MmuINT0006549 @ mm10
Intron Retention
Gene
ENSMUSG00000028794 | A3galt2
Description
alpha 1,3-galactosyltransferase 2 (isoglobotriaosylceramide synthase) [Source:MGI Symbol;Acc:MGI:2685279]
Coordinates
chr4:128761651-128762172:+
Coord C1 exon
chr4:128761651-128761740
Coord A exon
chr4:128761741-128762034
Coord C2 exon
chr4:128762035-128762172
Length
294 bp
Sequences
Splice sites
5' ss Seq
CTGGTAAGT
5' ss Score
10.65
3' ss Seq
CTCCTCCTGCTCATGTCCAGGGC
3' ss Score
7.42
Exon sequences
Seq C1 exon
GCTCATAGAAGGCTCCATCCCCATGGGCACCTGCCCTACAGCCATAATGCCTCTGCCGAGGGACAATTTCACAGGAGTACTGCACCACTG
Seq A exon
GTAAGTAGCCAGTGTTCTCACATGCAGGATGTCCACAAACTATAAAGGTCTGCCCCAGTCCCTGGCTTTCTGCTCACCCACACAAAGGCATTCTGGTTTGGGGAATCCAGAGGGGGCCCATTAGATCACATGCCACCCAAGTTATCACGTTGGTTCTAAGTCAGGGGTGCTTAGGGAACAGGTCTGATATGGCTGTGGGTGCCTAGGGCCCAGCAATGGGGCAGTGGCAATAATTAGCCGCCAAGCAGCTGAGTGGATACAACTATTTTTCTTACTCCTCCTGCTCATGTCCAG
Seq C2 exon
GGCCCGGCCTGAAGTCCTGACCTGTACCTCTTGGGGAGCACCAATTATTTGGGATGGCACTTTCGACCCTCATGTAGCCCAGCAAGAGGCGAGACGGCGGAACCTCACCATCGGGCTGACTGTGTTTGCTGTAGGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000028794:ENSMUST00000106077:3
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:
PF034148=Glyco_transf_6=PU(5.5=51.6)
A:
NA
C2:
PF034148=Glyco_transf_6=FE(15.8=100)
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:
TCATAGAAGGCTCCATCCCCA
R:
TACAGCAAACACAGTCAGCCC
Band lengths:
221-515
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