MmuINT0075923 @ mm10
Intron Retention
Gene
ENSMUSG00000004894 | Hapln2
Description
hyaluronan and proteoglycan link protein 2 [Source:MGI Symbol;Acc:MGI:2137300]
Coordinates
chr3:88023524-88024118:-
Coord C1 exon
chr3:88023765-88024118
Coord A exon
chr3:88023641-88023764
Coord C2 exon
chr3:88023524-88023640
Length
124 bp
Sequences
Splice sites
5' ss Seq
AGGGTGAGC
5' ss Score
7.75
3' ss Seq
CCAAGCTCTCCGCTCCCCAGGTG
3' ss Score
7.96
Exon sequences
Seq C1 exon
CCCCCCATCCGGGTCCCCACTACCTCCTGCCCCCCATCCACGAGGTCATTCACTCTCGTCGTGGGGCCACGGCCACACTGCCCTGCGTCCTGGGCACCTCGCCTCCCAGCTACAAAGTACGCTGGAGCAAAGTGGAGCCCGGTGAGCTGCGGGAAACGCTAATCCTCATTACCAACGGACTGCACGCCCGGGACTACGGGCTCCTGGGAGGGCGCGCCAGCTTGCGGAGAGGGCATCGGCTGGACGCCTCCCTGATCATCAAGAACGTGCGTCTGGAGGATGAGGGTCGGTACCGCTGCGAGCTCATCAATGGCATTGAGGACGAGAGCGTGGCACTGACCCTGCGCCTGGAGG
Seq A exon
GTGAGCTTTCCTGCGCCGGCACTGAGGTTCCCTAATTATATTGGGGCACCTCACCTCTGCCGGCCTCCCCTGCCCGCGCTCCCCTCCGCACCCAGCTGCCCTGTCCAAGCTCTCCGCTCCCCAG
Seq C2 exon
GTGTGGTGTTTCCGTACCAACCCAGCCGAGGCCGCTACCAGTTCAATTACTTCGAAGCGAAGCGGGCGTGTGAAGAGCAGGACGGACGCCTGGCCACTTACGGCCAACTCTACCAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000004894:ENSMUST00000005014:4
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:
PF0768612=V-set=WD(100=94.1),PF0019312=Xlink=PU(0.1=0.0)
A:
NA
C2:
PF0019312=Xlink=PU(41.1=97.5)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCTCATTACCAACGGACTGCA
R:
AGTAATTGAACTGGTAGCGGCC
Band lengths:
242-366
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