MmuINT0090289 @ mm10
Intron Retention
Gene
ENSMUSG00000036449 | Lcn8
Description
lipocalin 8 [Source:MGI Symbol;Acc:MGI:2135945]
Coordinates
chr2:25655115-25655388:+
Coord C1 exon
chr2:25655115-25655219
Coord A exon
chr2:25655220-25655298
Coord C2 exon
chr2:25655299-25655388
Length
79 bp
Sequences
Splice sites
5' ss Seq
TCAGTAAGT
5' ss Score
9.14
3' ss Seq
CACTCTGTTGTGCCCCACAGCTC
3' ss Score
9.69
Exon sequences
Seq C1 exon
GTAACAGGGAGATCCACGTGCTGGACACGGACTATGAGCGCTACACCATCCTGAAGTTGACCCTGCTCTGGCAGGGTAGAAACTTCCATGTGCTCAAGTACTTCA
Seq A exon
GTAAGTTCCGCCTGGGCTGGGCTCTGCCCTGCGACTACCTTCCTTCAGGCTGCCAGCCCCACTCTGTTGTGCCCCACAG
Seq C2 exon
CTCGGAGCCTTGAGAACGAGGATGAGCCAGGCTTCTGGCTGTTCCGGGAAATGACAGCAGACCAAGGCCTTTACATGTTGGCCCGACATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000036449:ENSMUST00000038482:4
Average complexity
IR
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(27.6=100)
A:
NA
C2:
PF0006118=Lipocalin=PD(19.7=80.6)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TAACAGGGAGATCCACGTGCT
R:
TTGGTCTGCTGTCATTTCCCG
Band lengths:
169-248
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- Ribosome-engaged transcriptomes of neuronal types
- Neural differentiation time course
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types