MmuINT0090054 @ mm9
Intron Retention
Gene
ENSMUSG00000008206 | Lass4
Description
LAG1 homolog, ceramide synthase 4 [Source:MGI Symbol;Acc:MGI:1914510]
Coordinates
chr8:4516873-4518358:+
Coord C1 exon
chr8:4516873-4516990
Coord A exon
chr8:4516991-4518239
Coord C2 exon
chr8:4518240-4518358
Length
1249 bp
Sequences
Splice sites
5' ss Seq
GAGGTGAGC
5' ss Score
8.7
3' ss Seq
CCTCATTACTCCCTTCTCAGACA
3' ss Score
7.02
Exon sequences
Seq C1 exon
ATTTGTGGCCTTGCCCCTGAGCCGGTGGATGGGTGTGCAGGATCCAATCAGGAGAAAGATAAAGCCCAACCCGGTGCTGGAGAAGTACTTCCTCAGGATGAAGCAGTGTCCAGAGGAG
Seq A exon
GTGAGCCCCATATTCTCTAGACAGCTGCATGGTGATTGCCCTGGGACCCAGGCATAGAAGTGGTGTGTGTCCCTTATTAGAGGTTGGACAGGGACCTCTGACACACCCACAGATTCAACTTGAACCCACAGATTCCCTGGTATGTTAGGCTCTCTCCTCTGTCTGCTGGTTTGTGAGACCCCCACCTCTTCCTGCTGTGCAGAGACTAGTGGATCAGTCACTCCTTCCCTGGTTCTGCGGGGCTTGAAACCACTTCTCTCTCAGTACGAGGCTACTCTTCCTAGCCTCAAGGCTTTGAAGCCCCATCCCTCATCTATCTCTTGAAAGCAAGGCCATGTTCCTCATCTCCCTGAGCCAAGAGTATCTGCCCGTTTAGGCTTCCTGGGTATGAAGCCCTGCCCTTCCTGTTCTCCTTGGGACCTGGGGAAACCTTATTTTCAAGGTCTTGAGGCATAAAATTGTCCTTGTGTAGCCTTTCTGGGACACAAGGCCATGTCTCTCTCTCCTGGTCTTCCTGAGACTTGAAGGTCCCATCCTTCTCAGGGTTCCCAGAGTTTGAAACTGGCATTCCAGCCTTCCTGGGTCATGAGTCTCTGTACCTCTAGGCTTCTTGGGGTTTAAGGCCCTGCTCCTTCCTCCCAGGTTTCTTGGGACATGAGGTCCTACCACTGTGAGGCTTCCTGGCATATGAAGCCCTCCTCTCTTAGTCTGGAACATCAACCTTATGATCACTCAACAAACAGAAGAGTAGGTTTCGTCCCAGTTCTGGGAAGGGACAAGATGCTTTTGATCCAGTGGAGTGCCTGGAGTGTCAGAAGCAGCCCTGTGGTTCTGCCTCCATTCCCATCCATGGTGTGGCAGCCCAGTTGGCCTGGTCTGGGTCAGGTTCTGTTGGGTAAGGTGGACGTGATGGCAGTGTGCCCTGTCTGGGAATAGAATAGCTTCTATAGAGCTGAGAGCTGAGTGCCTGCCTAGGGTAGTGTCCTACTCTGCTGCTTGTTGCAGTGCAAACAACTGCAAGCTGGAGAAGAAAGGGTTCATTTCAACTTAAACTTTCAGGTAACAGTCCATTGCTGAGGGAAGTGAAGGCAGGAAGTGAAGGCAGGAACTGAAGTAGATGCCACCTTACCCTCCTCTCTTTTCTCTGTGGGATAGATCTTAAGCTTCAGTGGGGAATCAAAGTAGGAACAAAGGGTACGAAACCGGCATTGGGCCTGTATAATCCTTCCCCTCATTACTCCCTTCTCAG
Seq C2 exon
ACACAGATGGTCCTGCTGGCTTCCCAGTGTGGCCTCACGCTTCGGCAGACTCAACGCTGGTTCAGGAGACGTCGGAACCAGGATCGGCCTTCCTTATCCAAGAAATTCTGTGAAGCCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000008206-Lass4:NM_026058:3
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0004624=Homeobox=PU(35.4=42.5)
A:
NA
C2:
PF0004624=Homeobox=PD(60.4=72.5),PF0379811=TRAM_LAG1_CLN8=PU(2.6=12.5)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCTGAGCCGGTGGATGGG
R:
CAGGCTTCACAGAATTTCTTGGA
Band lengths:
222-1471
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: