HsaINT0068655 @ hg19
Intron Retention
Gene
ENSG00000162676 | GFI1
Description
growth factor independent 1 transcription repressor [Source:HGNC Symbol;Acc:4237]
Coordinates
chr1:92948421-92949143:-
Coord C1 exon
chr1:92948930-92949143
Coord A exon
chr1:92948604-92948929
Coord C2 exon
chr1:92948421-92948603
Length
326 bp
Sequences
Splice sites
5' ss Seq
CAGGTGCGA
5' ss Score
7.75
3' ss Seq
CACCTGCCTCCTCTTTGCAGACA
3' ss Score
11.09
Exon sequences
Seq C1 exon
GTCTCCTCCGGGCTGGGGCTGAGCAAGCCCTCGGAGTGACCGTGGGTGACAGCGGCTCCAGGGACTCTTGGGGCGCAGTGGGGAAAGTGCCGGACCACCATGCCGCGCTCATTTCTCGTCAAAAGCAAGAAGGCTCACAGCTACCACCAGCCGCGCTCCCCAGGACCAGACTATTCCCTCCGTTTAGAGAATGTACCGGCGCCTAGCCGAGCAG
Seq A exon
GTGCGAGGCGCGCGCGGGCCAGGCGGGGCTGCTCCCCCGGATGCCTACTGCACCTCGGCACACCATTAGTCCGGAGCTGGGAGGGGCTGCCCCAACGTCCCTTTTGCTGCTGTTTTTGTTTCCTACTGTCCTGGTTCCTCCGGGTTTGTCTCCTAGGTGCCATGGCCTCTCTGCGCCTGCCCTCGGATCCGAGAGGGTTCCCGGCCGGGGTCTGGGTGGAGAGGGGAAGACGCTCGGCTGCCCTGGTCGGGGGATTGGGGGAGCCTTCAGCACCCTCAGACTCAACCGGTCCCAGCCTGAGCCCCTCACCTGCCTCCTCTTTGCAG
Seq C2 exon
ACAGCACTTCAAATGCAGGCGGGGCGAAGGCGGAGCCCCGGGACCGTTTGTCCCCCGAATCGCAGCTGACCGAAGCCCCAGACAGAGCCTCCGCATCCCCAGACAGCTGCGAAGGCAGCGTCTGCGAACGGAGCTCGGAGTTTGAGGACTTCTGGAGGCCCCCGTCACCCTCCGCGTCTCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000162676-GFI1:NM_001127216:2
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.974 A=NA C2=0.887
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
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:
CTGAGCAAGCCCTCGGAGT
R:
CTCAAACTCCGAGCTCCGTTC
Band lengths:
342-668
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- 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)