HsaINT1022199 @ hg38
Intron Retention
Gene
ENSG00000166159 | LRTM2
Description
leucine rich repeats and transmembrane domains 2 [Source:HGNC Symbol;Acc:HGNC:32443]
Coordinates
chr12:1827410-1828215:+
Coord C1 exon
chr12:1827410-1827594
Coord A exon
chr12:1827595-1828075
Coord C2 exon
chr12:1828076-1828215
Length
481 bp
Sequences
Splice sites
5' ss Seq
ATGGTGAGC
5' ss Score
8.27
3' ss Seq
AGTGCTCCTCCCTCCCTCAGGAC
3' ss Score
10.73
Exon sequences
Seq C1 exon
CTGCCGCAGCATGAACCCCTGAGCTGATGAGTCTTATTATAGCCCGGCTGGCGGAAGACAGAGTGCTGCTATTCACCTCTGCGTGGGCGTCGGTGGTGCAGGGGGAAGCAGCAGGCCATCCAGCGGCTCACACCCTACGCGGCTGCAGCTGCCAAGGGCCTGGCCCCTGCCTCCCTCGGGCCATG
Seq A exon
GTGAGCTGTGGCGGGGCTAGAGGAACCGGGACCCAGGTGAGGGGAGCCTCCAGGGACAGGTGACAGTTGTGGCCTGTGACCTCACTCTGCTCACCTCGGAGAGATGACCTCAGTTTCTCCACCCATAACTCAAGGAATGCCCAGATGGGAGACCAGGTTGCCATGAAAACATCTGAGTGATCAACATACTCGGGAGGCAACAAGAAGGCAGATGAGGCTGGGTAGGCCCATGGGTGCACCCCCAGCTTTGCGGCACTGTGCCCGACCCTCGGGCTCCTGGAAAGCCGAAGCCTGCCCCGCCCCCATCCCAGGGGCTTGAAGGCTTCCTGGCTCCTCTTCTTCCCCCACCCAGGGAATCATAACTGAGAGGAACAGGAGAGGGCATGAGGAGTGTAAAGAGACACCCGGGCCCTCTCCCTAACCCCTGGGCTGGAACGGGGCTCCCGCGCCTGCCTGTGCTCAGTGCTCCTCCCTCCCTCAG
Seq C2 exon
GACTGACAGGCGGCGCACCCAGGGGCTCCTCTCTCCCCAGAGCGACAGGGCCCGGAGAGCCGTGGGCCTCACCATGCTGGCGCCGGGCAGCAGCCCTGGGCAGAGGGGCAGGCTCGCCCTGCAGTGGAGGCAAGTCTCCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000166159:ENST00000299194:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
5' UTR
No structure available
Features
Disorder rate (Iupred):
C1=NA A=NA C2=0.130
Domain overlap (PFAM):
C1:
NA
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Conservation
Mouse
(mm9)
No conservation detected
Cow
(bosTau6)
No conservation detected
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CGCAGCATGAACCCCTGAG
R:
GAGACTTGCCTCCACTGCAG
Band lengths:
319-800
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains