HsaINT0065113 @ hg19
Intron Retention
Gene
ENSG00000184922 | FMNL1
Description
formin-like 1 [Source:HGNC Symbol;Acc:1212]
Coordinates
chr17:43323577-43323971:+
Coord C1 exon
chr17:43323577-43323697
Coord A exon
chr17:43323698-43323871
Coord C2 exon
chr17:43323872-43323971
Length
174 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGG
5' ss Score
11.08
3' ss Seq
CCTGCCCCACCCCCACTCAGTGA
3' ss Score
5.93
Exon sequences
Seq C1 exon
TCACCGCCAAAGGCCCGGCGGCCACAGATGGACCTCATCTCTGAGCTGAAACGGAGGCAGCAGAAGGAGCCACTCATTTATGAGAGCGACCGTGATGGGGCCATTGAAGACATCATCACAG
Seq A exon
GTAAGGGCTTGGCCAGGCCTTGGTCTTATCCTCAGTCTGTCCTTCTATGCTTTCTTCTGACCCAATGCGCTATCCTCTGGGGGACTGGCTGCCACACTGCTTCTTGCTACCTTTTCTGTTTTTCTTTCCTTTTTCCTTTCTCTACTCCCCTTCACCTGCCCCACCCCCACTCAG
Seq C2 exon
TGATCAAGACGGTGCCCTTCACGGCCCGCACCGGCAAGCGGACATCCCGGCTCCTCTGTGAGGCCAGCCTGGGAGAAGAGATGCCCCTCTAGCCCCTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000184922-FMNL1:NM_005892:25
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.756 A=NA C2=0.200
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ATGGACCTCATCTCTGAGCTGA
R:
CTGAGGGGCTAGAGGGGCAT
Band lengths:
194-368
Functional annotations
There are 1 annotated functions for this event
PMID: 19815554
This event
The study identified a novel splice variant (FMNL1gamma) containing an intron retention (HsaINT0065113, which also covers the downstream one, as it is associated with an AltEx) at the C terminus affecting the diaphanous autoinhibitory domain (DAD). FMNL1gamma is specifically located at the cell membrane and cortex in diverse cell lines. Similar localization of FMNL1 was observed for a mutant lacking the DAD domain (FMNL1DeltaDAD), indicating that deregulation of autoinhibition is effective in FMNL1gamma. Expression of both FMNL1gamma and FMNL1DeltaDAD induces polarized nonapoptotic blebbing that is dependent on N-terminal myristoylation of FMNL1 but independent of Src and ROCK activity. Thus, these results describe N-myristoylation as a regulative mechanism of FMNL1 responsible for membrane trafficking potentially involved in a diversity of polarized processes of hematopoietic lineage-derived cells.
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Genotype-Tissue Expression Project (GTEx)
- Autistic and control brains
- Pre-implantation embryo development
Other AS DBs:
FasterDB (Includes CLIP-seq data)
AS-ALPS (AS-induced ALteration of Protein Structure, links to PINs)
APPRIS (Selection of principal isoform)
DEU primates (Only for human)