MmuINT0075920 @ mm9
Intron Retention
Gene
ENSMUSG00000004894 | Hapln2
Description
hyaluronan and proteoglycan link protein 2 [Source:MGI Symbol;Acc:MGI:2137300]
Coordinates
chr3:87830807-87831433:-
Coord C1 exon
chr3:87831307-87831433
Coord A exon
chr3:87830863-87831306
Coord C2 exon
chr3:87830807-87830862
Length
444 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGG
5' ss Score
10.07
3' ss Seq
GCAACTTCTTCCTTCTGCAGGAC
3' ss Score
9.99
Exon sequences
Seq C1 exon
AGAAAAGAAAAGGACAGACAGACAGAAAGGGTCAGGGTCCTGAAGCAGCCAGACATCCTGAAAATCTGACTCCCATCTTGACAGCCTCTTCTGAAAGGCCATATATAGCCTGGCACAGAGGGCACAG
Seq A exon
GTGAGGGCTTTGGTGGGGGGGAGGGCAATTCTGTTGTTTGGATGGGGTCCATATGAAAATACAGAGCTGGATTCACAATTAGGGTTCGTCCCCGCTCCTCCTGGTCCAGCACCCTTGTACTTACAATTGGTCTGTCCCACCCCTGGTCTAAGGACAGAAGTAGCAAGGCCCGCTCTCCACACTCTTTTAGGTAATCTCCAGGATTGCTTTACTCTGCCCCCAACCGGTGTCTTGCCCTGGCCCCAGGACATCAACTGGCACAGATGCAATCACGGCTGACTTAGTGTGCTGCGTGAACATAGGCCTCAGTGCCTTGGCTTCTCTGAACACAGGAAACGAGTCTCTCTAGAACCGTGTCAGAGGAGCTGCAGTCCTGAGGCTCTAGGGTGCTTTGAACCCCCAGAATCCCTAATGAACCCCCACTGCAACTTCTTCCTTCTGCAG
Seq C2 exon
GACAGGAAGCTGCTGAGCACAGCTCGATTTGCCTCTGAGGAGAGATCATCTTGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000004894-Hapln2:NM_022031:1
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
5' UTR
No structure available
Features
Disorder rate (Iupred):
C1=NA A=NA C2=NA
Domain overlap (PFAM):
C1:
NA
A:
NA
C2:
NA
Main Inclusion Isoform:
NA
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGAAAAGAAAAGGACAGACAGACAGA
R:
TGCAAGATGATCTCTCCTCAGAGG
Band lengths:
182-626
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: