MmuINT0140528 @ mm9
Intron Retention
Gene
ENSMUSG00000026589 | Sec16b
Description
SEC16 homolog B (S. cerevisiae) [Source:MGI Symbol;Acc:MGI:2148802]
Coordinates
chr1:159465983-159467784:+
Coord C1 exon
chr1:159465983-159466044
Coord A exon
chr1:159466045-159467648
Coord C2 exon
chr1:159467649-159467784
Length
1604 bp
Sequences
Splice sites
5' ss Seq
TAGGTAAAG
5' ss Score
6.93
3' ss Seq
CTTCCTGAATCGTCCCACAGGGA
3' ss Score
9.47
Exon sequences
Seq C1 exon
GTTTTACTTAATGATTTTGAGGATCAGGAGGAGATGAGAGCTTTCCCAGGGCCCCTTATTAG
Seq A exon
GTAAAGTACTGTAAGTGTTGTTAAGGGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGATATGCACACATGTGTGAAGGCGTACACATGCATACATATGTGGAAGCCAGAGGAAGACATCTGTTGTTTTCTTCTTTCTCTCCCTCATCTTCTTTTGTTCTCTTAGTTTTTGAGAGAGGATCTCTCACTGAACCTGAAGCTTGCCATTTTGGCTAAGCTGTCTGACCACTGAGCTCCCAGTATATGCCTGTCTCTGTCCCCCAAACTCTGGCATTACAGGAACACATTGTCCATGCCTGGCTTTTATGGGGGTGTTTGGAATTTGATCTCATGTTCTCTTGCTTTCAGAGCAACTTCTCTGACCCCACTAAGTTATGTCACCAACTCCTAAATAAAGGCTTTTGAAAGCTGAGGACTCTTCCTGGCCAGGTCTTGGTTGTCAGGGAAGAAAATGTCTATTTTATTTGAACCAGATTTTTCTATGCCAGTAGGTAGAAAAAGAGATGACCTGAGTGATTTTAGCAAGCTGTTTCATATTTGAAGAGGAGAAAGAGAAGTAAGCTTAACAAGTTAGACCTTTAAAAACAGTTCCATTTCATAGAGGTTAGCTGGTAGGAAGCTTCAGTGTTCCAAGGACTTGATAGAGATTAGTGGGGAAATGGAGCACGGCCTGGAGAAACGTTCTTAAAACGGCTTTTTCTTGAGCTGATTTTTCCAGCTCCCTGCCATTGTGAACGTCTGCCCTCTGCAGGAATAAAGTAGAACTGCTGTAGCATTTTCAGCCACATTTCATCGGGTTTTAGCTGTGATGAGTCCTGGGTGGGTGGGTGTCAGAGGACCAGCATGCCAGGTAGCCTACTAAGTACTGGCTTATCAGCCATCTTTAAGTTTTTCCCTTGAGAAATGATATAGCACTCACTCTGCCTACTCCAAAGGCCGTGAAACTCTATTCATATGAAGGCCAGTGAATGTCGCTACTTCTTTGTACATGTAATCTGAAGCTAGCTCACAAGCACACGCTCACACATGTATGTGGGTACAAATGTAGAGGTCAGAGGAAAATCTCAAGGGTCATTCCTTAAGTACCTAACCCTTTTCCCCCTATGTCTTACAGGTTTGCAAAAAACTAAGTTGTGTATTAAATAGTATGAATGTTCTTGAACATTTAACAAGCACTTACTTGATGGATGCCATACAGTTTGCTTACCCCCTTTTTTAATGCAGGCAGTTGTTTTTAAAGTCCCGTCCTAAGTTAAGGATGGCACTGAGGCTCAGAGCAAGTGAGATGTTTACATAATCCAGACATGGACCCAGTCTTGTCTGACTTGAAACAGAACCCTTCTGAGAAGTCATTTAAGGTCTTTGGGTTTACTCTCCTCATTTAAAAGATGGAAGGATGCACAAGAGAATCTCTGAAACTCCTCCCTGTTCTACAGGAAAAAAACCCCCAAAACCCCAAAAAACCAAAAAACAAACGATCTTGCGATTCCAGACTTCCAGTCCTGGGCTCTCACCCTTCTGCCATGTTAGCGAGTTCATTGTACAGAGTCTGTACAGGGAGAGTCAGTCTGCTCAGGCCTTGCTTCCTGAATCGTCCCACAG
Seq C2 exon
GGAGGACATACACAAGGTGGATATCATGACGTTTTGTCAGCAGAAAGCAACGCAGTGTCTCAAATCTGAGACACCAGGGAGCAGAGACTCAGCTCTACTTTGGCAACTGCTGGTTCTCCTTTGTCGACAGAATGGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026589-Sec16b:NR_027641:9
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=0.000
Domain overlap (PFAM):
C1:
PF129322=Sec16=FE(19.6=100)
A:
NA
C2:
PF129322=Sec16=FE(44.1=100)
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:
TAATGATTTTGAGGATCAGGAGGAGA
R:
CCCATTCTGTCGACAAAGGAGA
Band lengths:
190-1794
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: