGAAGTCAGGAATGTCACAGAGACACCTTCTGGGGCACACAGGTGAGCAAGCACAGAGAGCAGAGCTGCCCAGGCCAGCTGCTGACTTTATTCCGTGTGTCCTCCAGGGGCACTGTGGAGAAAAGGGCAGTATGCCTAAGTGCTGGGAGAGGAAACAAACCTTTACATTCACCTGTGCTTCCGAACACACGCACGCGCCTCTCTCTGTACCTGACTTTGAATGGAACAAACCAGACTTTAACTAACAGGAACTTGAGCTTGTTCACTCAAAATCTGTCTAGGACTTTGTGTTGATCAGTCAGTGTGTTGCCCAGAACATTCCTTAGACTAGTTTTCTCAAAAAATTTTGACTACAATCCACAGTAAAACTCATTTTACATTTCATCTCAGTACACATATTTATACAATAAAAACTAAAGTTTAATGAAATGATCTTGCCATTCCATCCCATTCTCTTCATCTGATTTCCTGTTTTAGTTTTGATCCACTAAGGTGACTTTACAGCCCACGAGTGGGTTCTGACCTATAGTTTAGAAACCTGCTTAGACACTGTTGGGTGTGCAAGCTCACCCCTGGCTGTGAGCCCAGCGACGCCAGGGCAAAGGTGACATGGCTGTGGGGAAATGGGAGACTCCTGATGAGACAGAGGGGAGGGCATCTGGGGCGACTTTGAACATGACTTCAACCTGGCTGTTCACCTTCACAGCTCTGGCAAGAACTCATGAGGATGTGTGAGCAGAGTGTTTGTCATGACAGGGACGTGTGGAATTGGGTACATTCAATCTGATGAGACTTCTGTGCAGCTGGGCTGGCAGGGGAGGGTTGAGGCAGGGAGCTGAGCAGAGAAAGGACTGCTGTCCTCACTTTTCAGTGGCTTGGGAAGGCCCGTGGTGCAGGAGTCAGTGCCATGAGAGTGGGGACCTCTCCACTCTGATGTCCCCTGTGCCTCGCGCTGTCCTGCCTACAGCAGGCAGGCTTAGGTGCAGAAAGGATGGAAGGGAGGGTGTGGGAGGAGGCGCAGCTGCTGCAGATAGGCCGAAGCCAGTAAGCAGTGGTTTTTCCTTGCAG
Seq C2 exon
ATGACTCAGAGGCTGGAGCTAAGCGGCCCCGGACCACCATCACAGCCAAGCAGCTGGAGACATTAAAGAATGCATACAAGAACTCCCCCAAGCCTGCCCGGCACGTGAGGGAGCAGCTGTCCTCAGAGACAGGCCTGGACATGAGGGTCGTACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000121454-LHX4:NM_033343:3
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
No protein impact description available
No structure available
Features
Disorder rate (Iupred):
C1=0.029 A=NA C2=0.712
Domain overlap (PFAM):
C1:
PF0041217=LIM=PD(3.6=2.9),PF0041217=LIM=WD(100=87.0)
A:
NA
C2:
PF0004624=Homeobox=PU(77.2=84.6)
Main Inclusion Isoform:
NA
Other Inclusion 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]
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)