RnoEX0038235 @ rn6
Exon Skipping
Gene
ENSRNOG00000011353 | Gfi1b
Description
growth factor independent 1B transcriptional repressor [Source:RGD Symbol;Acc:1311727]
Coordinates
chr3:7192642-7195181:-
Coord C1 exon
chr3:7194910-7195181
Coord A exon
chr3:7193963-7194100
Coord C2 exon
chr3:7192642-7192807
Length
138 bp
Sequences
Splice sites
3' ss Seq
GACTCTTTGCTCTGCCTCAGGTG
3' ss Score
8.88
5' ss Seq
CAGGTGAGC
5' ss Score
9.6
Exon sequences
Seq C1 exon
AGGGGCCTCACGTGACATCCCAACCCCAGGATGGGGAATCGCCACTCTCCGAGTCACCCCCTTTCTATAAGCCCAGCTTCTCTTGGGATACGCTGGCCTCCTCCTACAGACACAGCTACCAACAGACCCCCTCCACCATGCAGTCAGCTTTCCTGGAGCGCTCCGTGAGGCTGTACGGCAGCCCGCTTGTGCCCAGCACCGAGTCCCCCTTGGACTTCAGCCTCCGTTATTCTCCGGGCATGGACACTTACCACTGTGTCAAGTGTAACAAG
Seq A exon
GTGTTCTCCACCCCTCATGGGCTAGAAGTGCATGTCCGCCGCTCTCACAGCGGAACCCGGCCCTTTGCCTGTGACATCTGTGGCAAAACCTTTGGCCACGCTGTGAGTTTGGAGCAGCACACGCACGTGCATTCCCAG
Seq C2 exon
GAGCGTAGCTTCGAGTGCCGGATGTGTGGCAAAGCCTTCAAGCGCTCATCCACTCTGTCCACCCACCTGCTCATCCATTCGGACACTCGGCCCTACCCCTGCCAGTTCTGTGGGAAACGCTTCCACCAGAAGTCGGACATGAAGAAACACACCTACATCCACACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000011353-'13-12,'13-10,15-12
Average complexity
C2
Mappability confidence:
100%=100=100%
Protein Impact
Alternative protein isoforms (Ref)
No structure available
Features
Disorder rate (Iupred):
C1=0.240 A=0.130 C2=0.107
Domain overlap (PFAM):
C1:
PF153561=SPR1=PD(69.4=54.9)
A:
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)
Main Skipping Isoform:
ENSRNOT00000015236fB5933
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCTCCTCCTACAGACACAGCT
R:
GAATGGATGAGCAGGTGGGTG
Band lengths:
256-394
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]