MmuINT0077575 @ mm10
Intron Retention
Gene
ENSMUSG00000029102 | Hgfac
Description
hepatocyte growth factor activator [Source:MGI Symbol;Acc:MGI:1859281]
Coordinates
chr5:35046884-35047264:+
Coord C1 exon
chr5:35046884-35047024
Coord A exon
chr5:35047025-35047115
Coord C2 exon
chr5:35047116-35047264
Length
91 bp
Sequences
Splice sites
5' ss Seq
AAAGTGAGT
5' ss Score
8.4
3' ss Seq
GAAAGTGCAGTCCTCCACAGATG
3' ss Score
1.42
Exon sequences
Seq C1 exon
TCTTGATCCGGCTAAAGAAGAAGGGAGAGCGCTGTGCTGTCCGCTCCCAGTTTGTTCAACCCATCTGCCTGCCTGAGGCAGGCAGCTCCTTCCCTACTGGACACAAGTGTCAGATTGCAGGCTGGGGCCACATGGATGAAA
Seq A exon
GTGAGTGGAAGGCAGTCCCTGCCAGTGGGCGTCGAGGCGGGAGGAAGACAGGCAACAAACCTGCCTGCCCTGAAAGTGCAGTCCTCCACAG
Seq C2 exon
ATGTGAGCAGCTACTCCAACTCCCTGCTGGAGGCACTGGTCCCTCTTGTTGCTGACCACAAGTGTAGCAGCCCAGAGGTATATGGTGCTGACATCAGCCCTAACATGCTCTGTGCCGGCTACTTCGACTGCAAGTCCGATGCCTGCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000029102:ENSMUST00000201038:10
Average complexity
IR
Mappability confidence:
NA
Protein Impact
In the CDS, with uncertain impact
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(20.9=100)
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:
GCTCCCAGTTTGTTCAACCCA
R:
CTCTGGGCTGCTACACTTGTG
Band lengths:
176-267
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- Ribosome-engaged transcriptomes of neuronal types
- Neural differentiation time course
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types