HsaINT0092590 @ hg19
Intron Retention
Gene
ENSG00000162761 | LMX1A
Description
LIM homeobox transcription factor 1, alpha [Source:HGNC Symbol;Acc:6653]
Coordinates
chr1:165177300-165180013:-
Coord C1 exon
chr1:165179936-165180013
Coord A exon
chr1:165177370-165179935
Coord C2 exon
chr1:165177300-165177369
Length
2566 bp
Sequences
Splice sites
5' ss Seq
AAGGTAACC
5' ss Score
9.24
3' ss Seq
TATGGTCCTCTCCTTATCAGATG
3' ss Score
9.2
Exon sequences
Seq C1 exon
GTGAGAGAGACTCTGGCTGCAGAGACAGGGCTGAGTGTCCGTGTCGTCCAGGTGTGGTTCCAAAACCAGAGAGCGAAG
Seq A exon
GTAACCTGCTTCTTACTTTTATCTGTCCCCATGTTGCTGGTTTCCTGAAATAATCACAGTAGGACATTGTACTTGCTGCCAGGTTTTCTCGCCTTAGCTCATTGGATAGAGTAGTTCTCTTGATTCAAAAATTCTGTTATCAATAATTATTTTGGCCACAGCAGCCCTGCAGAAGGGGAGAGAGAAGGCATTCATTTTAGTGAAATTGCTTGTATTTTCCTAGCAGCCATGACTGTGGTTTTGGCCAGCCATCTGTATGAATAAATGTCTTTCTGTGTCTTTTGGTAAAAGCATGTTCTTTAATTCATATTTATTTAATGCAAATACCAAAGTTATTTTAAAAGTAGCATGCATATAACTGGTCCAAGACAATTTTATGACAGGGTAGAATGAGTGCCTTTTCTTACTTCTCCCAGGGCCCAGCCCTCACTAATATAGGCCCAAGCCATCATACTGTCCTCTGGATCCAATGAAGCTCTATATTCCCTCATCATGGTTTTAGTTTTAGACCTTTTGCTCATTCATCTACCTACCTCTAAAAATACATGTGCCCTGTGGACTGTTTCTCAAGAGCCCTGATCTTTAGTGGATGATATGAGGAAAAAACAAACTCTATGTTTCCTCTGCTCTTACACTACAACAATCAGCGCAGAATGCTTCTGTGACAAAATATGTGGAGATATTCTCCATACACCAAGCAAGCAATCAATTGTGCAGTGGATACCAACTGGGTGTCCTCTAATTCTGACACTCTCTACCTGGAAATAGTGTCAGATTTCACAGGTTGAGGGTTCAGCCCCACAAGACTGCCCTCCTCTTCAAATGCCAATTGCAAGCTCCAGGTGGTTTTACCTATGCTTCGGATCAACTGGCTATAAATTGGGATTCCAGTGACCCCACCCCTTGGATTTGATTAATTTGCAGAGCATCTCACAGAATTCAGGGAAATACTTACTTATATTTACTGCTTTATTACAAAGGATATTACAATAGATGTGAATAATGTGATGCATATGGCGAGAAATGGGGGAAGGGTGTGAAGCTTCCATGCCCTCCCTGTGCACCCCAGCCTCCAGGAAATTCCATGTATTCAGCTGTCTGGAAGCTCTCTATCCCCATCCTTTTGGGATTTTATGGAGGTTTCATAATGTAGGCATGATTAATTAAATCACTGGGCATTGATGGTCAACTTAACTTTCAGCCCATCCCTTTTCCACAGAGGTTTGGGGGTGGGGCTGAATGTTCCAACCATCTAATCATACCTGGGTCTTTCTGATTATCATTCTCCACCCTGAAGCTACCTAGGGGCTGACAGCTGTCAGTCAGTCATTAACATTCACATAGGTATCACTCTGGAGAGTCCAAAAATTTTAGGAACCGTATGCCAAAAAACAGGGTCAACGACCAAATATATGCTTTACAGTATCACAGGTTATCTCACTATTTGATCATGATTGGTTAAGGTAGCATTTCTCTAACTGACATCCTCAGAACAGGGCTGTTGATGTGTACCAAAGAAAGACTCCATAGTGCAATAAGTTGCAGAGGCCCTATAGCCTATGGATTCATAAAGCACAGGGACACATTTAAAGCTCTGAAAAATCTTGCAATAAAGAAAATTTTTACAAAAATCTAGTGTTTCCTACACACAGACACATACACACACTCAAAGTATATGTCATCATCTCGTGGAACCCTAATGCTCTATGGAACACAGTTTGAGAAATATTGAGTTAAAATATTCCTTCAGGGGGCCGGGCGTGGTGGCTCACGCTTGTAATCCCAGCCCTCTGGGAGGCCGAGGCGGGTGGATCACGAGATCAGGAGATCGAGACCATCCTGGCTAACATGGTGAAACCCCGTCTCTAGTAAAAATACAAAAAAATTAGCCAGGCGTAGTGGCGGGCGCCTGTAGTCCCACCTACTCGGGAGGCTGAGGCAGGAGAATGGCGTGAACCCGAGAGGCGGAGCTTGCAGTGAGCCGAGATCGCGCCACTGCACTCCAGCACTCCAGCCTGGGTGACAGAGCGAGACTCCGTCTCAAAAATAAAAAATAAAAAACTATTCCTTCAGGGAAGCTTGCGTGTTAGCAGGGTGCTTTGGAAGAGGCATGAATCTCTGGGTAGGCTCATCTCAATCTTAAGGGCCAGCAGACAGGGAGGAGGAAAGGAACAGCCTCTTAGCTTACCCCAAATCACAACCTCTTGTTCCATACGTCTAGGCTGGGCTGCAGATTTCACAGTCACACACTTATTACCTAATGTAAAATGGTCACACCACAAGCAGCAAGTTTTATTTACTGAGGAAAAAATCCCTATTCCTGCTAAGACAAGCTGCACCCCTGCTTCCCAGCCAGCTGTCTTTATACTGCTGCAGAGTGGAAGAGCTCTCAGCTGCAATGCTTCTCGCATATGGGGCTGGCCACTGTTGCTCCTTTACTAAGTAAGAGCCAGAGCTTTGCCAACAAGCCCTCTCCCGGGGAAGGTGTCACTTCCAGGCCCCCCCTTACTTTGTGAACATGCTGCAGGCCACCTGACTTCTAATCCTATGGTCCTCTCCTTATCAG
Seq C2 exon
ATGAAGAAGCTGGCCAGGCGACAGCAGCAGCAGCAGCAAGATCAGCAGAACACCCAGAGGCTGAGCTCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000162761-LMX1A:NM_001174069:6
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
No protein impact description available
No structure available
Features
Disorder rate (Iupred):
C1=0.122 A=NA C2=0.925
Domain overlap (PFAM):
C1:
PF0004624=Homeobox=FE(43.9=100)
A:
NA
C2:
PF0004624=Homeobox=PD(3.5=8.3)
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)