MmuINT0140511 @ mm9
Intron Retention
Gene
ENSMUSG00000026589 | Sec16b
Description
SEC16 homolog B (S. cerevisiae) [Source:MGI Symbol;Acc:MGI:2148802]
Coordinates
chr1:159486896-159488279:+
Coord C1 exon
chr1:159486896-159487036
Coord A exon
chr1:159487037-159488165
Coord C2 exon
chr1:159488166-159488279
Length
1129 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGC
5' ss Score
9.6
3' ss Seq
TGCCTGGAAACTCGGCTCAGCTC
3' ss Score
-0.63
Exon sequences
Seq C1 exon
GTGTATAAGCTCCTCTATGCCTCCCGTCTGGCAGATTATGGCCTGGCATCCCAGGCCTTGCATTACTGTGAAGCCATTGGTGCAGCTGTCTTGAGCCAGGAAGGGAGCAGCCACCCTGTGCTATTAGCGGAGCTCATCAAG
Seq A exon
GTGAGCGTCTCAAAGGGATCTCTGTAGGTGTTTTATCTTCAGTGTTCAGAGAAGCCATTGTAGAGAGGCTTAAACTCCACATTTCATCTTCTTTGAACACACTGCAAAATTGGAGCCCACGGCTGTCTTTGACCATGTATGCATGCCCCGATGTGATAAGCAGAGGTCCTGTTTGCACAAAGAACAACTGGCTGGGCAGGGGGCAGAGGGGTTGGGGGACTGCAAAGCAGGCGTGTTCTGCTTGAGAAGTTCTGTGCATCTGCTTTTCTGGTACAGTTAAACTGCAAGCTACGGTGAGCCGTCCTAATTACAAAAGCGAGCCTTTGAAAATAGATTTTAGTGATTAAACCAGGAAATGATCCTTATTAAAATACTTTTAAATGCATGGAATATTTTATCACGTGTGGGACACATTTAAAAAAGAAAACAAAAACCGTACCAACCCTTAGTTTCTTGGGAAGAAACAACAATCAGGAAAATAGTTGTTTCAATTAATTGAAGGAAAAAAAAACCCACTCCATTAGCTAGAGAGTAAAAGGCAGGGTGCTCTACAGTATCTGTACCGCTTTACATGAGGCCCAAGTGCTGGATTCTATAACCAATAAAATCTGTGCTGCCTGAGCCCCTGCCCACACTGCTAGTGGGCTGATGCCCAGGATGAGTAATTAGAGTTTCTAGGTACAGAACATAATGACACCTTGAGGCAGAAAGCAGCATCAGGTGGTGAGCAATGTAGATCTGAGTCCCATCCAGACCAGAATCAGAATTAGCATTAACAAGGTCCCTGAATTTTCTCGAATTTCTATTCTAGAAGTTTCTCGAAGAGAAGGCAGCAATGCACGGACACAAAGCTGGAGAGCTCTCTTTTTCCTCTCATATTTTGGGGGCAATAATACCAAAATGGGTTGCTTATATATTTATACTGCAATTTTGGGAGGAGATCTGCTGAATTTGTTATTTCTCAATTATTCTTTGTTATGTGATGTTTGAGTAAATTATGGCTTCTCCTCCCTTCTTATTGCCTCTCTCCCCTGTTGTCTTTCCACATGCCCCATTTCTCTCTCTTGTCCTTCTCACTTTCTGCCCCTGACCTGCCTGGAAACTCGGCCTGCCTGGAAACTCGGCTCAG
Seq C2 exon
CTCGCAGAGAAACTGAAGCTGTCAGATCCTCTGGTTTTAGAAAGACGCCGTGGGGACAGGGACCTGGAACCAGATTGGCTTGTGCAACTGCGGAGGAAGCACAAGGACCTGGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026589-Sec16b:NR_027641:17
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=0.105
Domain overlap (PFAM):
C1:
PF129312=Sec16_C=FE(18.7=100)
A:
NA
C2:
PF129312=Sec16_C=PD(5.7=36.8)
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:
TGTATAAGCTCCTCTATGCCTCCC
R:
CTCCAGGTCCTTGTGCTTCCT
Band lengths:
254-1383
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: