HsaINT0097334 @ hg19
Intron Retention
Gene
ENSG00000166159 | LRTM2
Description
leucine-rich repeats and transmembrane domains 2 [Source:HGNC Symbol;Acc:32443]
Coordinates
chr12:1940101-1945918:+
Coord C1 exon
chr12:1940101-1940691
Coord A exon
chr12:1940692-1943432
Coord C2 exon
chr12:1943433-1945918
Length
2741 bp
Sequences
Splice sites
5' ss Seq
GAGGTGAGC
5' ss Score
8.7
3' ss Seq
TTTTTCTCTTCTGCATGTAGGGG
3' ss Score
9.2
Exon sequences
Seq C1 exon
GGATCACCTGCTGGATCGCCCTGTATGCTGTGGAGGCCCTCCCCACCTGCCCTTTCTCCTGCAAGTGTGACAGCCGCAGCCTGGAGGTGGACTGCAGTGGCCTTGGCCTCACCACGGTGCCCCCAGACGTGCCCGCAGCCACCCGAACCCTCTTGCTCTTGAACAATAAGCTGAGTGCCCTGCCAAGCTGGGCTTTCGCCAACCTCTCCAGCCTGCAGCGGTTGGACCTGTCCAACAACTTCCTGGACCGGCTGCCCCGCTCCATTTTCGGGGACCTGACGAATCTGACTGAGCTTCAGCTGCGCAATAACAGCATCAGGACCCTGGACAGGGACCTGCTGCGGCACTCGCCGCTGCTCCGCCACCTGGACCTGTCCATCAACGGCCTGGCCCAGTTGCCCCCTGGTCTTTTCGACGGGCTCCTGGCTCTGCGCTCCCTCTCGCTTCGCTCCAACCGTCTGCAGAATCTGGACCGGCTGACATTTGAACCCCTAGCAAACCTGCAGCTGCTGCAGGTCGGGGATAACCCCTGGGAGTGTGACTGTAACCTGCGTGAGTTCAAACACTGGATGGAGTGGTTCTCCTACCGAG
Seq A exon
GTGAGCGCAGCCGGCCCTGCTGGGGCCCGAGGGATTGGGACGATCACCTCTGGCCCCACACTTTCCTCCTGGTGGCTGGGTGCTGACTCAGAGAGCAGGCCAGGGGAAAGAAGGGGGCGACCCTGCCTCTGTGCCAGCTCGGCTAGAAAAGTCACAAGCCTCCCCTCACATGAGCCATCACCCTTCCTGCCAATGGGAGAGAGGCTGGTGCTGCTCCCTCCACCCCCACCCTCCCCTCCCTGCTCTGCATCCCCTCCCCCAGCCAGCTCCCCACTTTCTCCTAGGACTCACTGAACTGGATCTCCCTTTCTTAGGTTACATAAGGGCAGTAAAGACACCTGGGCTTTGTATCCCGCCAAGTTTGCCTGTGGGCTTCCCCAGTGTGGTAGAAGGAGGGAGAAAAACAGCTCTTCTGAAGAATACAGCCATCTCTTAAACATCTCCCCTTACATGAGAGGGGAATAGAATGAATCCTCAGTAAAACCAAATCTTCCTTTTGGTGACAGTGCCAACTTCCTCTCCCAAGTTTTATTATCCAAACTTTAAGAAGAAGTCAAATGGGTTAGGCTTTACTTTCTTCCCTTCCCATTTTCTTTAATATGGGAAAGTGCTGTAATGACCTATGACATGATCACATGACATGGGAGAGGAGGGTGCGCAAGATGGTGGTGAGGAGGGCCAGGTCTGCGTCTGAATTTCGGCTCTGCCACCTGCCAGCTGTGTGATCTTGAGAAAGCTGGTTACCCTTTCGCTGTGGCAGGGCCTGGTCTGTAAAGTGGGAAGGAAACAATATCTATTTCGTAGGGTCATTATGAGAATTAAATGTGGCAATGCACGGAACGTGGCTTGAGAGGTGCCCAGCACAAAGTGAGTCCTCAATAAAACGTCCATTTATCCGTTCACTTCCTGGTAATAATCAAATACTAAGTGGACTTGAAACACCATTTGGCACGAAGAAGATGCTCAATGAATGTTTGCTGGGCTAAGGAATCAACATTTAAGTGGTGAAAATAATGCCAATGCTTTTTGTTAAAGTCTTACTACTTTCATTTAATCTCCAGCCACAATTTCAATTATTTCCATGAAATTCTCCTGTGTTAGTTAATTAAAAATGTTTTACAAACTATAAAGTGCCACAAAATGTTAGTCACTATGATCATTTCCCCCATTTTCATGAGCGGGGAAATAATGATTACTACTTATATAGTTTCCAGTTTACCAATGTCTTTTCATGTACATGATTTTAAACCTTACAGCAGCTAATTGAGATAGACCTTCTTATTTTACAGCTAAGAAAACTAAAACTCATAAGTAATTAAATAAATTAAATAATTTTCACAAGATGACACAGCCAGGATTCAACCGTGGGTCTTCCCAGCAGGGAAATGAGGCTGCATCCCTGTCAGCACCCAGCTTTGCATCCCCAGGCAGCACTGATACGTGTTCCTGGGATGTGAGGTTTGCTGCAGGCCACCGAGGTGTCAGCCGCACAGGGGAACTAGGCCGGGTGTCTTCAGACCCTCCTCTCCTGTGGTCGCCGGGAACTGAATTCCCAGCACAAAAATGCATGCCATGAGAATGTGCAGTTTTCAGACTTTTTCAATAGCGGAGTTGCTTTCAACATTGCATTTCTTAAAAACAAAATCCTGGAATATTTCCATCGGCATCCCAGGGAAAGATTGATGCCTATTGTATGAGGAGACTTGCGGCAGATGGGCTGCAGAGGGAGCTGCCAGTGACGGAGTGGCTGCAGCCCGCATCTTTTCGGCAGGGGGTCTAGTGCCTGCATCCAGATTTCACTGGAAGCTGAAAGAGGGCCAGAATCCAACTTTCACTTCCTAGGGGAGGTCTAGACAGATTATTGTCCTCAACCACCTTCTCTCTCACCCCAGCCCTGTCCTGCATCTGTGTCTCCCTCTGTCCAAGCCAGCCTCCACCATCATCATGAAGACATCCTGGCGAGCCCGTGCGCCCAGGTACCCACACCTCCTCATCAACACCAGCCTCCTCTCCTTGGCCTCGTGTGCCTCCAGGATTCCCCCTCCAGATGCCTTTGTACTTACAGGGCTGTGGTTGGGGCACCGATGGGGCCATTGGATTGCTCCTAAGGAGGAGAAGGAGAACATTCCTGCCCAACTCTTTTCCTCTTTACGCCAGGAAGGGAGCTGCCCATTCTTAGGCAACCAAAAGGTCTTGCGTGGAGGGGCAGCGGCAGGGGCAGTGGGTTTTGACTGCTGTCCTTTGAGTGAGAGGTAAGAACCCTAGAAGGATAAGATGCTGTGTTGAGAACGGTATCCTGGGCTCACAGACAGGTGATGAGCAGGCAGATTCGGGGGCAGAGAGTGTGGCAGGGACGCTCAGCTCTCTAATGACAGCCCTTTCCTGGGAACCTCCCCATGTTAGCACTGCCTTACTCTGTGGGTCCGTTTGGCCTGGGAGAGGACAGGCCGGATGGAAGTGGCTGCGTGCTTCTCTATAAAATGGGAATAAAGACAATATCCATTTCACATGGCTTCTGCGAGGATGAAATGGCACGATATACGTAACTCACTGTGGACTTGGCTCAATCAATGCTGTTTTCCCTCCTCCGCTTCCTCTTCTATAGATGGTGATTCCAGGATTGACTACATTGCTGATAAAAACTACCTTCTGGGGCTTCCGTTTTGGGGAGCTGGGGATGGGGAGAGGGAGTGCAAGTTCTAGATGCCTGGTCAGCCCCTCTTTTTCTCTTCTGCATGTAG
Seq C2 exon
GGGGACGCTTGGACCAGCTTGCCTGCACCCTGCCCAAGGAGCTGAGGGGGAAGGACATGCGGATGGTCCCCATGGAGATGTTCAACTACTGCTCCCAGCTGGAGGACGAGAATAGCTCAGCTGGGCTGGATATTCCTGGGCCACCCTGCACCAAGGCCAGTCCAGAGCCTGCTAAGCCCAAGCCCGGGGCTGAGCCGGAGCCGGAGCCCAGCACAGCCTGCCCACAGAAGCAGAGGCACCGGCCGGCGAGCGTGAGGCGAGCCATGGGCACGGTGATCATTGCAGGGGTCGTGTGCGGCGTCGTCTGCATCATGATGGTGGTGGCCGCTGCCTATGGCTGCATCTACGCCTCCCTCATGGCCAAGTACCACCGGGAGCTCAAAAAGCGCCAGCCCCTGATGGGGGACCCCGAGGGCGAGCACGAGGACCAGAAGCAGATCTCTTCTGTGGCCTGAGCGCCCATCCCCACCCGGCCAGGTAGGAAGGGCGGGGAGAGCACACGGCATTGCTCAGCCACAGCTCCCACCTTGACCCGGCGCTGGCCACTGCCTCCCCGAGTCCACCCTCCTCCCCGCCCTCCAGCAGACAAGCCACACCGGGTTCTCTCCCTGCACTTTCGAGGCTCCCTGAAAGCCACCGTGCTGGGGGCTCCTGCTGATGCTCCTGTCTGGGCCAGTAAATCTTTGGAACATGTGGGGGATCTCCCTAAGCTCTGGCCACAGCAAAGCAAGGAGGTGTGTGCAAGAGGAGGCTTCCGGACTGGGCATTCCCCTGTCGCCCTTCCTGCCCTGGGGTGGCCATAGCTGGTGACTCTTCCTACCTTGCTGGTCCCACCTCACCTGCATTGAGGGGACGGGGAGGGAGGGATCTGAGGGATGAAGGTAGATTTCTGAGACTCTCTCCTAAGCCAGAAAGACGTTCTTAACACCCCTGCAGTGTGAAAGCTGGTCCAGCTCTACAACTGTTGGTACCAATGTGCAAACACACCAGCCCTGCCATCTGGACCCAGCACTCAGAAACACCATACACCCCTGGCCGACGCCATCATGCCCCTGGATCTGCTATAGGCCACACTGACCACATGCTCCTGGATTCGCTAATTCACTCACACACCCATTGCATCACCAGTGCGGTCACATGGATTGAAAGAATTAATACACACACACACACACACACACTCACACGGTCACACGGAGACCGAGGCTATGAGCGCTCGAACAGCAGAGACATGCTCTTCCCCAGGGGTCTCCCTGAGACCACAGAGCCTCTCGCGTGCTCACTGCAATCTTCTCAAGTCAACAGCAGGAAGGAACTCAACCAGTAACACCAGGATCCTTTGAGATCCTCTAAAGTGGGCCAAAGTGGTGCCCCTGGAGGAGCCCTCCTGTCACCATGGTAACCCTCTCACACCTCTCCTGCTGGGCTTTCCCGGGATACCACCCAGGGGCCTGGAGCGGCTGCATGTGTGCATGGCGGCCTCCTGAGGACCCAGCCACACACCACTGGTGTTGCCTCGGTCCTGCCCACGCATCTCACAGCACCAGGCCCTGTGGGGCCCCCACTGATTCCTCCACAGCCTGCAGCCTGGCACCGTGACTCTGTGCCTCTCGCCCTCCATCTTCAGTACTCCTGGCCTGTGACTTCAGGGCTGGGACTTGGTGGTGCTTTGCCATTGGTGGCACCCTCTGGGGAAAGCAGGTGGCAGGCAGAGAACACGGTGGCTCCCCTGAGGCTCATTGCCTGCCAGCTTATTGCAGACAGAGCCCAGGAGCAGGAGCGGGTGGCCACGTGCTGCCCAGAGGCTCCCAGGATGGGGCCTCTGTTCCCGGGCTTTGTCTGCTCAGTGTGGCTCCCTAGAGCACCCAGCCGGGGCCAAACCAGAGAGTGGGTGGGGAGCCTGTCTGGGACAGAGCCACCTGCTGCCAAGGCAGTGCAAGTTTTCCAGGTTACCTGTCCCCCTCCCTAGCTCTGCCCCTCCTCAGAGTGTGAAGATGGTGGGTACCTAGGTGTCATGCTCACAGGCTCAGGAGGCATCAGGCTCGTCCCTGGCTCTGGGATGGAATCTCGATGGGGGCTCAGGAAGAGGCCAGCAAGAACCCTGAAGCCAAGGGTCTGAGCAGAGGGAGTTGGCAGGCCTAGCTCCTGTGCCCCACTCCGACCCTCCCTGCTCATGCGGCAGTGGGTGGGTGAGGTGGGCTGGGGGCCTGGAGGAGTGCCTTTGAGGAGGTCAGTCCTGGCAGGTGGACAGAGGACGCCTGGCATGGGCTGCTTACTGGGACCCCAGGCGGCCCTGGCCATGGCCACAGTCTTCCTTCTTTTGGCGTGTGGGCTGGTACCAGATCTGGGGATTTTCTAAAGGGACTGGGGGGAGGGGAGGGCATTGTCAATGGTGGTATCTTTAGCCTGAGACAGAAGATTTTTAAAGGCAAAATTATATTTCTGGTTTGTTGTTTCAGAAGACCAATAAAGACTGTATTTTCCTATGT
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000166159-LRTM2:NM_001163926:4
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.444
Domain overlap (PFAM):
C1:
PF0146213=LRRNT=WD(100=15.2),PF138551=LRR_8=WD(100=30.8),PF127992=LRR_4=WD(100=23.2)
A:
NA
C2:
PF0248011=Herpes_gE=WD(100=57.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal4)
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
- Pre-implantation embryo development
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)