HsaINT0068656 @ hg19
Intron Retention
Gene
ENSG00000162676 | GFI1
Description
growth factor independent 1 transcription repressor [Source:HGNC Symbol;Acc:4237]
Coordinates
chr1:92946158-92948603:-
Coord C1 exon
chr1:92948421-92948603
Coord A exon
chr1:92946646-92948420
Coord C2 exon
chr1:92946158-92946645
Length
1775 bp
Sequences
Splice sites
5' ss Seq
CAGGTAGGA
5' ss Score
9.79
3' ss Seq
CTCCCCTTGTGCCTCCACAGCCT
3' ss Score
9.51
Exon sequences
Seq C1 exon
ACAGCACTTCAAATGCAGGCGGGGCGAAGGCGGAGCCCCGGGACCGTTTGTCCCCCGAATCGCAGCTGACCGAAGCCCCAGACAGAGCCTCCGCATCCCCAGACAGCTGCGAAGGCAGCGTCTGCGAACGGAGCTCGGAGTTTGAGGACTTCTGGAGGCCCCCGTCACCCTCCGCGTCTCCAG
Seq A exon
GTAGGAACCCACTGGGAACCTCTTGGGCGGGAGCTGCAGGGACCCGGCAGTGCTGGGGGGGAATTGGCGCGACCTTGGGCGTAGAAATGCTAACGGGGAGTTGGAGAGTCTTTCCGGGAGAAGGGAGCTGATTCGTAGGGGAAGGAGGCATCCGGCTTCTCTGGGACTTGGACAGCTTGCCCGCTGGGGCTGCTGCCTCCATCCCAGGCGGCAGGACCCTAGCTGCTTGTCGCTTAGATTCGTTTGCGCGGAGCTGGCCAGTGACGGAAAACAAACCAGTCGTTTCGACTGGCGGCAACGCTGACCTTTCATTTTCTGACCAGACCTGACTGTTTTATAAAGTGCTAGGATCCTGCAATCTAGACCCCCAAACCTCAAACAGAGAACAGGGCAGAACGGGCCAGGCAGAGGAGCTAGGCGCTGGGCGGCAGGGAGGGGGCAGGACGAAAATCTCAGCCCGCGGCTTGGTCTTCACAGGCGCAGATTGGGGGCCTGTTTCATTTTTCGTTTTGCCGGGTTAACCTAGCCTCAGGGGCCTGCTCTCTGGGTTTCATTTCCAGCGAGCAATCCAGCTTCAGGCAAACTAAGTGACCACACGTTGGGTGGGGGCGTCTCGAGTCCCGGCCGGGGGAAGGAATGAGCAGACCAGCCGGATTCTGTCAAGGGCCGGTTATATCCAGAATATGTTTGCTAGTTTTAGAAGATACCACCACCCGTCCCACAATCAGTGAGTTGACTTGGCGAAAACCATAGCTCCAGCAAGTGTGTCTGGGAGCCGGCGGCGGGAGGATTCTTCCTGCCAGGGCGTCAAGTGGCCAGACAAGGATTGGGCGCGCCCCGAACCCCTCCGAACGAAACTCCGGGTACAGCCTCTCACTGAAGTGGCCAGCCTGAACTGGAGTGTTGTGCGCACACACACACACACACATTTGTAAATGCCGTATGCACTCACATGCGTTGGGGTCACTAGTTTTAGCAAAATTCACGTGGGTGGGGGCGTAGCAGGCCGAGAATTCAGAGCTGTCTCCTTGCAGGTGGTGGCTAAACCTTATGAGTTATAGTTATTCTCTGAGAAATTCAGGTTCCCCGCCTCCATCAAACTGTAACAGGAATGGGGAGTATTTGGCTGTCAATTTAAGCCCAAAAGCCCCTTTCCTGCTGCTCCTTTGCTACGTACACTGGGCACTTAACTTCGTGAAATCTTAATACCTTCGGGTTTATTCAGACAGCAGCCTTTCGGGTAGTTCGGGGCCGCATTTATGGACCTTCTCCCTCCTTCCTCTTGGATTCTGGGAAGAAAAAGAATTGAATGGGAACATGTAGGGGCTGGGAGAGTGCCTGCGCTGGTGGCTGGACCCTTCCGCCCTTGAGTGCTGTGAGGGGCCGAACGGCCGCCACCTTCTCCTTCTTAACAGCTCAACTACGGGCATTTATAGATGCGCCCTTCCCTGTAGGATCTCCAGGTGCGCGGGTCCAGCCAGAAAAGATCCTCGGAACGCCGAGCGCCTCCGCTGCACTCGCACAGAATTTACGACCTCCTCTCCCGAGGTCTTTTCAATGATCTGTTTACTGTTCTGCCTCCTATAGTGGCCTGCGAGGCCCCAGGGCCCGGGCCACGTTTTACCCTGGGGCGAGCCTGGCACCTGGCGCACGCAGTGTTCTACAAGCGCTGGGTGCCCCGCAGTCCGCGAACACGCCACGCTCGCAGCCGCAGCCCGGCGGCCTCCGCTCTGCCGTCTGAAGCCTGACCGGACGCTCCCCTTGTGCCTCCACAG
Seq C2 exon
CCTCGGAGAAGTCAATGTGCCCATCGCTGGACGAAGCCCAGCCCTTCCCCCTGCCTTTCAAACCGTACTCATGGAGCGGCCTGGCGGGTTCTGACCTGCGGCACCTGGTGCAGAGCTACCGACCGTGTGGGGCCCTGGAGCGTGGCGCTGGCCTGGGCCTCTTCTGCGAACCCGCCCCGGAGCCTGGCCACCCGGCCGCGCTGTACGGCCCGAAGCGGGCTGCCGGCGGCGCGGGGGCCGGGGCGCCAGGGAGCTGCAGCGCAGGGGCCGGTGCCACCGCTGGCCCTGGCCTAGGGCTCTACGGCGACTTCGGGTCTGCGGCAGCCGGGCTGTATGAGAGGCCCACGGCAGCGGCGGGCTTGCTGTACCCCGAGCGTGGCCACGGGCTGCACGCAGACAAGGGCGCTGGCGTCAAGGTGGAGTCGGAGCTGCTGTGCACCCGCCTGCTGCTGGGCGGCGGCTCCTACAAGTGCATCAAGTGCAGCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000162676-GFI1:NM_001127216:3
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.887 A=NA C2=0.141
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:
AGTTTGAGGACTTCTGGAGGC
R:
GAAGTCGCCGTAGAGCCCTAG
Band lengths:
356-2131
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)