HsaINT0075908 @ hg19
Intron Retention
Gene
ENSG00000109758 | HGFAC
Description
HGF activator [Source:HGNC Symbol;Acc:4894]
Coordinates
chr4:3449219-3449762:+
Coord C1 exon
chr4:3449219-3449358
Coord A exon
chr4:3449359-3449621
Coord C2 exon
chr4:3449622-3449762
Length
263 bp
Sequences
Splice sites
5' ss Seq
TCGGTGAGC
5' ss Score
9.1
3' ss Seq
CTGGCCACTCTTCTGATCAGTCC
3' ss Score
4.23
Exon sequences
Seq C1 exon
CCCCCCCAGGGACAGCGTCTCCGTGGTGCTGGGCCAGCACTTCTTCAACCGCACGACGGACGTGACGCAGACCTTCGGCATCGAGAAGTACATCCCGTACACCCTGTACTCGGTGTTCAACCCCAGCGACCACGACCTCG
Seq A exon
GTGAGCTCCGGCGTGTCGTGGCTGCACTCTGGGCAGGTGGGCCCTGTGCTCCCCAGGCCAGGCCCAGACAGGGGCAGGAGCTGGGCAGACATGTGGTGCGGGGGAAGCTGGGGGCAGGGCAGGGAGGACAGGGCACCGCTCCCTTCTGGATCTCCCAGGCTGCCCTGTGGACCCCACTGGCTACCCTCCCTCCACCACGGGCCCCGACAGCCTCCCGTTCAGCCCGCACACCACAGGCTGACCCTGGCCACTCTTCTGATCAG
Seq C2 exon
TCCTGATCCGGCTGAAGAAGAAAGGGGACCGCTGTGCCACACGCTCGCAGTTCGTGCAGCCCATCTGCCTGCCCGAGCCCGGCAGCACCTTCCCCGCAGGACACAAGTGCCAGATTGCGGGCTGGGGCCACTTGGATGAGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000109758-HGFAC:NM_001528:11
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0008921=Trypsin=FE(20.1=100)
A:
NA
C2:
PF0008921=Trypsin=FE(20.1=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCCAGGGACAGCGTCTCC
R:
TCTCATCCAAGTGGCCCCAG
Band lengths:
277-540
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)