MmuINT0090241 @ mm9
Intron Retention
Gene
ENSMUSG00000026943 | Lcn12
Description
lipocalin 12 [Source:MGI Symbol;Acc:MGI:1924951]
Coordinates
chr2:25347761-25348027:-
Coord C1 exon
chr2:25347951-25348027
Coord A exon
chr2:25347884-25347950
Coord C2 exon
chr2:25347761-25347883
Length
67 bp
Sequences
Splice sites
5' ss Seq
GAGGTGAGA
5' ss Score
7.66
3' ss Seq
CTGACATGTGTGTCCCTCAGGGT
3' ss Score
9.98
Exon sequences
Seq C1 exon
GGGCAAGCACTGCAACACTTGGTCCTATACCCTGATCCCAGCAACCAAGCCTGGGCAATTCACCAGGGACAACAGAG
Seq A exon
GTGAGAGAGACATGGGTGTGCGGGAGGGACATGGCTGTCTTGGGAACCTGACATGTGTGTCCCTCAG
Seq C2 exon
GGTCAGGGCCTGGGGCAGACAGAGAGAATATACAGGTCATAGAGACAGACTACATCACGTTTGCCCTGGTGCTGTCCCTCAGACAGACAAGCAGCCAGAACATCACAAGGGTCAGCCTTCTGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026943-Lcn12:NM_029958:3
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.259 A=NA C2=0.167
Domain overlap (PFAM):
C1:
PF0006118=Lipocalin=FE(17.8=100)
A:
NA
C2:
PF0006118=Lipocalin=FE(28.1=100)
Main Inclusion Isoform:
NA
Other Inclusion 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:
GCACTGCAACACTTGGTCCTA
R:
CTGGCTGCTTGTCTGTCTGAG
Band lengths:
169-236
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: