MmuINT0140479 @ mm9
Intron Retention
Gene
ENSMUSG00000026924 | Sec16a
Description
SEC16 homolog A (S. cerevisiae) [Source:MGI Symbol;Acc:MGI:2139207]
Coordinates
chr2:26279403-26280077:-
Coord C1 exon
chr2:26279937-26280077
Coord A exon
chr2:26279517-26279936
Coord C2 exon
chr2:26279403-26279516
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-Sec16a:NM_153125:17
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.058
Domain overlap (PFAM):
C1:
PF129312=Sec16_C=FE(55.4=100)
A:
NA
C2:
PF129312=Sec16_C=PD(41.0=89.5)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
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
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types
Other AS DBs: