MmuINT0077580 @ mm9
Intron Retention
Gene
ENSMUSG00000029102 | Hgfac
Description
hepatocyte growth factor activator [Source:MGI Symbol;Acc:MGI:1859281]
Coordinates
chr5:35386209-35386604:+
Coord C1 exon
chr5:35386209-35386331
Coord A exon
chr5:35386332-35386472
Coord C2 exon
chr5:35386473-35386604
Length
141 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGA
5' ss Score
9.22
3' ss Seq
GAACACTGTGTGACTCACAGAGA
3' ss Score
5.04
Exon sequences
Seq C1 exon
CTATCCTTGACCCTTGTGCCTCTGGGCCCTGCCTCAATGGGGGCACATGTTCCAGTACACATGACCATGGGTCCTACCACTGCTCTTGCCCGCTGGCCTTCACAGGCAAGGACTGTGGCACAG
Seq A exon
GTGAGAGGACCTCGGGGACCCAGGAGTGGGGCCATTCTAGGAGGCTGGGAGAGCAGCTGCTGAGTCCAGCCTGGGGTGGGTAGTGCCTACCTGGGGGAGGGGACCTGCACGGGCACTGTGGGAACACTGTGTGACTCACAG
Seq C2 exon
AGAAATGCTTTGATGAAACACGCTATGAGTATTTTGAGGTGGGCGACCACTGGGCCCGTGTGAGCGAGGGACATGTGGAGCAATGTGGCTGTATGGAGGGCCAGGCCCGGTGTGAAGACACCCACCACACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000029102-Hgfac:NM_019447:5
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:
PF0000822=EGF=WD(100=78.6)
A:
NA
C2:
PF0003913=fn1=WD(100=80.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ATCCTTGACCCTTGTGCCTCT
R:
CTGTGTGGTGGGTGTCTTCAC
Band lengths:
253-394
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: