MmuINT0090242 @ mm10
Intron Retention
Gene
ENSMUSG00000026943 | Lcn12
Description
lipocalin 12 [Source:MGI Symbol;Acc:MGI:1924951]
Coordinates
chr2:25492008-25492363:-
Coord C1 exon
chr2:25492241-25492363
Coord A exon
chr2:25492110-25492240
Coord C2 exon
chr2:25492008-25492109
Length
131 bp
Sequences
Splice sites
5' ss Seq
TGGGTGAGT
5' ss Score
8.73
3' ss Seq
ATGTTGTCCTCTGGCCACAGGTA
3' ss Score
9.65
Exon sequences
Seq C1 exon
GGTCAGGGCCTGGGGCAGACAGAGAGAATATACAGGTCATAGAGACAGACTACATCACGTTTGCCCTGGTGCTGTCCCTCAGACAGACAAGCAGCCAGAACATCACAAGGGTCAGCCTTCTGG
Seq A exon
GTGAGTCCCTGCTTCCCTGGGCCCTATGCATAACCTTCCTCAGGAGGGTGCTTTCCTGGGTTTGGGACAGCTTGGGGGCAAATACCTCTCTACCGAAAAGTACTGAGAGCCATGTTGTCCTCTGGCCACAG
Seq C2 exon
GTAGAAACTGGAGACTTTCTCATAAGACAATAGACAAGTTCATCTGCCTGACCAGGACCCAAAACCTCACAAAGGATAACTTCCTCTTTCCTGATTTGAGTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026943:ENSMUST00000028312:4
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.167 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0006118=Lipocalin=FE(28.1=100)
A:
NA
C2:
PF0006118=Lipocalin=FE(23.3=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:
CCTGGGGCAGACAGAGAGAAT
R:
CACTCAAATCAGGAAAGAGGAAGT
Band lengths:
217-348
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