MmuINT0077583 @ mm9
Intron Retention
Gene
ENSMUSG00000029102 | Hgfac
Description
hepatocyte growth factor activator [Source:MGI Symbol;Acc:MGI:1859281]
Coordinates
chr5:35387006-35387498:+
Coord C1 exon
chr5:35387006-35387180
Coord A exon
chr5:35387181-35387412
Coord C2 exon
chr5:35387413-35387498
Length
232 bp
Sequences
Splice sites
5' ss Seq
CCGGTCAGC
5' ss Score
4.61
3' ss Seq
ACTCCCTTGTCTGCTTCCAGGAA
3' ss Score
10.91
Exon sequences
Seq C1 exon
TTCCCACAGAGCACTGCTTCCTGGGAAATGGTACAGAGTACCGAGGCGTGGCCAGCACCGCTGCCTCGGGCCTGAGCTGCCTGGCCTGGAATTCTGACCTGCTCTACCAGGAGCTGCACGTGGACTCAGTGGCTGCTGCTGTCCTGCTTGGCCTGGGCCCTCACGCTTACTGCCG
Seq A exon
GTCAGCACCTAATGGCTGCTATACATACTCTTTCTGCATAAGCAAAGGATTGGACAGAGGGTCTTCCCAGACTCTGCAGGGGACAACAGTGCCTAGATGGCTGTTAGCCTCTGCCTCTTGGGATGGTGGGTTCATGTGTGCCCACCGTGGTCTGCAGAGAGAGCACATAGCTCTGGGTGTTAGGATGGTCCTCTAGGGAGAGTGATGGTGTGACTCCCTTGTCTGCTTCCAG
Seq C2 exon
GAACCCAGACAAGGATGAGAGGCCTTGGTGCTATGTGGTGAAGGACAACGCACTGTCGTGGGAGTATTGCCGCCTGACAGCCTGTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000029102-Hgfac:NM_019447:8
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:
PF0005113=Kringle=PU(64.6=89.8)
A:
NA
C2:
PF0005113=Kringle=PD(34.1=93.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCACAGAGCACTGCTTCCTG
R:
CTGTCAGGCGGCAATACTCC
Band lengths:
252-484
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types
Other AS DBs: