MmuINT0090288 @ mm9
Intron Retention
Gene
ENSMUSG00000036449 | Lcn8
Description
lipocalin 8 [Source:MGI Symbol;Acc:MGI:2135945]
Coordinates
chr2:25510265-25510739:+
Coord C1 exon
chr2:25510265-25510335
Coord A exon
chr2:25510336-25510634
Coord C2 exon
chr2:25510635-25510739
Length
299 bp
Sequences
Splice sites
5' ss Seq
CTGGTAAGT
5' ss Score
10.65
3' ss Seq
TGCCACTGCCACTCCTGAAGGTA
3' ss Score
4.68
Exon sequences
Seq C1 exon
CTCAGGAAGTTGTGTGACAGAAAGTTCACTGGGTTCAGAAAGAGACACTGTGGGGGAATTTGCTTTTCCTG
Seq A exon
GTAAGTACTGTTGCCTTGTTGCTGAAGTTGCAGCTGCTGTCTGAGCCTGGACATCTCCCCCTGGCCTCGCTTCCTGTGCCCTTCCAAGGATTCTCAGGCCCTGGACTCCAGCCCCCTCATCTCTACTAGTGTACTGAGTTGATCTTCAGAATTTGTCTTCTCAGATGTCACAGGCAGGTCCCAGCACTAGGCAGAAATAGAAAGGAGTTAGATTCTGCAAATCCAGCCTTCAAGGTCAGCTCCCTGGAGTGTTCAGGTCTGAGCAAGCCTCCTTAACCCTGCCACTGCCACTCCTGAAG
Seq C2 exon
GTAACAGGGAGATCCACGTGCTGGACACGGACTATGAGCGCTACACCATCCTGAAGTTGACCCTGCTCTGGCAGGGTAGAAACTTCCATGTGCTCAAGTACTTCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000036449-Lcn8:NM_033145:3
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:
PF0006118=Lipocalin=FE(18.9=100)
A:
NA
C2:
PF0006118=Lipocalin=FE(27.6=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTCAGGAAGTTGTGTGACAGA
R:
TGAAGTACTTGAGCACATGGAAGT
Band lengths:
176-475
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: