BtaEX6047021 @ bosTau6
Exon Skipping
Gene
ENSBTAG00000012772 | GFI1B
Description
growth factor independent 1B transcription repressor [Source:HGNC Symbol;Acc:HGNC:4238]
Coordinates
chr11:103048402-103050445:+
Coord C1 exon
chr11:103048402-103048673
Coord A exon
chr11:103049230-103049367
Coord C2 exon
chr11:103050280-103050445
Length
138 bp
Sequences
Splice sites
3' ss Seq
CCCTCTGCCCCCACCCGCAGGTG
3' ss Score
13.47
5' ss Seq
CAGGTGGGC
5' ss Score
8.07
Exon sequences
Seq C1 exon
AAGGACCTGCTGTGACGTCCCGACCCCAGGATGGGGACTCGCCCTCCTCTGACTCACCCCCGTTCTACAAGCCCAGCTTCTCCTGGGACACCCTGGCTTCCTCCTACGGCCACAGCTACCGGCAGGCCCCCTCCACCATGCAGTCTGCCTTCCTGGAGCGCTCCGTCAGCCTGTATGGCAGCCCTCTGGTGCCCAGCGCCGAGCCACCTTTGGACTTCAGCCTCCACTATTCCCCGGGGATGGACGCGTACCACTGCATCAAATGCAGCAAG
Seq A exon
GTGTTCTCCACCCCCCATGGGCTGGAAGTGCACGCCCGCCGCTCCCACAGCGGGACCCGGCCCTTCGCCTGCAACGTCTGCGGGAAAACCTTCGGCCACTCCGTGAGCCTGGAACAGCACACACACGTCCACTCCCAG
Seq C2 exon
GAGCGCAGCTTCGAGTGCCGGATGTGCGGCAAGGCCTTCAAGCGCTCGTCCACCCTGTCCACACACCTGCTCATCCACTCGGACACGCGGCCCTACCCCTGCCAGTTCTGCGGCAAGCGCTTCCACCAGAAGTCTGACATGAAGAAGCACACCTATATCCACACTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000012772-'5-9,'5-6,6-9=AN
Average complexity
A_C1
Mappability confidence:
100%=100=100%
Protein Impact
Alternative protein isoforms (Ref)
No structure available
Features
Disorder rate (Iupred):
C1=0.242 A=0.152 C2=0.107
Domain overlap (PFAM):
C1:
NO
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:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TTCCTCCTACGGCCACAGCTA
R:
GATGAGCAGGTGTGTGGACAG
Band lengths:
250-388
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]