MmuINT0075922 @ mm9
Intron Retention
Gene
ENSMUSG00000004894 | Hapln2
Description
hyaluronan and proteoglycan link protein 2 [Source:MGI Symbol;Acc:MGI:2137300]
Coordinates
chr3:87827687-87828393:-
Coord C1 exon
chr3:87828252-87828393
Coord A exon
chr3:87828041-87828251
Coord C2 exon
chr3:87827687-87828040
Length
211 bp
Sequences
Splice sites
5' ss Seq
CGGGTAAGA
5' ss Score
9.84
3' ss Seq
ACTGTGGCCCCTCTGCTCAGCCC
3' ss Score
5.82
Exon sequences
Seq C1 exon
TACTAGGGAGTGCCCACCACCTGTGCCCTGCAGACGGTGCTTGCTGACACCATCATGCCAAGCAGGATCCCTCTCCCTGCGTTCTGCTGCTTCCTTCTCCCCTGGGCCTTCACCAGCTTTCACAAAGCCCTGGGGAATCCGG
Seq A exon
GTAAGACCGTAGCCCAGCCCCCAACCAGAACACTGGGGTAGGGGACCAAGGGATGGAGGAATAAAAAGGGCAGCTGTTGAAAGTCCCTAGGGAGTGAGAATCAGTGGGGAGAGGTAAGGCTGAGCCCGAGGAGAGCCTCTGGGGACTAGGTCTGAATGGGCACTTGGGGCAGGGAAGATCAGAAGCCTGCCACTGTGGCCCCTCTGCTCAG
Seq C2 exon
CCCCCCATCCGGGTCCCCACTACCTCCTGCCCCCCATCCACGAGGTCATTCACTCTCGTCGTGGGGCCACGGCCACACTGCCCTGCGTCCTGGGCACCTCGCCTCCCAGCTACAAAGTACGCTGGAGCAAAGTGGAGCCCGGTGAGCTGCGGGAAACGCTAATCCTCATTACCAACGGACTGCACGCCCGGGACTACGGGCTCCTGGGAGGGCGCGCCAGCTTGCGGAGAGGGCATCGGCTGGACGCCTCCCTGATCATCAAGAACGTGCGTCTGGAGGATGAGGGTCGGTACCGCTGCGAGCTCATCAATGGCATTGAGGACGAGAGCGTGGCACTGACCCTGCGCCTGGAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000004894-Hapln2:NM_022031:3
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0768612=V-set=WD(100=94.1),PF0019312=Xlink=PU(0.1=0.0)
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:
GGTGCTTGCTGACACCATCAT
R:
CGTGCAGTCCGTTGGTAATGA
Band lengths:
293-504
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: