HsaINT0092592 @ hg19
Intron Retention
Gene
ENSG00000162761 | LMX1A
Description
LIM homeobox transcription factor 1, alpha [Source:HGNC Symbol;Acc:6653]
Coordinates
chr1:165171104-165175271:-
Coord C1 exon
chr1:165175101-165175271
Coord A exon
chr1:165173278-165175100
Coord C2 exon
chr1:165171104-165173277
Length
1823 bp
Sequences
Splice sites
5' ss Seq
ATGGTAAGA
5' ss Score
9.48
3' ss Seq
GTGTTTCATCTCCATTTCAGGTG
3' ss Score
11.64
Exon sequences
Seq C1 exon
CTCAGACAAACGGTGGTGGGAGTGCTGGGATGGAAGGAATCATGAACCCCTACACGGCTCTGCCCACCCCACAGCAGCTCCTGGCCATCGAGCAGAGTGTCTACAGCTCAGATCCCTTCCGACAGGGTCTCACCCCACCCCAGATGCCTGGAGACCACATGCACCCTTATG
Seq A exon
GTAAGAGGGACTTAAGCCCCTCGGGCCCTCTCATAACTTGTGTGGGTTTCTCATTCCCTCCTAAACACATCTAGGCAGTTCCCAGATGCTCACCGAAGTTCCAAAGCAGAATAATGTGCCCTACAAAATACTGCCAGAATCGCCTAACCAATGACTACAGGAGAAAGACCTTCATGCATATTCATTATTGACACTTCCATTTATCTTGTTTTCAAAGCTTCTTGTTTGTTGGTTTTAAATGGGAAGTTGTGCTCTCCTTGTAGACCTGTTTGTTGTCATTGAATTGCAAGTCTTGCGCTTCATGCCAGAGATCAGCAGTATCAGTGCTACAGAAGGCCTTAATTAAGCAAACGTTTACCTAAAGTAAGAAAAGAAATAAAAAGCACAGAAGACAAATTTTCTAACTGGACTATCCTACTATGGATACTAATAGGTGCTCTAATTTAACTAGTGAAACATAAACTGACTTGTAAAGTGAAAGTATCTCCCTTATACCCACCCCACCCAAAGAAGCATTGATTTAAATGCTGCATATATGGGTAGCTGAGCCTCTCCCACTTACCCAGCTTCGTGCTTAAGCTAATGGACAACAACCGGGGGCCTGAGGACCCAGAGTAGGGGGCTGGGTGAGCTTTGGAGTGAAGGCTCAAGTTCAACCTCAGCCAAGTATAGGGCATTACATTTTATACAGAGAAGGTTAGTGTTGTATGTAATGCATTGGTCTGTACTGTGTAATCTGATAGATTACACTGATAGTTAAAAAATAATCTTATGCAGCAAGTCTTCAAAACATTAGTATCAGAGATTCACGCCACAGATCACAGATTTTGCCAAACAACTTTTTTTTTTGCCTTCATGAAAAAAAATTCTGTTGTTAAAATCACGCCTACTTTCCCATATCACACATTCAGCAAACATTTATTAAGATTTGGCCCTTGACAAGCCCTTCACTGGCTGACCCCACTCATTGGATGTTCAGTGATAGCCACCCTCTTGGCTTCCTTAGAAGGCACAGGTCACATCTGTACCATTCTTTACTCCACAGCTATCGGAAAACAGGGCAAACACATTTTTTTGCAAATTCTTTTCAGAGTCTCAGGGATTGTGTTACATGAAGTATCCCTGTGATGAGTCCTTTCATAAAATGAATATTTAAAGCCCCATGACAAGTTGTATAAACTCCAGTTTTCACCTCTCCTATTTACTTGAAGCAGAGGCAGAACATTCTTTGCCTCCAGATCCTGGTTGCAGTGATTTCTCAGCTGTTCCAATGTGTGCCCTACTGGCTTCCCTATCAAAGGTGTAAATTAGTTGAAGGTAGGCACCTAACCTTCCTTTTCTTTGCATTACAAATTTGGGGTAACAGCTGATAGTAGACCCTTGGTGTTTGAAAGAACAAATGTTATCACAGGAGTTTTCATTAGCTTCACTCAAAGAGCTTTCTTTTTGTTTTGTTTTTTTGTTTGTTGGTTTTACCATCCCTCCTTCAAGCATCATTTTTCAGGCCCAAGTCCTATAGGAGCTCTGCCCTGTCTCTCCAGCCTCTGGTGACATGTCCTGCCTACTCCCCACACTCCCTGTCTAGACATTGTGACATTTGCTTATGCTGCACTCAATTTAGCACTTTGTCATATCCTGGTTTAGATTGTTTTCACTTGTTGCACTTTGGACTTGAGCCCCCTAAAGAGAATATAGACTTTTTGTAGAAAGTTTCACCTGGAGCCTGTGCTCAGGCAACACTTGTTGAATTCAGCTGAATATCCTAGCACTGAAATGAGTCACTTCTTCAAGACCCTCATGCCAGTGTTTCATCTCCATTTCAG
Seq C2 exon
