HsaINT1021937 @ hg38
Intron Retention
Gene
ENSG00000162761 | LMX1A
Description
LIM homeobox transcription factor 1 alpha [Source:HGNC Symbol;Acc:HGNC:6653]
Coordinates
chr1:165201867-165206034:-
Coord C1 exon
chr1:165205864-165206034
Coord A exon
chr1:165204041-165205863
Coord C2 exon
chr1:165201867-165204040
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:ENST00000342310:8
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.707 A=NA C2=0.588
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
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]
SPECIAL DATASETS
- Autistic and control brains