MmuINT0140499 @ mm10
Intron Retention
Gene
ENSMUSG00000026924 | Sec16a
Description
SEC16 homolog A, endoplasmic reticulum export factor [Source:MGI Symbol;Acc:MGI:2139207]
Coordinates
chr2:26428815-26429123:-
Coord C1 exon
chr2:26429062-26429123
Coord A exon
chr2:26428954-26429061
Coord C2 exon
chr2:26428815-26428953
Length
108 bp
Sequences
Splice sites
5' ss Seq
CAAGTAAGG
5' ss Score
7.66
3' ss Seq
GGTGTTCATTCTCTCCCCAGAGA
3' ss Score
9.42
Exon sequences
Seq C1 exon
ACCTTGCTGCAGCACACACCTGAGCAGGAAGAGATGCGCTCCTTCCCAGGACCTCTCGGCAA
Seq A exon
GTAAGGTTCCCTGTTGTGGGGTCTCTTGATGTCTGCCATAGTGGTGGCTGCTGGGTTTGGCTCACAGTTTTGGAACCACCATTCACTGGGTGTTCATTCTCTCCCCAG
Seq C2 exon
AGATGATACCCACAAAGTAGATGTTATTAACTTTGCACAGAACAAAGCAACAAAATGTTTGCAGAATGAAAGTTTAATTGATAAAGAGTCTGCAAGTCTTCTTTGGAAATTCATTATTCTGTTATGCAGACAGAATGGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026924:ENSMUST00000114082:9
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.876 A=NA C2=0.043
Domain overlap (PFAM):
C1:
PF129322=Sec16=FE(19.4=100)
A:
NA
C2:
PF129322=Sec16=FE(44.7=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:
GCTGCAGCACACACCTGAG
R:
TGAATTTCCAAAGAAGACTTGCAGAC
Band lengths:
170-278
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