HsaINT1022233 @ hg38
Intron Retention
Gene
ENSG00000227507 | LTB
Description
lymphotoxin beta [Source:HGNC Symbol;Acc:HGNC:6711]
Coordinates
chr6:31581559-31581859:-
Coord C1 exon
chr6:31581814-31581859
Coord A exon
chr6:31581631-31581813
Coord C2 exon
chr6:31581559-31581630
Length
183 bp
Sequences
Splice sites
5' ss Seq
TGGGTAAGA
5' ss Score
8.91
3' ss Seq
GGACTCTTTGCCCCTTCCAGGGT
3' ss Score
7.75
Exon sequences
Seq C1 exon
GTAACGGAGACGGCCGACCCCGGGGCACAGGCCCAGCAAGGACTGG
Seq A exon
GTAAGAGCAGACTGTCTCTCCTTCCCCGCTTCAGACCCTCAGGGGCTCCCAGCTCCCTGCTGCGTCCCCAGATACCTCTTCCTCTAGGAATCCAGGCTCCCCATCCCTGCGCCCTGTTCTCTCAAGGGTAGCCTGCATGGGTGGCTGCCCTGCCCCCAATCGTGGACTCTTTGCCCCTTCCAG
Seq C2 exon
GGTTTCAGAAGCTGCCAGAGGAGGAGCCAGAAACAGATCTCAGCCCCGGGCTCCCAGCTGCCCACCTCATAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000227507:ENST00000429299:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.750 A=NA C2=0.646
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
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:
CACAGGCCCAGCAAGGAC
R:
CTATGAGGTGGGCAGCTGGG
Band lengths:
93-276
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains