MmuINT0093652 @ mm9
Intron Retention
Gene
ENSMUSG00000024399 | Ltb
Description
lymphotoxin B [Source:MGI Symbol;Acc:MGI:104796]
Coordinates
chr17:35331452-35332310:+
Coord C1 exon
chr17:35331452-35331628
Coord A exon
chr17:35331629-35331994
Coord C2 exon
chr17:35331995-35332310
Length
366 bp
Sequences
Splice sites
5' ss Seq
CGGGTGAGT
5' ss Score
9.89
3' ss Seq
AACCCTACCTACCCATCCAGGTT
3' ss Score
6.89
Exon sequences
Seq C1 exon
TAGTTCTGAGTCTGGATGGGGACACGGGGACTGCAGGGCCTGGGTGGGAGACCCCAGGGGAGGGGCTGCCTCTTGCTGGCTGTGGCAGGAGCTACTTCCCTGGTGACCCTGTTGTTGGCAGTGCCTATCACTGTCCTGGCTGTGCTGGCCTTGGTGCCGCAGGATCAGGGACGTCGG
Seq A exon
GTGAGTGGCTGCAACGGGCTCCAGAGGGCTGCCTCTTGTGACTGTTTATTTACTTATGGCTGTGCTTCTGCCCACCGCGCTCAGCTGGCCGCTCTCCCCAGAGGGAATGTCTGGTCTGTCTTTGCCTCTCCAGGCAATCCTAGCCTGAATTTTCAAGCCCCTTCCTGGTTGGCTTCTTTTCCAGATAACACTGCACTTGCGTCTCTCTGCCTGCATACATCGTCTTTGTTTGTTCTTCTAGCAAGATGCAGTCTAGGGAGGACACAGCAGGCCCAGGCCTTGGGGCTGGGCTCTACGGTGGGAGGGGTGGAGTTGCCATTAGCCAAATCTGACCTCTGGGCACTCTAACCCTACCTACCCATCCAG
Seq C2 exon
GTTGAGAAGATCATTGGCTCAGGAGCACAGGCTCAGAAAAGACTGGATGACAGCAAACCGTCGTGCATCTTGCCCTCACCCTCTAGCCTCTCAGAGACTCCTGACCCCCGTCTGCATCCTCAGAGATCCAATGCTTCCAGGAATCTAGCCTCCACATCCCAGGGCCCTGTTGCGCAGTCCTCTCGGGAGGCATCTGCATGGATGACCATCCTGTCTCCAGCTGCGGATTCTACACCAGATCCAGGGGTTCAACAGCTGCCAAAGGGGGAACCAGAAACTGACCTCAACCCTGAGCTCCCTGCTGCCCACCTCATAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000024399-Ltb:NM_008518:1
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.167 A=NA C2=0.868
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
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:
AGGAGCTACTTCCCTGGTGAC
R:
GCTGTTGAACCCCTGGATCTG
Band lengths:
347-713
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types
Other AS DBs: