HsaINT0092589 @ hg19
Intron Retention
Gene
ENSG00000162761 | LMX1A
Description
LIM homeobox transcription factor 1, alpha [Source:HGNC Symbol;Acc:6653]
Coordinates
chr1:165179936-165183050:-
Coord C1 exon
chr1:165182878-165183050
Coord A exon
chr1:165180014-165182877
Coord C2 exon
chr1:165179936-165180013
Length
2864 bp
Sequences
Splice sites
5' ss Seq
AAGGTATAG
5' ss Score
7.98
3' ss Seq
TCTCGTTCAATTTTTCCAAGGTG
3' ss Score
6.62
Exon sequences
Seq C1 exon
GTAAAAGTGATGATGAAGAAAGTCTCTGCAAGTCAGCCCATGGGGCAGGGAAAGGAACTGCTGAGGAAGGCAAGGACCATAAGCGCCCCAAACGTCCGAGAACCATCTTGACAACTCAACAGAGGCGAGCATTCAAGGCCTCATTTGAAGTATCCTCCAAGCCCTGCAGGAAG
Seq A exon
GTATAGGAGGGAGCAGGGAGGAAAAGGAGCTGGGCCCCACTTCTCTGTGTGCACTCAGACCCCTCTGGGATCTCAGTGGGCATTGGGGGTCACAGTGGTGAGGAAGGCTGTTCAGACAGAGCCTGCACAGGCGGCTCAAGCCTGTTGGAGACTCCAGAGATCACTAAGCTGTGGCCAGGGTGTGATAGACTCTCCTGAAGCTTTCATGCATGCACACCAACTCCAAATGGCCCCTGTCACACCTTTCATTTCATAGAGCACAATGGGAACAGTAATAATGATAGGTGTCCATTGTGGTGTAGACCCAGATGCTGTAAAGCAAAGAGTATAAAAACACAGTGGCTTGCAGTACTCTTTTTTGAGTCTGGCTTTTTCCACTTGGTGTGGTGGTTTGGGGATTCATTCATTCCTATTTCAGCATTCCACTGTATAGGTGTGCCATGATTGGTTTGTCCATGCACCTGTTGATGGGTGTTTGGGGTTGTTTCTAGTTTGGGACTGTTTCAAATAGGACTGCTATGGACATTCATGTAAAAAAAAATACAGTGGTTTAATGAGACAGGAGTTTATTCTCTTCTGTCACAGTCCAGAGGTGAGCAAGGCAAGGCTGGTGGGTGGCTCTGTTATCCATCTCCTGTGTCCAAGCGACTGCTCCAGTTGTCACCATGTTTCCAGTCACCAGGTAGAGAAAGAGGAAATGGAGGGCAAGCGCCCTGCTTTTTAAGGATGTATCCAGGGGTTGCTCAAATCATTTCTCCTCATATGTGTTGGCCAGAATGTAGTCCTGTGGCCACACTTCCTGCAGGGAAAGTTGGGAAATGAGTCTGTCTGGGTGACCAAGAACTTGCTAAACTTAGTGATTCAATTACTCATAGGATGAAGAAAGAATAGATATTGGGGACAATTAGCAGTCTGCCATAAATAGCAGCGCCCATTTATTGAGTACTTATTGTTTATCGACTGCCTGTCATATACTGAGTACTATCTTTTACATGATAAAAAGAAAGAAAATAGGGTATTCTTTACTGAAATTCATAAAGGAAATACATTTTGAAAAAATGTTAGCATTATTTTTCCTGCATCCTTTTTTGCATTAGTCAGCTTTGTCTGTGATAAAAAAAAAACAAACAAAAAGTCACCATGGTTCCCAACAAACATGTATTTTCTTTTCTTGGGCTGTGCATTGGCTGTGGCCCAGCTGGGTGCAGGTTCCAGCCTGCTCCACCTGTCTATCATTCGAGGGTCCAGGCTGAAGGAGCAGCCCCCTCCTGGGCTTGTTGTTCTCATGAGGTTGGCAGGAAGCAAGAGGCCAAGTCAAAGTGGGAAGCCCATCGAAAATCTCTTGCTGGATATCAGACACATCACATCCCACAGGCCAAAGCAAGGCATGGGCTTAGCCCAGCGTAGGTGCAGTGGTGAAGCACACACCCACCACGGAGCAGGGGAGGGAAGGATAGATATTTGTTGAGCAATAGTCCAGCCTATCACAACTTCTGATATTTGGAAAGATTCAGCTGCAGACTCACTTTTTCTGCCCTTGCAGCTCCTTATGCTCCAAGAGAGGTATCAGTAGAAAGTAAAATGCCCCCAAATTGGGCTTGCACTAGGACAAATTACAGTCTTCCTCACTTATTTACTTCTTCCATGTATACTAAACTCCCAGCCCATGTAGGGCTTTGTGCTGGGTGCTTGTCCCCGGGCAGCTTCCAGGTAACCAGCAAGAAGGAGATGCGTGTACACATTACTGTAACACCAGAGAGGGGGCTCTGAGGACCATAACAGAGGGGAAGCCAGGAAGCAAGGGAAGGGAAAGGTCACTTTGGTCTGGGCAATCAGGCAAGGCTTTGTGGAACAGGTGGCTTTTGAGCTGGGCCTCTGAGGAATGGATAGGGTTTCAGCAGGTGGAGGTGGGCCCCTGAGTACACTCCTATTTTAGTTGGCTTAGCAGAAGGATGTGCTATAAAAACCTGTTCTAATCATTCCACTTCTAAGCCTTTCCCCAAGTGGCATGATAAAGGGGAAGTATTTCTCAAGGCTTCCATTTGCTCTACTCACACGTTTATTCAAGGAGCTCTTTCAATCCCATCTCCTCCCCAGGATCTAATCAAGAGAGGTCAGTGTCTCTCAGGCCCCCCTCTGAAAATCTGTGCTTCTTGCCCCTTCTCTTCTCAACACCTTGCCAGACCCTCACTGTGTGCCTGTATGGTAGGCAGATGTTTAAATGCATCTCTTTATTATCTGGATCCCAGTTGTCCTGTCTCCACCACAGCCCTGGCACATGTGCTGGCCTCAGAGTTGCCTACCTGGCTCTGCCGGGTTCCAGATGGCTCTCATTTTATTCTCTTTGGGCAGGGCTCACTTGGGGTAGCAGTCACTATGGATATTCATGAAACACCCAAAGTTACCTAGAGATATGAGGGACAAAACCAAAAATTAAGGTCAATGAATTTAGGCAAGAGAGGAGACCAAGAGAGAGCCATTTGTTTTTCCAAAGTGATTTTCACTCTCAGATCTCCTTAAGTAGGTCAATGCATATGCATGGCTTATAGCTAAAGCACAACAATAGACTAAAGTCTAAACCACTTGAAGGCCTAATTTCCAGAGCAAGAGAAATCCAGAAACACCTCTTGGGAATGCACATGTAAATTAATAATTATTATTTTGTTTCTTTACCTGGTGAAGGACTTTCTTTCTACCTGAAGGGAAGCAATGTTCTCGTGTTTGTGTGTATGCTCAACATTAAAAACTATTCAGCTCCTAAAGCAGATACAGTCTTTTGGCCTCCTCAAGTATTATATAGGAGATGTTCTACCTCCTACCCTGAGATGCCAGTGTGTCTACATTTCTCGTTCAATTTTTCCAAG
Seq C2 exon
GTGAGAGAGACTCTGGCTGCAGAGACAGGGCTGAGTGTCCGTGTCGTCCAGGTGTGGTTCCAAAACCAGAGAGCGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000162761-LMX1A:NM_001174069:5
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
No protein impact description available
No structure available
Features
Disorder rate (Iupred):
C1=0.483 A=NA C2=0.122
Domain overlap (PFAM):
C1:
PF0004624=Homeobox=PU(47.4=46.6)
A:
NA
C2:
PF0004624=Homeobox=FE(43.9=100)
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)