GTGCCGAGCCCCTTTTCCATGACCTGGATAGCGACGACACCTCCCTCAGTAACCTGGGTGATTGTTTCCTAGCAACCTCAGAAGCTGGGCCTCTGCAGTCCAGAGTGGGAAACCCCATTGACCATCTGTACTCCATGCAGAATTCTTACTTCACATCTTGAGTCTTCCCCTAGAGTTCTGTGACTAGGCTCCCATATGGAACAACCATATTCTTTGAGGGGTCACTGGCTTTAGGACAGGGAGGCCAGGGAAGAGGTGGGTTGGGGAGGGAGTTTTGTTGGGGATGCTGTTGTATAATGATATGGTGTAGCTCAGCATTTCCAAAGACTGAATACATTATGGATTGCATAGTTTAATGTTTCTAATAAGAGTCTTAGCATTAGATATGAAGACGTGTTTATCATTAAGGACAGAGACTTTTAATATAGACATTCTCATGCAAACTAGATACTTAGGGACTCCTAACAACTTCCCACCATGTCGGGGAAGCTCTTGTCAAGAGGTGCATATGTCTATCCATCTACACACCAATAGACAGAAGGACAGATAGATAGATGTGTGTGTGTGAGTGTGTAACCTTTCGTATTTTACCCTCAAAGTTTATTCCTAATTATAACAGACACCAACTGTACAGCAAAAGTAACTTTATTTTCAGTGTGAACTATATTTAAGGAAATGCTTGATGCACTTAAGTTATAAAATGAGATAATTTACTTTTATAAACTTTATTTTTAGCTTGACAAGACTTGTCAGCAGGGCAGAGAGGGCTGCTCCACCTAGCCCCATAGCTTTGAGTGCTGGGGTTCATTCTGTTTTCAGAGTGTCTTTCAGATCTGGAAAGAAATTCTGTGTGGCTGATGGTGTTCTCTCTTGCATTCTTGCTCTCTTTGGGGTTGAATCACTGGGCAGGGGTGGGACAGAATAATCTCTGATCATGTTCTGAGAAAATGTAAAGCCCAGACTCCTGGGCTTTCTTTTAAATTCTGACAAGTGGTTGTTGGGCAGTGCTAGGATGATTGGTTCAGCTCTTGAGCTTCAGCATCTGCAAATGTGGATGAGGCTAATAGTATGTACCTACCTCACTGGGAAACACCAAGGCTTAATTCATTCCCAGGACACATGAGCAGGGCTGAGACTAATATCTGATATTTGTTTAAGATACAACCAGGCCACTCACTTGGCAAAGGAGGGTACATAGGGTTGCAGAGCAGGAGGGCTCCTGAACTCCAGAGGGCAGTTCTGCCTGCTGAAGTCCCTCTGCAAAGCCTGTGCTGAAGGAGACACCAGCTCAGAGCAGTTCAGAGGGATCCCAGAGTCCCAGAGTGGGGAGGAGGTGAAGGCTGAGGGGATAGAGGAGGGCCTGGTGGTGTTCTAGAGCAGGGTTGGGCAAACTCCTGCTTGCGGGCCTGCTTTCTATGGCTTGCCAGCAAAGAATGGTTTTTACTTTTTTTTTGAGGTCATTAAAAAAAAGGAGAAGAAGAATATATAACAGGCTGTCTGTGGCCTGGAAAGCCTGAAATATTTGCTATCTGTATTGTCTGGCCCTTACAGAAAAAGTTTGGGGCCCCTTGTTTTAGAGGGTCTGTTTCTAAAGAACCTCATGGCGCTCATAGAGGCAGAAGGTTCCAGTGGAAACCCTTGGCTCTTCCTTCCAACTCACTCCTCTGATCCTCGGCACAGAAGACCCAGCAGCCATTGTACATGGGGACAGTTCCACACCCTGGTCTCCAGTTGCGGTGCTAGGATGGTATTGTTCTGTGCTAGGAAGTCTCCTGGGAACCCAGAATGAGTTGGTGGGGAAGACAGCGGGTCACTGTGGACCCATCCAGGAGGGGCCAGGATAGGCTTGGCCTCATTTCTGGGGACATCATTGGAGACTTGAACACAGAGACACGTCCCTATCACTCTGGCAAGGCCAGAGGGAACATGTCCCCTTATGGTAGAGTCTATGTTGTGTGATTTTTGTGCTCTTGTTTATAATTTATGCAAACCACCAAGAAACCCAAACCAGTCTGATGAGTGAAAATTATGCAGATGCTGTATGGCCCCACAGGTTTCTGTGGTAAAGACCAGTTGGAGAATGTAGGAGATACTATGTGAGTGAAAATGAATAGAGATCCTTATTCCACTCCTTAATGGCATACCAAGATGAAATTAAAATCTCTTACAAATGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000162761-LMX1A:NM_001174069:8
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
No protein impact description available
No structure available
Features
Disorder rate (Iupred):
C1=0.700 A=NA C2=0.548
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
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:
AGCTCAGATCCCTTCCGACAG
R:
GCATCCCCAACAAAACTCCCT
Band lengths:
354-2177
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)