HsaINT1022232 @ hg38
Intron Retention
Gene
ENSG00000227507 | LTB
Description
lymphotoxin beta [Source:HGNC Symbol;Acc:HGNC:6711]
Coordinates
chr6:31581814-31582425:-
Coord C1 exon
chr6:31582256-31582425
Coord A exon
chr6:31581860-31582255
Coord C2 exon
chr6:31581814-31581859
Length
396 bp
Sequences
Splice sites
5' ss Seq
CTGGTGAGT
5' ss Score
10.1
3' ss Seq
CTGTGACCCCACCCAACCAGGTA
3' ss Score
5.68
Exon sequences
Seq C1 exon
CAGTCTCAATGGGGGCACTGGGGCTGGAGGGCAGGGGTGGGAGGCTCCAGGGGAGGGGTTCCCTCCTGCTAGCTGTGGCAGGAGCCACTTCTCTGGTGACCTTGTTGCTGGCGGTGCCTATCACTGTCCTGGCTGTGCTGGCCTTAGTGCCCCAGGATCAGGGAGGACTG
Seq A exon
GTGAGTGGCTGCAACAGGCCCTGGTGGAGAGTTGTATCTTGCGGATGCTTGGCTCCCTCTGGTTGTGCCTGTGGTCTTTTGCCCCCTCTGGCTCAGCTGGCTCGGCTGTCCCTGGTGGGGATGTCTTGTCTCTTTGCTGACTCTCTTTCCATGTTCCTGTGATGTTGTGCTTGTGTCCCGACATAAGCCCCTTGTGTCTCCTCTCCTCTTCCCGAGGTACATCTGTTTCTCCGCCCAAGTACCTATGCCTTGCTTGTTCTCCCTTCTAAGGAGGTGTGTGTTGGGGATGGTGCTGGTAGGAGAAACCCCAGGCCTGCAGCTTGGGTCCACTTTCAGAGGGGTAGGGGTGACATGAGCTGAATCTGAACTCTGGGCACTGTGACCCCACCCAACCAG
Seq C2 exon
GTAACGGAGACGGCCGACCCCGGGGCACAGGCCCAGCAAGGACTGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000227507:ENST00000429299:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.750
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
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:
CAGTCTCAATGGGGGCACTG
R:
AGTCCTTGCTGGGCCTGT
Band lengths:
214-610
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains