HsaINT1021935 @ hg38
Intron Retention
Gene
ENSG00000162761 | LMX1A
Description
LIM homeobox transcription factor 1 alpha [Source:HGNC Symbol;Acc:HGNC:6653]
Coordinates
chr1:165208063-165210776:-
Coord C1 exon
chr1:165210699-165210776
Coord A exon
chr1:165208133-165210698
Coord C2 exon
chr1:165208063-165208132
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:ENST00000342310:6
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.143 A=NA C2=0.938
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
Chicken
(galGal3)
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]
SPECIAL DATASETS
- Autistic and control brains