MmuINT0140524 @ mm10
Intron Retention
Gene
ENSMUSG00000026589 | Sec16b
Description
SEC16 homolog B (S. cerevisiae) [Source:MGI Symbol;Acc:MGI:2148802]
Coordinates
chr1:157532053-157533178:+
Coord C1 exon
chr1:157532053-157532173
Coord A exon
chr1:157532174-157533078
Coord C2 exon
chr1:157533079-157533178
Length
905 bp
Sequences
Splice sites
5' ss Seq
CCAGTAAGT
5' ss Score
9.09
3' ss Seq
CTTCTGTCATTTCGCTGCAGATT
3' ss Score
9.54
Exon sequences
Seq C1 exon
TGGCAAGGCAAGGGAGTCCTTATATCTGGCATGAAGATCATGGAGACCAGAGGTACTTCGGCGAGCATCATCGGGAGAAGCACAATGGTACATTTGGAGCAAACAGTGATACCCAGTTCCA
Seq A exon
GTAAGTGTGAAAACACAAGCCACGCCGACAAGATTTAGTTAGACTCTGTTGGGACAATCTTAGGGCATCTGGTAGTGGTTCCGGTCCTATGGAAGACACAGTCTGCTTTTATGCCAGCCACAGAGAGTGGCCCAGGTCTATTTTTCTCCCTGAGAGCTGCGCTGTTCCCATTCAGGACTAGTCTACATCCTGTAAGGTTACTTTAGGTCCTCAGTGGGAGAGGATGCATTTAGTTCTGCTGTGACTTGATGTCCCAGGACTGATGGGTCCCCAAAGGGGGACTCCCCTTCTCTGAGGAGAAGGTAAGGGGATCGTAGGGGAGGAATTTGGGAGGATAGGACTGAGAGGAGAGGAGGGGGGATATGACTGGATTATAAAGTGAATAAATAAACAACTTAAGGAAAAAGTTACTTGAGGCTCATCTAAAGGTCAAATCCTATAATGGCCTCAGAAACAATGTGGTCTCCCAGTGATTGCTGTGGCTGGAGCCTTTCTGGGGCTGGAATGTTTCTCCATCCACTCTTCCTGGTCATAAGCATGGAACAATCTTGTAGCATAAGACACAGAAGGGCTGGACGTTACTGGAGCACTTGTCCTGGTGCCCTTAGTCTTGGAACTCACCAGTGCAAGGGCTCTGAGTCAGGCTCCTCCAGGAGGGCAGGCTGTAGCAACCAGTCACTCTCCCCAAGGTCTGGATCTTTTTTAGTAAATGTGTGTGGAACCCAAAGATGCCATCTTTCGAGTACATTGAGATAGGAAAGAGAGAGAAAATGCTTTTTGCTGGAGCACTCAAAATGGCCTGACAGGTGCCCACACTTGGCGTTGAGCCTGCCTCCAGCAGAGCGTATTTCAGCCTTGCTGGCTTGCCCAGGACCTGTCTCAACACTTCTGTCATTTCGCTGCAG
Seq C2 exon
ATTTACCAGTAAGAATCCATACCGAGACAGCCCTGCTTCTGTGTCTGGACAGGAACAGCCTGGGGAATTCTTTCCAGAGAGTGAAGCCCAGAAACAAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026589:ENSMUST00000027881:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.951 A=NA C2=0.970
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGGCAAGGCAAGGGAGTCC
R:
TTCTGGGCTTCACTCTCTGGA
Band lengths:
214-1119
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