GgaEX6015296 @ galGal3
Exon Skipping
Gene
ENSGALG00000003478 | GFI1B_CHICK
Description
NA
Coordinates
chr17:7412952-7414113:+
Coord C1 exon
chr17:7412952-7413214
Coord A exon
chr17:7413398-7413535
Coord C2 exon
chr17:7413948-7414113
Length
138 bp
Sequences
Splice sites
3' ss Seq
AATGGCATTTTGTTTTTCAGGTG
3' ss Score
11.02
5' ss Seq
CAGGTGCGT
5' ss Score
9.73
Exon sequences
Seq C1 exon
ACATGAGCATCTCAGGTCTGCAAGTCAAAGACTGCACTAACCCAACAAGCATGCCTACCTTCTACAAAACCGGCTTTTCTTGGGATGCTTTCCAGCTGCCATACAGCTACAGACAGATGTCTTCCACCATGCAGTCAGCCCTCCTGGAGCACCCCGTCAGCCTGTATGGAAGCCATCTCCTGCCAAGCGCCGAGCCCCCTCTGGATTACAGCATGCGGTACTCCTCAGACATGGAGACCTACCACTGTGTGAAGTGCAACAAG
Seq A exon
GTGTTCTCCACTCCCCATGGCCTGGAGGTCCACGTGCGAAGGTCTCACAGTGGGACCCGACCCTTTGCTTGTGAAGTATGTGGCAAAACCTTCGGGCATGCTGTGAGCCTGGAGCAGCACACCAACATTCACTCCCAG
Seq C2 exon
GAAAGAAGTTTTGAGTGCAAGATGTGTGGGAAGACATTCAAGCGTTCCTCCACCCTCTCCACACATCTGCTGATCCATTCTGACACACGGCCCTATCCCTGCCAATACTGCGGCAAGCGCTTCCACCAGAAGTCGGATATGAAGAAACACACTTACATCCACACTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000003478-'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=0.068 A=0.043 C2=0.107
Domain overlap (PFAM):
C1:
PF0403211=Rpr2=PU(43.4=26.1)
A:
PF0403211=Rpr2=PD(52.8=60.9),PF134651=zf-H2C2_2=WD(100=58.7),PF134651=zf-H2C2_2=PU(38.5=21.7)
C2:
PF134651=zf-H2C2_2=PD(53.8=25.0),PF134651=zf-H2C2_2=WD(100=46.4),PF102764=zf-CHCC=WD(100=39.3),PF134651=zf-H2C2_2=PU(38.5=17.9)
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCGGCTTTTCTTGGGATGCTT
R:
GGTGGAGGAACGCTTGAATGT
Band lengths:
248-386
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]