MmuINT0077573 @ mm10
Intron Retention
Gene
ENSMUSG00000029102 | Hgfac
Description
hepatocyte growth factor activator [Source:MGI Symbol;Acc:MGI:1859281]
Coordinates
chr5:35045212-35046628:+
Coord C1 exon
chr5:35045212-35045506
Coord A exon
chr5:35045507-35046488
Coord C2 exon
chr5:35046489-35046628
Length
982 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAAC
5' ss Score
5.56
3' ss Seq
CCTGCCAGCTTCCTGTGCAGCCC
3' ss Score
6.23
Exon sequences
Seq C1 exon
GGGAATCCAGGGGTATGAACCGATGACCTCCACTCCCAGAATCCCTGGCCAGAGTCCACTCCCAAACCCCGGAGATCCTAGCAGCCCTGCCCGAGTCAGCCCCGGCTGTGCGTCCTACCTGTGGCAAGAGGCACAAGAAGAGGACGTTCTTGAGACCACGCATCATCGGGGGCTCATCATCTTTGCCTGGCTCACACCCCTGGCTGGCTGCCATCTACATTGGGAATAGCTTCTGTGCCGGGAGCCTTGTCCATACCTGCTGGGTAGTGTCTGCAGCCCACTGCTTCGCCAACAG
Seq A exon
GTGAACACACCTCCTCAGGGGCCACCCACATGTCATATCCCTACCCTCATTCTATCCCATGGGCCCCTACCTGCGACTCACACTCCTCTCCGGCATCAGCATACTTCCATCCAGACGGAAGTATGTTGACCATTTTTTCTGTTCCCCTAACACACCTTTTGGTCCCACTGTGGCCTAACGTGTGTGCTGGGCACTGAGGTAGGCATGGAGCATCGGAGCAGGGCATTTTCTGCAGCTAGCCTTATATCCCTGTGCGGGGATGTGGGGGAACACTCTCCTGTCACCTGCAGAGACCCTGCCTCTCCCAGAGCTGAGCAGTGGGATGGAGTTAAGGTGCCCGAGTTGAAGACATGCCCCATGTACCACCCTGTGTCAGTGCCTAGGTGTTTAAGGGGCACTTACCTGGGCAAGGAGTCAGGAGGCTCAGTTACAACATGTAGTAGACCCTCTAGAGTCACTGCACAGCCAGGGAAACTGAGGCCCAGCTCACTGGATGGGCTCCTAGGAGTGAGGACCTGAGGTCCACTCTGTCTCCACCTAACACGGCTGTAGCCTGAGACACCGAGACTACCTGGACTGAATAGAAAAGCCCAGCAATTCCTCCTAGCTTCATGCCCTGGGGGTAAAGCATTTGCACCTGAGGATCCTCTAGGCCAGACCAAGCCAGGCCGAGGCACAGCATATAGGCAGATCAAATCTCCATCCATGGGACTTATTCTCAGAGCAGACCTTGTCTGAAGGCTCTACTGGTTTATCAATGAAACCCATGAAGCTCGGGCTCCTGGGCCAGGGTCGCTGTGGCTCTGCCTCCCTTGTCAGTCCTGATTCTACTGTCACATGGGTTGAAAATGTCTACAGACCTTTCCCAGGGCTGGGACCCTCTTGCTTGGCCATGACCAACAAAGTACAGGGGCCAAGGTTGGGGAGACCTGATAGTGCCGTGGAGAGGGCTGGGTTTCACTCCTGCCAGCTTCCTGTGCAG
Seq C2 exon
CCCCCCCAGGGACAGCATCACAGTGGTACTGGGTCAGCACTTCTTCAACCGCACCACGGATGTGACACAGACATTTGGCATTGAGAAGTATGTGCCCTACACCCTGTACTCGGTGTTCAACCCCAACAACCATGACCTTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000029102:ENSMUST00000201038:8
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=0.000
Domain overlap (PFAM):
C1:
PF0005113=Kringle=PD(0.1=0.0),PF0008921=Trypsin=PU(36.4=50.0)
A:
NA
C2:
PF0008921=Trypsin=FE(20.1=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGACCTCCACTCCCAGAATCC
R:
GTCTGTGTCACATCCGTGGTG
Band lengths:
344-1326
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