MmuINT0075927 @ mm10
Intron Retention
Gene
ENSMUSG00000030606 | Hapln3
Description
hyaluronan and proteoglycan link protein 3 [Source:MGI Symbol;Acc:MGI:1914916]
Coordinates
chr7:79121647-79123551:-
Coord C1 exon
chr7:79123370-79123551
Coord A exon
chr7:79122016-79123369
Coord C2 exon
chr7:79121647-79122015
Length
1354 bp
Sequences
Splice sites
5' ss Seq
AAGGTGGGT
5' ss Score
8.23
3' ss Seq
GTGCCCCACCTTGTCCCCAGGCC
3' ss Score
9.95
Exon sequences
Seq C1 exon
TTTTCCCAGGGCCCAGCCTCGTCTAAGAGACCCTGGCACTGCCACCATCCTGGCCGGGATGAGCCTGCTGTTCCTTGTCCTTCTCTCGCCATTTCCCTGCGTTTTGGGACTTCCATTCTACAATGGCTTCTACTATTCCAATGATCTGAGTGGCAGGACCCTGGGAAATGGCTACGGGGAAG
Seq A exon
GTGGGTGTCTCATAGGCCTATGTCCTGGCTTCTGCTGTGATATGCAAGTTCTGGGCTGGGATGGAGACAGCAGGATCTTCCTTGTCCAGGCCTCCAGAGGTGGACAAACTCTGCTTCTAAGATGAGAGGAGATGGTTTAGAGTTTGCTGGTACCAAAGACTGAGTTCTCCTGGGGTGGCCCTAGTTCCTAGAACTGCTAGTTCATTAAGATCTAGCCCGAGTGTAGCTACCTGTGGTGTCCCCTGCAGAAGGGACTTTGGAGTCACAGAGGTGTGAGTTTGAATATCACTTGTAACCTCTTTTGGGCTGGGAGGCCTTGGGCACGGGGCTTTTGAGATGGTGGTCACTGTGTCCTGCAGTGAGTTCTGTTGCTTAGGAAGTTCTGTCATTTGGACCCTGAGCTCTGACAGCCTCTTGCCTTGGCTAAGAGATCTGGGTCTTTGGGAGGAGCCCTGGTCAAAGGTTGGCTCAGACTGTCAAAAGGAGGTGTGCTGTGCTTTCTGGTGGCCATTATAGAATGAAGGGGACTCAGGAACACTTGAAGCAGGGCTCTCGCTGGAACTGCCTTGTCCCTTGGTGTTCTTTCCACCTTCTCTCCCACCGTGTTCTCTGAGCCATGGGTGCCTATTGGAGGGCTGAGCACTGAGCCTCCTCTTCGCAGGTCTTTGACCTCATTAGCCATTTTGACAATCTCAGTTGGTTATGTGAAACAGGAGAGTGAGGGGGTCCTACCTTCCCTTGGGTCTCCTCTGTCTCCTAACTATCGGTCTCAGGACTTGCAAATGGCCTGCTATTGGAGCCTCTCACAGGTGGTTGGTATAGGATGACCCCAGCTGAGGAAGATGCATTCTGCTTCCCATTGTCTCTTGTGCTCTAGGCAGGCAAGTCTGGGCTTGTACTCTTAAGAGACTGGCATTAAACGACCACAGAGAAGGTGGAGTCAACAAGGGCTCCTGGACCCAAGCCTCAGGGTAGGCACAGTGGGACCATCATTTCCATCTTTCATCCAAGCAGCAAACAAGTGGCAAGGCCAGTACAAATCCAAGGAACTGACATCACCCCTCCTCCCTTTTTTAAGACAGTTTCACTGCATGTAGTCCATGCTGGTCTCAGACTAATGTTAATCCTTCAGTCTCAGCCTTCCTACAGGTGCGCCAGCACACCCAGCTCAGTGGAAGTAGACGCAAAGTCGCACCGTTGGGTAGTGGAGGAGTGGAGGAGCAGGCACTTGTAGGAATGGGGAAGGATAGCTCTTTTTGCATCCTGCAACAATTGAGTCTGAAGGGGCTTGGGATGAGGGTATGGGTGCTCCTTGCAAGACCATTATCCCATCTGTGCCCCACCTTGTCCCCAG
Seq C2 exon
GCCTATTCAATGGCGTGAAGTTAGTGGTGGAGACGACGGAGGAGTCCCTGTTCAGTCACCAAGGAGCCAGCGTGACCCTGCCCTGCCACTACCACTATGAGCCAGCCCTGGCATCCCCAAGACATGTGCGTGTTAAGTGGTGGAAGTTGTCAGAGAATGGAGCCCCAGAACAGGACGTGCTGGTGGTCATCGGGCAGAGGCACCGCTCCTTTGGGGACTACCAAGGGCGAGTTCAACTGAGACAGGACAAGCAGCAGGAAGTCTCGCTGGAGCTTCGAGACCTGCGGCTGGAGGACTCTGGGCGCTACCGCTGCGAGGTCATCGATGGCCTGGAAGATGAGAGTGGCCTGGTAGAGCTGGAGCTTCGGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000030606:ENSMUST00000206092:2
Average complexity
IR
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=0.055
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0768612=V-set=WD(100=92.7),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:
TCCTTCTCTCGCCATTTCCCT
R:
CTGTCTCAGTTGAACTCGCCC
Band lengths:
350-1704
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