MmuINT0140479 @ mm10
Intron Retention
Gene
ENSMUSG00000026924 | Sec16a
Description
SEC16 homolog A, endoplasmic reticulum export factor [Source:MGI Symbol;Acc:MGI:2139207]
Coordinates
chr2:26423883-26424557:-
Coord C1 exon
chr2:26424417-26424557
Coord A exon
chr2:26423997-26424416
Coord C2 exon
chr2:26423883-26423996
Length
420 bp
Sequences
Splice sites
5' ss Seq
CAGGTAGGA
5' ss Score
9.79
3' ss Seq
CTCTGTTCTCTGGGGTCTAGATG
3' ss Score
6.55
Exon sequences
Seq C1 exon
GTGTTTAAATTCATCTACTTGTGCCGCCTGGCTGAAATGGGACTTGCCACACAGGCCTTCCACTACTGCGAAGTAATAGCCAAGAGTGTCCTGACACAGCCTGGTGCATACTCTCCAGTACTGATTAGCCAGTTGACTCAG
Seq A exon
GTAGGATCTTCTGGTGCCTTCCTGTTAGCATCTTGCCAACTCTGGGGAAGCACAGGCTTCATCTTGCTGAGCTTGGGGTGGTGAGTGGTACTTAACAAAGAGATATCCAGAATGTGCTTTAGATACCTCAGTGCTCTGGGGCGGCTGTTTTGGACTTTGCATCATTAATAGTCACTACTTAACAAATTCATCTTGATCCATTCAAATCCTTTAAAGGCCCTATCAAAGAACTTCATCTTCCCTGGTTAGTTGAGTACTTGGACAGGCCTGCTAATATCCATATAAGTGTGAACTGCACCCTGGCGCACTCGATGATTTATACAACCCACACATGACCTCCTTCAGGCCCAGGGAACACTTGGGAACAATTTTATTGGTGCCATTTGGCAATAACAAGGACCTCTGTTCTCTGGGGTCTAG
Seq C2 exon
ATGGCTTCCCAGTTACGCCTCTTCGATCCTCAACTGAAGGAGAAGCCAGAAGAGGAGTCCTTTGTGGAGCCTGCCTGGTTGGTGCAGCTGCAGCACGTGGAGAGGCAGATCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026924:ENSMUST00000114082:17
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=0.052
Domain overlap (PFAM):
C1:
PF129312=Sec16_C=FE(17.4=100)
A:
NA
C2:
PF129312=Sec16_C=PD(12.1=84.2)
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:
TGTTTAAATTCATCTACTTGTGCCGC
R:
CTGGATCTGCCTCTCCACGT
Band lengths:
254-674
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