MmuINT0063785 @ mm10
Intron Retention
Gene
ENSMUSG00000026938 | Fcna
Description
ficolin A [Source:MGI Symbol;Acc:MGI:1340905]
Coordinates
chr2:25627278-25627549:-
Coord C1 exon
chr2:25627436-25627549
Coord A exon
chr2:25627332-25627435
Coord C2 exon
chr2:25627278-25627331
Length
104 bp
Sequences
Splice sites
5' ss Seq
GAGGTAGCA
5' ss Score
4.75
3' ss Seq
TTTAGTCCTTGTGTTTACAGGAG
3' ss Score
8.17
Exon sequences
Seq C1 exon
ATGTTAAGGTCGTAGGTCTGGGGGCCCAGGACAAGGTGGTTGTCATCCAAAGTTGCCCTGGCTTTCCTGGCCCACCTGGGCCCAAAGGGGAGCCTGGAAGCCCTGCTGGAAGAG
Seq A exon
GTAGCAATCTGGATGGGAGAGGGATTCCCCTTAGCCTCCCCTTGGCCCAGCTCCCTCCAATCCTACCTAGGAGATGAGATCCAGTTTAGTCCTTGTGTTTACAG
Seq C2 exon
GAGAACGGGGCTTTCAGGGCAGCCCAGGAAAGATGGGACCTGCCGGCAGCAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026938:ENSMUST00000028307:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.590 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PU(32.8=51.3)
A:
NA
C2:
PF0139113=Collagen=FE(29.5=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGTTAAGGTCGTAGGTCTGGGG
R:
CTGCCGGCAGGTCCCATC
Band lengths:
162-266
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