MmuINT0077578 @ mm10
Intron Retention
Gene
ENSMUSG00000029102 | Hgfac
Description
hepatocyte growth factor activator [Source:MGI Symbol;Acc:MGI:1859281]
Coordinates
chr5:35042566-35042934:+
Coord C1 exon
chr5:35042566-35042662
Coord A exon
chr5:35042663-35042854
Coord C2 exon
chr5:35042855-35042934
Length
192 bp
Sequences
Splice sites
5' ss Seq
GTGGTGAGT
5' ss Score
8.95
3' ss Seq
CCTCTGACTCGACCCTCCAGGTG
3' ss Score
9.35
Exon sequences
Seq C1 exon
TGCTCACCGAGTCTGGGCAGCCGTGCAGGTTCCCTTTCCGCTACGGTGGCCGCATGCTGCACTCCTGTACCTCTGAGGGAAGTGCCTACAGGAAGTG
Seq A exon
GTGAGTCCCAGAGTGGGGTAGCGGCTGAGGAACCTACACAGGTTCCCACTGTGGACCCTCATGAACCCTGAAGCTAGTAGGTCTTGATGCCCAGCAGGTACATTTAGTGAACAGGGGCTCCAGGGTGCCCAGGCAGAGATGGGTGGGGCTCTGGGCAGGGACTCAGTTTTATCCTCTGACTCGACCCTCCAG
Seq C2 exon
GTGCGCTACAACACACAACTATGACCGAGACCGGGCCTGGGGCTACTGTGCAGAGGTGACCCTGCCTGTGGAAGGTCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000029102:ENSMUST00000201038:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.106 A=NA C2=0.404
Domain overlap (PFAM):
C1:
PF0004014=fn2=PU(58.5=72.7)
A:
NA
C2:
PF0004014=fn2=PD(39.0=57.1)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTCACCGAGTCTGGGCAGC
R:
CCTTCCACAGGCAGGGTCA
Band lengths:
170-362
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