MmuINT0075925 @ mm9
Intron Retention
Gene
ENSMUSG00000004894 | Hapln2
Description
hyaluronan and proteoglycan link protein 2 [Source:MGI Symbol;Acc:MGI:2137300]
Coordinates
chr3:87825672-87827325:-
Coord C1 exon
chr3:87827143-87827325
Coord A exon
chr3:87826748-87827142
Coord C2 exon
chr3:87825672-87826747
Length
395 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGC
5' ss Score
9.6
3' ss Seq
TCACCCACTCGCATTTCCAGGCC
3' ss Score
8.3
Exon sequences
Seq C1 exon
CGTGGACCGAGGGGCTGGACTGGTGCAACGCCGGCTGGTTGCTCGAGGGCTCCGTGCGTTACCCTGTGCTCACCGCGCGGGCTCCGTGCGGCGGCCACGGGCGGCCAGGCATCCGCAGCTACGGGCCCCGCGACCGCAGCCGCGACCGCTATGACGCCTTCTGCTTCACCTCGGCCCTGGCAG
Seq A exon
GTGAGCCAACTGCGGGCAGGCGGCGCCCGGCCTGGGGACTCCGCCTGCAGGAAGGGCCGTGTCGGGTCAGAGCCTGGACGAAGGACTCCCGGGCGTGGGAGAAAGGACCTAGGAGGTGGCAGGAGCTGGACTTGTTGGCGGAGCAGGGGCTGGTCAGCTCCCTGTGTCGTGGGCGGGACCAGGAGGAAGAGATGGGCGGGGCCTGGGCCCGGGGCGGGGCCGGTGTCAGAAGCCAGGCAGAGAGACAGCGTGTGGGCGTGGTCTGATGTCAGGGCGAGCGCATCCTAGACAATTTTCCTCCGCACGGTCCTGTGAGGGCTTCTCGGAGCTTCGCGGCCGGGTCCCCGTCCCACACCAGCTGCTTTGGGCGGCCGGTCACCCACTCGCATTTCCAG
Seq C2 exon
GCCAGGTGTTCTTCGTGCCGGGGCGGCTGACGCTGTCAGAAGCCCACGCGGCTTGCCGGAGGCGCGGAGCCGTAGTAGCCAAGGTCGGGCACCTCTACGCCGCCTGGAAGTTCTCCGGCCTGGATCAATGCGACGGAGGCTGGCTGGCGGACGGCAGCGTTCGCTTCCCCATCACGACGCCGCGGCCGCGCTGTGGGGGTCTCCCTGACCCAGGGGTGCGCAGCTTCGGCTTCCCCCGACCCCAGCAGGCGTCCTACGGGACCTACTGCTATGCCGAGAAGTAGGAGTGCGACAGAGTGGCGGGTCCCCTCTGGACAGACTAAGGCCCAGCCCTCACTTCTGCCTTCCCCAGGCCAGCGCGGTGCTTCGGGCTGCTGGGCAAAGGGGCGTCCCGGGCATTAACTGACCAATAAAATAACATGGCACCTTCTTTGTTCCATAAGAACAAACATATATTGCATCTATGGCTCAGCAATATACTGGGTTTGTGATTAGAGAGCACCCACAGCACGAAGGACAGAGGAGAGGAAGGAGGAGAGGAAGTCTCAGCAGACCTGGCCATCTACACGGGAGAATACAGGCTGCCCTTTATGTCTAACCAGTCACTCAAAGGTTTCTTATTCAAAATTTCCAGGAACTCCAAACTTCCAGAGCTGTCTGGGCCCTACAAAACAAATATTCAAACTAAACTCATTTCTAAATGTACTTATCACTTCCAAGGTCTGTTTTATTTAGTTTATTAATTTTATTTATTTATTTTGAGACAAGGCCTCTCAATTTTTCCTTGACTGTCCTGGAACTTCCACTGTGGACTAGGCTGGCCTTGAATTCACACACATCAGCCTCCCTCTACCTCCTAAGTTCTGGGATCACATCTGGCTAAAGTCTACAATGAAAGACGGTAAATTCCGTGTGGACTGAGAACTCAGCAGCTAAGCTAACTTGATGCTCTTTCAGAGGACGAGGACCCACAATCATCTGTAACTCCAGTTCCAGGGAATCCAACAACCTCTTCTGACCCCCACAGGCACCAGGCAGGCACACTGTGAGCTTGTCTACTATAATAAATCCACTTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000004894-Hapln2:NM_022031:6
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.081 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0019312=Xlink=PD(57.9=88.7),PF0019312=Xlink=PU(0.1=0.0)
A:
NA
C2:
PF0019312=Xlink=WD(100=95.8)
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:
GACGCCTTCTGCTTCACCTC
R:
GCCTTAGTCTGTCCAGAGGGG
Band lengths:
357-752
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: