MmuINT0063784 @ mm9
Intron Retention
Gene
ENSMUSG00000026938 | Fcna
Description
ficolin A [Source:MGI Symbol;Acc:MGI:1340905]
Coordinates
chr2:25482956-25483494:-
Coord C1 exon
chr2:25483269-25483494
Coord A exon
chr2:25483070-25483268
Coord C2 exon
chr2:25482956-25483069
Length
199 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGA
5' ss Score
9.22
3' ss Seq
TTTTTTTTTTTTCTATGCAGATG
3' ss Score
11.83
Exon sequences
Seq C1 exon
TTTTAACTTGCACTCCTTCTCAGGAGAAAAAGCTGAGCCGTGAGGAATCCAGGCAGTGAGGGTCTTCACTTCGTTCATCAGTGCCTCAGCCTCCGTCCAGAGCCAGGGAGTCAAGGAGTGGCTGCTGTACCCAGAGCAATGCAGTGGCCTACGCTGTGGGCCTTTTCAGGACTGCTCTGTCTCTGTCCCTCCCAGGCCCTGGGTCAGGAGAGAGGTGCCTGTCCAG
Seq A exon
GTGAGAGGGGTCTGCTCAGAAGTGTGGGCACACACATACCTGCATATGCCTGCACATGTGGCAGCAGGAGATGGGACATTTTAGAAGGGCAGCCTGAAAACACATCCAGAGACAGGCTGCATGAATGCTAGTGGGTACGGAGAGCTGTGGTTTTCAATGCTGCTCCAAAGCCACCCCTCTTTTTTTTTTTTCTATGCAG
Seq C2 exon
ATGTTAAGGTCGTAGGTCTGGGGGCCCAGGACAAGGTGGTTGTCATCCAAAGTTGCCCTGGCTTTCCTGGCCCACCTGGGCCCAAAGGGGAGCCTGGAAGCCCTGCTGGAAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026938-Fcna:NM_007995:1
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=0.017 A=NA C2=0.513
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0139113=Collagen=PU(32.8=51.3)
Main Inclusion Isoform:
NA
Other Inclusion 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:
AATCCAGGCAGTGAGGGTCTT
R:
CCAGGGCAACTTTGGATGACA
Band lengths:
242-441
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
Other AS DBs: