MmuINT0090247 @ mm9
Intron Retention
Gene
ENSMUSG00000062061 | Lcn13
Description
lipocalin 13 [Source:MGI Symbol;Acc:MGI:2387617]
Coordinates
chr2:25557082-25557798:+
Coord C1 exon
chr2:25557082-25557195
Coord A exon
chr2:25557196-25557696
Coord C2 exon
chr2:25557697-25557798
Length
501 bp
Sequences
Splice sites
5' ss Seq
TGGGTGAGG
5' ss Score
6.74
3' ss Seq
ACCTGCCCCCCTCCTCACAGGGA
3' ss Score
11.31
Exon sequences
Seq C1 exon
TTCATAACACGAAGGTTATTCATGTGGAAAAGACGTCGGTGAATGAGCACTACATTTTCTACTGCGAAGGCCGGCACAATGGGACGTCGTCATTCGGGATGGGAAAGCTCATGG
Seq A exon
GTGAGGTGCCATGGAAGCCCCATGTCCCGTCCCTGGTCTCTACTTCTGGTAGCCACGAGAAGGGCAGGAGATGGGCCTGGCACTGGTGCTGCCCAGGAAATGTGTGAGATCCAAAGTGGAAAATGGGGAAAACTGCTTAGGAATGGGGTTTGTGTGGCCTTTGGAGGCCTGAGTGCTCAGGAGTGGGTCCCACACCTGGAGCCAGCAAATGCTACTCCCAGGGCTCTCAGTCACGTGAACATAAAAGGACGTCTTGGCAGGGACATTTTATTGTAGGTAAGAACCCTCCAGGGCCGGGGACAGCCTCATGACCTTGAGATTCAGTGTTCATATAGGGCTGTGTGGCAACCCCGCAGGTCTGCTTGGGTCTGAGGACGTCCACAGGTGATGTCTACTGCCAGGGTCCTCTCTGACCTCTGTCCTGGTTTGCACCTCCCTCTTGTGTCTCTGGCTCTCTGCGGAGCTGAGTGCCACCCCTCAAACCTGCCCCCCTCCTCACAG
Seq C2 exon
GGAGAGACTCTGGTGAAAATCCAGAGGCCATGGAAGAATTTAAGAATTTCATAAAGCGCATGAATCTCCGACTGGAAAACATGTTTGTGCCAGAGATCGGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000062061-Lcn13:NM_153558:4
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.179 A=NA C2=0.143
Domain overlap (PFAM):
C1:
PF0006118=Lipocalin=FE(27.1=100)
A:
NA
C2:
PF0006118=Lipocalin=FE(24.3=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CATAACACGAAGGTTATTCATGTGGA
R:
CTCCGATCTCTGGCACAAACA
Band lengths:
214-715
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: