MmuINT1022136 @ mm10
Intron Retention
Gene
ENSMUSG00000026943 | Lcn12
Description
lipocalin 12 [Source:MGI Symbol;Acc:MGI:1924951]
Coordinates
chr2:25493222-25493911:-
Coord C1 exon
chr2:25493743-25493911
Coord A exon
chr2:25493359-25493742
Coord C2 exon
chr2:25493222-25493358
Length
384 bp
Sequences
Splice sites
5' ss Seq
CAGGTACAG
5' ss Score
8.68
3' ss Seq
GCCCACCACCAGCCATGCAGTTT
3' ss Score
-3.5
Exon sequences
Seq C1 exon
CCAGCAGCCGCTCCTCGGGCAGGCTGTGTCCTTCTGGAGCCTGGTGGCTGTTGGGATGGGCCCTTGGTGGGCTCTGTGGCTGATACTCACCCTGCCCCAAATCCTGGAGAGTCAGATCTCAGCCATGTCTCAAGGCTTTCCCCAGATGACAAGCTTCCAAAGTGACCAG
Seq A exon
GTACAGGGCTTTCAAAGGAGAAGAAGCAGGTGGCAGCTGGCCAGGGTCCCGGCTTGTGGAGGGAGGGAGCATGCAGGCCTGTGGGCACTGCTCAGGGAGGCCAGGGCAGAACCTGAATTAAGAGTGAACCCATGACCAATAACTTTCTGTACTTACACTAATAGCTTCCTCCATGAAAGGAGATGAGCAGAGACTTGGGACCACCACCTGGCTCCCGGCCAAGGCCACCTTCTACCTGGCAGATCAAAGGCAGATTGAAGGTCTGCCAATGTCACTGACATAGACCTGGCCTGCAGTTGCCTCCTAAGGAGAGGTCCTAGCTGACTGTGGGCTGCTCAGGGTAGGGTGGGCAGGGGCTACCTATGCCCACCACCAGCCATGCAG
Seq C2 exon
TTTCAGGGAGAGTGGTTTGTCCTCGGTCTGGCAGACAACACCTTCAGGAGAGAGCACCGGGCCTTGCTGAATTTCTTCACTACATTGTTTGAGCTGAAAGAGAAAAGTCAGTTTCAGGTGACCAACTCCATGACTCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026943:ENSMUST00000028312:1
Average complexity
IR
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(30.1=95.7)
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
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:
CTCCTCGGGCAGGCTGTG
R:
CGAGTCATGGAGTTGGTCACC
Band lengths:
296-680
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- 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