HsaINT0068657 @ hg19
Intron Retention
Gene
ENSG00000162676 | GFI1
Description
growth factor independent 1 transcription repressor [Source:HGNC Symbol;Acc:4237]
Coordinates
chr1:92945905-92946645:-
Coord C1 exon
chr1:92946158-92946645
Coord A exon
chr1:92946043-92946157
Coord C2 exon
chr1:92945905-92946042
Length
115 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGG
5' ss Score
9.16
3' ss Seq
TCTGGCCCCACCCGCCTTAGGTG
3' ss Score
6.98
Exon sequences
Seq C1 exon
CCTCGGAGAAGTCAATGTGCCCATCGCTGGACGAAGCCCAGCCCTTCCCCCTGCCTTTCAAACCGTACTCATGGAGCGGCCTGGCGGGTTCTGACCTGCGGCACCTGGTGCAGAGCTACCGACCGTGTGGGGCCCTGGAGCGTGGCGCTGGCCTGGGCCTCTTCTGCGAACCCGCCCCGGAGCCTGGCCACCCGGCCGCGCTGTACGGCCCGAAGCGGGCTGCCGGCGGCGCGGGGGCCGGGGCGCCAGGGAGCTGCAGCGCAGGGGCCGGTGCCACCGCTGGCCCTGGCCTAGGGCTCTACGGCGACTTCGGGTCTGCGGCAGCCGGGCTGTATGAGAGGCCCACGGCAGCGGCGGGCTTGCTGTACCCCGAGCGTGGCCACGGGCTGCACGCAGACAAGGGCGCTGGCGTCAAGGTGGAGTCGGAGCTGCTGTGCACCCGCCTGCTGCTGGGCGGCGGCTCCTACAAGTGCATCAAGTGCAGCAAG
Seq A exon
GTGAGGCTCCCGAGCTCACCACCTCGCCTGCCGTGCGCCCGCTTCCCCTACCCGCGCCTCGCCTGCGCCCCGCGGCCCCTCTCAGCGGCCTTCTCTCTGGCCCCACCCGCCTTAG
Seq C2 exon
GTGTTCTCCACGCCGCACGGGCTCGAGGTGCACGTGCGCAGGTCCCACAGCGGTACCAGACCCTTTGCCTGCGAGATGTGCGGCAAGACCTTCGGGCACGCGGTGAGCCTGGAGCAGCACAAAGCCGTGCACTCGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000162676-GFI1:NM_001127216:4
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.141 A=NA C2=0.065
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF134651=zf-H2C2_2=WD(100=58.7)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCTGTATGAGAGGCCCACGG
R:
GAAGGTCTTGCCGCACATCTC
Band lengths:
253-368
Functional annotations
There are 0 annotated functions for this event
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)