MmuINT0090272 @ mm10
Intron Retention
Gene
ENSMUSG00000026919 | Lcn4
Description
lipocalin 4 [Source:MGI Symbol;Acc:MGI:102668]
Coordinates
chr2:26667674-26668363:-
Coord C1 exon
chr2:26668337-26668363
Coord A exon
chr2:26667898-26668336
Coord C2 exon
chr2:26667674-26667897
Length
439 bp
Sequences
Splice sites
5' ss Seq
GTGGTAAGT
5' ss Score
10.36
3' ss Seq
TGTATATCTCTCTGTCACAGCCC
3' ss Score
8.96
Exon sequences
Seq C1 exon
ATCGGTGTATTCCCATACATGACAGTG
Seq A exon
GTAAGTGACCCTCTGAAGAAACCCTGAGAGAACTCAGATTCCTCTGTTCCATGGTGGATGTTTTTATCTGTTGTTGACCCATCTCTCAACATCCCACTCAGGAAGGAATGTGCTTAGCCAGGAAGCAGTGACCACTCCAGGAGGAGTCCTCAAGTGGAATTCTTGGATACTTGGGAATTCCATCATTCATTTTCCTTGAGTTCTGCCTTTGCAGTGGTCTATTTTCATGCCTTAGGTACCCACAAAGCTGATTAGAGATCTAAAATGTCAAGGAAGTTAGGATACTTCTGTGGCCCATGTATTCTCAGGATGAAATTCCCAAAGGCTCAATGAATGGAAAAATTTTAATAGGCATGTATCTCCTAAGTAGCTACTCTCCGACAGCTATTGCCGTGATAGAGGGAGGGATCTCTCAGTTGTGTATATCTCTCTGTCACAG
Seq C2 exon
CCCACCAGGACCACAAATGCTGAGACAGACTTGCCAGTAGGACCTGACCATGACCTTAGTGGACTGACTACTATTCTTCCTGGACAACATTTCTCTGAGCTGCATTTCCCCAATCTGTGTTCTACTCCTTAAATTGTACCACCCTCTGGACTTCCTAAGCTCCTGATTTACCTTCTAACCCTTGCTCTGAGACCCCTCTGAATCCAATAAAAAAATTAGCAGTT
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026919:ENSMUST00000028283:6
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.150 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0006118=Lipocalin=PD(0.1=0.0)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Human
(hg38)
No conservation detected
Human
(hg19)
No conservation detected
Rat
(rn6)
No conservation detected
Cow
(bosTau6)
No conservation detected
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:
TCGGTGTATTCCCATACATGACA
R:
TTTTATTGGATTCAGAGGGGTCTCA
Band lengths:
238-677
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