HsaEX0027327 @ hg19
Exon Skipping
Gene
ENSG00000165702 | GFI1B
Description
growth factor independent 1B transcription repressor [Source:HGNC Symbol;Acc:4238]
Coordinates
chr9:135863584-135865294:+
Coord C1 exon
chr9:135863584-135863855
Coord A exon
chr9:135864448-135864585
Coord C2 exon
chr9:135865129-135865294
Length
138 bp
Sequences
Splice sites
3' ss Seq
CATGCTGCCCCTGCTCCCAGGTC
3' ss Score
10.56
5' ss Seq
CAGGTGGGC
5' ss Score
8.07
Exon sequences
Seq C1 exon
AGGGCCCCATTGTGCTGTCCCGACCCCAGGATGGGGACTCTCCACTGTCCGACTCACCCCCATTCTACAAGCCTAGCTTCTCCTGGGACACCTTGGCCACAACCTATGGCCACAGCTACCGGCAGGCCCCCTCCACCATGCAGTCAGCCTTCCTGGAGCACTCCGTCAGCCTGTACGGCAGTCCTCTTGTGCCCAGCACTGAGCCCGCCTTGGACTTCAGCCTCCGCTACTCCCCAGGCATGGATGCGTACCACTGTGTGAAGTGCAACAAG
Seq A exon
GTCTTCTCCACCCCTCACGGGCTCGAAGTGCATGTGCGACGCTCCCATAGTGGGACCCGGCCCTTCGCCTGTGACATCTGCGGCAAAACCTTCGGCCACGCTGTGAGCCTGGAGCAGCACACGCACGTCCACTCCCAG
Seq C2 exon
GAGCGCAGCTTCGAGTGCCGCATGTGCGGCAAGGCCTTCAAGCGCTCGTCCACGCTGTCCACCCACCTGCTCATCCACTCAGACACGCGGCCCTACCCCTGCCAGTTCTGCGGCAAGCGTTTCCACCAGAAGTCCGACATGAAGAAGCACACCTACATCCACACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000165702_CASSETTE1
Average complexity
S
Mappability confidence:
100%=100=100%
Protein Impact
Alternative protein isoforms (Ref)
No structure available
Features
Disorder rate (Iupred):
C1=0.215 A=0.065 C2=0.093
Domain overlap (PFAM):
C1:
PF0403211=Rpr2=PU(45.5=27.5)
A:
PF0403211=Rpr2=PD(50.9=60.9),PF134651=zf-H2C2_2=WD(100=58.7)
C2:
PF0009621=zf-C2H2=WD(100=41.1),PF134651=zf-H2C2_2=PU(38.5=17.9)
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CAACCTATGGCCACAGCTACC
R:
TGTCTGAGTGGATGAGCAGGT
Band lengths:
258-396
Functional annotations
There are 1 annotated functions for this event
PMID: 27486782
This event
Whole-exome sequencing identifies a GFI1B variant associated with low platelet counts. By performing CRISPR/Cas9 genome editing in hematopoietic cell lines and follow-up targeted knockdown experiments in primary human hematopoietic stem and progenitor cells, th authors demonstrate an alternative splicing mechanism by which the GFI1B rs150813342 variant suppresses formation of a GFI1B isoform that preferentially promotes megakaryocyte differentiation and platelet production.
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)