DreEX6083910 @ danRer10
Exon Skipping
Gene
ENSDARG00000079947 | gfi1b
Description
growth factor independent 1B transcription repressor [Source:ZFIN;Acc:ZDB-GENE-091118-129]
Coordinates
chr21:17246257-17254305:-
Coord C1 exon
chr21:17254076-17254305
Coord A exon
chr21:17248607-17248744
Coord C2 exon
chr21:17246257-17246422
Length
138 bp
Sequences
Splice sites
3' ss Seq
ATTTGTGTGGTCTTATCTAGGTG
3' ss Score
10.27
5' ss Seq
CAGGTAAGA
5' ss Score
10.77
Exon sequences
Seq C1 exon
AACCTCAGCTGGCAGAGTTTCCTCCATACTACAAGAGCTCTTTTGGCTGGGATCATGGTCCTGCCTCATATCAGGAGTTCAGACATATGGGCTTTTCTCCGTCTCTCCTCCATCATGCCAGCAGTCTGTACGGAGCTCATCTGAAGCAGAGCGCAGAGCCACAGCCGCTGGACTGCAGCACTCACTACTCGCCCTCCTCCAACACATACCACTGCATCACCTGCGACAAG
Seq A exon
GTGTTTTCCACGCCTCATGGGTTGGAGGTTCATGTCCGCCGCTCTCACAGTGGTACAAGACCTTTTGAATGCAGCATCTGCAGAAAGAGCTTCGGCCATGCAGTCAGTCTAGAGCAACACATGAACGTCCACTCACAG
Seq C2 exon
GAAAGAAGCTTTGAGTGCAAAATGTGCGGTAAAACCTTCAAGCGCTCCTCAACTTTGTCCACTCACCTGCTGATCCACTCAGACACACGGCCATATCCCTGTCAATATTGCGGGAAACGCTTCCATCAGAAATCCGACATGAAGAAACACACCTACATTCACACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000079947-'3-4,'3-3,4-4=AN
Average complexity
A_S
Mappability confidence:
100%=100=100%
Protein Impact
Alternative protein isoforms (Ref)
No structure available
Features
Disorder rate (Iupred):
C1=0.019 A=0.108 C2=0.107
Domain overlap (PFAM):
C1:
NO
A:
PF134651=zf-H2C2_2=WD(100=58.7),PF134651=zf-H2C2_2=PU(38.5=21.7)
C2:
PF134651=zf-H2C2_2=PD(57.7=26.8),PF134651=zf-H2C2_2=WD(100=46.4),PF102764=zf-CHCC=WD(100=39.3),PF0136316=FYVE=PU(48.4=55.4),PF134651=zf-H2C2_2=PU(34.6=16.1)
Main Skipping Isoform:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ACAAGAGCTCTTTTGGCTGGG
R:
AAGTTGAGGAGCGCTTGAAGG
Band lengths:
255-393
Functional annotations
There are 1 annotated functions for this event
PMID: 27486782
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]