MmuINT0090244 @ mm9
Intron Retention
Gene
ENSMUSG00000062061 | Lcn13
Description
lipocalin 13 [Source:MGI Symbol;Acc:MGI:2387617]
Coordinates
chr2:25555594-25556363:+
Coord C1 exon
chr2:25555594-25555697
Coord A exon
chr2:25555698-25556229
Coord C2 exon
chr2:25556230-25556363
Length
532 bp
Sequences
Splice sites
5' ss Seq
GATGTGAGG
5' ss Score
4.17
3' ss Seq
CACAGTTTTGTCTCCTACAGTAC
3' ss Score
7.66
Exon sequences
Seq C1 exon
GAGCCCAGTGCCTGGAGATGAAGAGCCTGCTCCTCACCATCCTGCTGCTGGGGCTGGTGGCTGTCCTGAAGGCTCAGGAAGCCCCGCCAGATGACCTGGTGGAT
Seq A exon
GTGAGGATGGGAGGGACAATGGGTGGTGGCAGGAGATGGCCTGGCCTACTGCTTGACGCTGAGGGGAAGGATGTTACCTTGAAGGTTGAGTTTGACTCCATACTTCATCTCAGCAGTCTGATCAAGGACTCCTGAGTCCTTCTGTTAGAAGATAGGGGCCTCCCTGAAAACATGGGTCCTCCGAAGACTTGAGTTAGAAGAAAGAGCAGATTTGGGTGGAGGATCCTTGTTCAAGTAAAGCTCAGAGCTAGAACATTTAGAGCAGGACGTTCCGGGCAGAGGATTCATCCAGTGCCCTCTTTGACGTGTAGACCTCAATGAGTGCATTCACTGGGATGGGGGAAGACACTTCTGCCATCATGGGATTGGGTACCCAAGTGCTGGTATCTCTCTATTGACCACACGTCTTGGAACATGTGAGGTTAGCTCACCTCAGTGGCTGCACCCTGGGCTCAGGAGCTAGCTCATATGCTGGACCCTGGGGTAGACTCCTGGGAAGGCTCGGGTGTGCTCACAGTTTTGTCTCCTACAG
Seq C2 exon
TACTCTGGGATCTGGTACGCAAAGGCCATGGTACACAATGGTACCCTACCCAGTCACAAGATACCCAGTATAGTTTTCCCTGTGAGAATAATAGCTCTGGAAGAAGGAGACTTGGAGACCACAGTTGTATTCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000062061-Lcn13:NM_153558:1
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0006118=Lipocalin=PU(30.7=95.6)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Human
(hg38)
No conservation detected
Rat
(rn6)
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:
CAGTGCCTGGAGATGAAGAGC
R:
CAGAATACAACTGTGGTCTCCAAGT
Band lengths:
233-765
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: