MmuINT0077576 @ mm10
Intron Retention
Gene
ENSMUSG00000029102 | Hgfac
Description
hepatocyte growth factor activator [Source:MGI Symbol;Acc:MGI:1859281]
Coordinates
chr5:35047116-35048461:+
Coord C1 exon
chr5:35047116-35047264
Coord A exon
chr5:35047265-35048156
Coord C2 exon
chr5:35048157-35048461
Length
892 bp
Sequences
Splice sites
5' ss Seq
CAGGTAGGC
5' ss Score
9.88
3' ss Seq
GAGCCTAGTCTCTGTTCCAGGGG
3' ss Score
3.82
Exon sequences
Seq C1 exon
ATGTGAGCAGCTACTCCAACTCCCTGCTGGAGGCACTGGTCCCTCTTGTTGCTGACCACAAGTGTAGCAGCCCAGAGGTATATGGTGCTGACATCAGCCCTAACATGCTCTGTGCCGGCTACTTCGACTGCAAGTCCGATGCCTGCCAG
Seq A exon
GTAGGCTGCTGCCAGGCCCCCACCAAGATGACACAGATGGGGTATTACTGGAATTTTCTGACTCCTAGGGAGTCTGGGGCTAACGGGGAACCTAAGGCAGAGGGTCCACGCACTGTGGAGCACTTGGCACTTCCTGGAAGGCATCCTTACAGTAGGAAGAGAGCTGTCTAAACAGATGGGAAAGTGAGTCCAGTTAAAGCCCCACTGTCCAGGCAACAGTTAGGGCCGTCCACATGACATCGGACCTCAAAAGCTACAATGCTCTGTCCAGATTTCTCTTGAATCCTCAGCAATCAATCAATCAATAGTGAATGTTTGTCAAGGGTTTCATAGGCCAGGCCATGGTCATGGTTACGTGTCAACCTGCTTCACCATGGAGGGGCTGTTTTATGCCCTTTAAACAGGCAAAGAAACCGAGTCTTAGAGAGGTTGGATCCCTTTTCTGAAGTGATACAGGGTCAAGTGGACGGAACTTGATGCTGGGACAATGAGGGCTTCCCAGGAAAGAGGACAGTAGCACTGGTTCTAGGAGATGTAAGAAAAGCATGCCAGGCACGAGGAGGCATTTCATACGGTGGCCTAGCACGCAGGGACTGCCCACTCATTCCTCACAGAGTAGGACCAGAGCTGTGGGTGGTAGAGGTGAGAAAGCTTTCCCAAACGTTTGGAAATAGGACACATTCCTGACTGATTGGGGTCAGGAAGAGAGGCCACACTTCTCAGAAAAACCTGTCATCTGCCCCTAGGCAGTCAGCCTTGAAAATCCTGTGAGCACCAGAGACTCTTGCTCACTTATTACTTCAGGATCTTTACAGGGTTGGAAGCCTAGGTGATCCTGAGTCAGGACTCTGGCTGCTGGTGCACAGACAGCTGAGCCTAGTCTCTGTTCCAG
Seq C2 exon
GGGGACTCAGGTGGGCCCTTGGTCTGTGAGAAGAATGGTGTGGCTTACCTGTATGGCATCATCAGCTGGGGTGATGGCTGTGGGCGCCTCAACAAGCCAGGAGTCTACACCCGTGTGGCCAATTATGTGGACTGGATCAACGACCGTATTCGACCGCCCAAGCGACCCGTGGCTACGTCCTGAACCCCGGTCCCCAAGGAAGGGATGCTCATAGTACCCCTTCTACTACCAACAATAAAACTGTCTCCAAGGACCTGGCTTCACAGAGGCACTGCCCTGAGCCAGGCAGCTCTTTGTGTCCAAGC
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000029102:ENSMUST00000201038:11
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.083
Domain overlap (PFAM):
C1:
PF0008921=Trypsin=FE(20.9=100)
A:
NA
C2:
PF0008921=Trypsin=PD(19.2=73.8)
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:
CAGCCCTAACATGCTCTGTGC
R:
TTGGACACAAAGAGCTGCCTG
Band lengths:
358-1250
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