MmuINT0140477 @ mm10
Intron Retention
Gene
ENSMUSG00000026924 | Sec16a
Description
SEC16 homolog A, endoplasmic reticulum export factor [Source:MGI Symbol;Acc:MGI:2139207]
Coordinates
chr2:26425194-26425587:-
Coord C1 exon
chr2:26425476-26425587
Coord A exon
chr2:26425300-26425475
Coord C2 exon
chr2:26425194-26425299
Length
176 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGG
5' ss Score
11.08
3' ss Seq
ACTTTTCACTTCTTCCACAGTTT
3' ss Score
9.27
Exon sequences
Seq C1 exon
CATCAAAAGGCCTGTTGGATGCTGCACACTTCTGCTACCTGATGGCCCAGGTTGGATTTGGGGTTTATACAAAGAAAACTACAAAACTTGTCTTGATAGGCTCAAATCACAG
Seq A exon
GTAAGGAATCAAGTCACTATAGCAGCGTCCGTTTTCCTCTAAGAAGCAAATGGTCCTGACCTTCAGTTAATTTGGAAGTGGCCAGCCTTACGCCTTAGCTGCATGATGGGCATACTTGGGTTTACCTGCTTGGGTTTATGGTGCCAGTAATTGGCCACTTTTCACTTCTTCCACAG
Seq C2 exon
TTTGCCCTTTTTAAAGTTTGCCACCAATGAAGCCATTCAAAGGACGGAGGCTTATGAGTATGCTCAGTCCCTTGGGGCACATACCTGTTCCTTACCTAACTTCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026924:ENSMUST00000114082:15
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:
PF129312=Sec16_C=FE(14.0=100)
A:
NA
C2:
PF129312=Sec16_C=FE(13.3=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:
CATCAAAAGGCCTGTTGGATGC
R:
CTGGAAGTTAGGTAAGGAACAGGT
Band lengths:
218-394
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