HsaALTA0004763-2/2 @ hg38
Alternative 3'ss
Gene
ENSG00000050405 | LIMA1
Description
LIM domain and actin binding 1 [Source:HGNC Symbol;Acc:HGNC:24636]
Coordinates
chr12:50192452-50195887:-
Coord C1 exon
chr12:50195830-50195887
Coord A exon
chr12:50192562-50192564
Coord C2 exon
chr12:50192452-50192561
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
ENSG00000050405-55-44,55-43-2/2
Average complexity
Alt3
Mappability confidence:
NA
Protein Impact
Protein isoform when splice site is used (Ref)
No structure available
Features
Disorder rate (Iupred):
C1=0.955 A=NA C2=1.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Mouse
(mm9)
No conservation detected
Cow
(bosTau6)
No conservation detected
Chicken
(galGal4)
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:
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