HsaALTA0004763-2/2 @ hg19
Alternative 3'ss
Gene
ENSG00000050405 | LIMA1
Description
LIM domain and actin binding 1 [Source:HGNC Symbol;Acc:24636]
Coordinates
chr12:50586235-50589670:-
Coord C1 exon
chr12:50589613-50589670
Coord A exon
chr12:50586345-50586347
Coord C2 exon
chr12:50586235-50586344
Length
3 bp
Sequences
Splice sites
5' ss Seq
CCCGTAAGC
5' ss Score
4.37
3' ss Seq
TCTTCCTTTTGTAACTCAAGCAG
3' ss Score
1.76
Exon sequences
Seq C1 exon
ATTTCTGCAAATGAGAATAGCCTGGCAGTCCGTTCCACCCCTGCCGAAGATGACTCCC
Seq A exon
CAG
Seq C2 exon
GTGACTCCCAGGTTAAGAGTGAGGTTCAACAGCCTGTCCATCCCAAGCCACTAAGTCCAGATTCCAGAGCCTCCAGTCTTTCTGAAAGTTCTCCTCCCAAAGCAATGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000050405-13-16,13-15-2/2
Average complexity
Alt3
Mappability confidence:
NA
Protein Impact
Protein isoform when splice site is used (Ref)
No structure available
Features
Disorder rate (Iupred):
C1=0.950 A=NA C2=1.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Rat
(rn6)
No conservation detected
Chicken
(galGal4)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GAATAGCCTGGCAGTCCGTTC
R:
TCTGGACTTAGTGGCTTGGGA
Band lengths:
105-108
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- The Cancer Genome Atlas (TCGA)
- 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)