MmuINT0090240 @ mm9
Intron Retention
Gene
ENSMUSG00000026943 | Lcn12
Description
lipocalin 12 [Source:MGI Symbol;Acc:MGI:1924951]
Coordinates
chr2:25347951-25348878:-
Coord C1 exon
chr2:25348742-25348878
Coord A exon
chr2:25348028-25348741
Coord C2 exon
chr2:25347951-25348027
Length
714 bp
Sequences
Splice sites
5' ss Seq
TCGGTGAGT
5' ss Score
11.11
3' ss Seq
CCTGCCTATCCCTCCCACAGGGG
3' ss Score
11.51
Exon sequences
Seq C1 exon
TTTCAGGGAGAGTGGTTTGTCCTCGGTCTGGCAGACAACACCTTCAGGAGAGAGCACCGGGCCTTGCTGAATTTCTTCACTACATTGTTTGAGCTGAAAGAGAAAAGTCAGTTTCAGGTGACCAACTCCATGACTCG
Seq A exon
GTGAGTGGGGTGTCTGTTGTGCAAGCAGTCAAGGACTTGGGGCTGTGTTCTGGGAGCCTGGCATGGCCTAGACATACTGCGGGTTGAGGAACCACATTTGGAGGCCATGCCTAGCACAGCCTGCTTAATGACATAAAGTCCAACCCAGCTGATGGGCTGAAGACCAGAGGAAGGCATCTGGTGACTTACTCGGGCCAGTGTGACTTACCAGATGGGTTTTGGAGACTCTTGTGTGGTCAGGGAACCCTTTCTCGGTCTCTGTCTTGGTTCTGCCTGCCCTACCTTGATTTCTTGGGCAGGTTCTTGTTCTCTTAGTCTCAACAGTGGCAGACAGCTCCAATTTGTAGTCTGTTCTTGACCCTTTTTGGAGCTAGTTGGCTTGGGTGCCAGAGGGGGCTAGCTGCTGAGACCCAGAAACGCTTTCTTTTTAACATGACAAGTCCCTGTAGATTTGAGTCCCTGTGCTTGCTTGAGCAGGAGCCACTCTTGTGGCATTGGGCCAGACTTCTAGGAAGGGCACAGAGTAGCTGAGAGGATCCCAGAGCCAAGGCCTGGGGAACGGGGGAGGCCTCCAGTCCTCTCCATCCTTCTGGGATGCAGACCCCTCCAAATGAATAGCTGGATATTTTTTTTTCTTGGTGGTCTACCAAGATGGGCCTGGTTGACTTCCTTAGTCTTCTGCCCCACCTCTGCCCCTGCCTATCCCTCCCACAG
Seq C2 exon
GGGCAAGCACTGCAACACTTGGTCCTATACCCTGATCCCAGCAACCAAGCCTGGGCAATTCACCAGGGACAACAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026943-Lcn12:NM_029958:2
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.259
Domain overlap (PFAM):
C1:
PF0006118=Lipocalin=PU(30.1=95.7)
A:
NA
C2:
PF0006118=Lipocalin=FE(17.8=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:
TTTCAGGGAGAGTGGTTTGTCC
R:
CTCTGTTGTCCCTGGTGAATTG
Band lengths:
214-928
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: