HsaINT0075907 @ hg19
Intron Retention
Gene
ENSG00000109758 | HGFAC
Description
HGF activator [Source:HGNC Symbol;Acc:4894]
Coordinates
chr4:3447769-3449358:+
Coord C1 exon
chr4:3447769-3448021
Coord A exon
chr4:3448022-3449218
Coord C2 exon
chr4:3449219-3449358
Length
1197 bp
Sequences
Splice sites
5' ss Seq
CAGGTGCAC
5' ss Score
4.29
3' ss Seq
CTCCAGCCCCCCTTGCACAGCCC
3' ss Score
4.36
Exon sequences
Seq C1 exon
AATCCCTCACCAGAGTCCAACTGTCACCGGATCTCCTGGCGACCCTGCCTGAGCCAGCCTCCCCGGGGCGCCAGGCCTGCGGCAGGAGGCACAAGAAGAGGACGTTCCTGCGGCCACGTATCATCGGCGGCTCCTCCTCGCTGCCCGGCTCGCACCCCTGGCTGGCCGCCATCTACATCGGGGACAGCTTCTGCGCCGGGAGCCTGGTCCACACCTGCTGGGTGGTGTCGGCCGCCCACTGCTTCTCCCACAG
Seq A exon
GTGCACCTCCTCTGGGCCCCAGTCACCTGCCCTGAGGCCCCACACACCATCCAGCGTCACTATGCGCCTGTCCCCACCCGCTTGCGGACCCCATCCCGGTGCCTCTGCTGACCCCTTCCCGGGGTCCCCGGTAACCCTCTCTGACCCCTCTGGGTCTTGGGGCTCAGTCCTGAGCTGGGCATGCATGGACACTCCAGAAACCCTGTCCCTATTGAGGGAGGCCAGGGGTCAGTGGCATTTCCACAGAGGACCCAGCGCCTGCGGAGAGTGCAGTGGGCCAGGTCCTGTCCTCCCCGCAGGCCCCGCCCCTCCCAGAGTCCTGGCTCTCAGTAGGGAGCCAGGGAGCGCAGTGACAATGCGTCAGAGCCCTAGGAGCCCAAGCACAGCCAGGGAAACTGAGGCCCAGCCCACTCAGCCGGCTCCCCTCAGTGGGGGCGCACAGCCACCCAGGCCCACACTCTGGGAGGCGGGCCTCGAGTGGGGAGACCCTGAGACGGAGCAGCCTGGGCCAGACGCCCTTCCACCTTCGATGGGCACCCCAGTGATTAGGGGCAGGGGTCCGGCCAGCCGAGGGTCTGGCGGCCTTTCGAGGACCACAGCTCCCAGGGTGGGGTCCTGCGTGGCCCTGCAGAACCTGCAGCCGGCGGCTCCTGGGCCTGCAAATGGGGCCAGAGCCTTCCTCAGTGTGGAGAAATGGGGTTCCCCACATGGAGCCCAGGGCAGGAGGCCGAGGCAGGGTGGAGCGACCTCCACACAGCAGATGGGAGCCAGGCTCAGGGGCCCAGGCTCTGTGCCCAGCAGGAGTGAGGGCTGCATCTGGGGACCCCACAATGTGGATGGAAGCTGGGGCAGGGCCTGAGCAGGCCAGGTCTCCACCCACTCGGGTCGGCCTTGCAGCCGATCCTGCCTGGGCTTGGCCTGAGACTCCCCCCAGGGCTTGTGACCAGTGTTGTCAGGAGGGATGGCACCGCACTTCAGCTCCCATGCCTGGATCTGGGGGTGACTGGCAATAGCCCCTGCTTGGTGGTCCCTGTCTCCCCAGTATCAACAGCCCACACCCAGGCACCTGCTCAGACCCCTCCCCGGGACCAGGGTCCCACACCATTGGCCTCCGTGGGCCTGACAGGGGGTGGGGAGAGGTGAGCCCGGTGGCTGGGGGAGGGCTGGTCCATGCAGCCTCCAGCCCCCCTTGCACAG
Seq C2 exon
CCCCCCCAGGGACAGCGTCTCCGTGGTGCTGGGCCAGCACTTCTTCAACCGCACGACGGACGTGACGCAGACCTTCGGCATCGAGAAGTACATCCCGTACACCCTGTACTCGGTGTTCAACCCCAGCGACCACGACCTCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000109758-HGFAC:NM_001528:10
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.024 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0008921=Trypsin=PU(18.8=51.8)
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:
TCCCTCACCAGAGTCCAACTG
R:
GGGATGTACTTCTCGATGCCG
Band lengths:
347-1544
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)