MmuINT0139212 @ mm9
Intron Retention
Gene
ENSMUSG00000040722 | Scamp5
Description
secretory carrier membrane protein 5 [Source:MGI Symbol;Acc:MGI:1928948]
Coordinates
chr9:57293179-57293980:-
Coord C1 exon
chr9:57293879-57293980
Coord A exon
chr9:57293297-57293878
Coord C2 exon
chr9:57293179-57293296
Length
582 bp
Sequences
Splice sites
5' ss Seq
CTGGTAAGT
5' ss Score
10.65
3' ss Seq
CAGCTGGCTTCTTCCTACAGCGG
3' ss Score
7.23
Exon sequences
Seq C1 exon
GACAGACAGTTCCTTCAGCTTCATGGCATTCTTCTTCACCTTCATGGCTCAGCTGGTCATCAGCATCATCCAGGCTGTGGGAATTCCAGGCTGGGGTGTCTG
Seq A exon
GTAAGTGCCAAAGGTCTGACCTGGGCTGCTGGAGTAGCATTCGGGCTGTTCGCTTGCCTGGGTGCTAAGGTACTTTGCTTTTATGGGCACTGAGTGGCTTGTTTTCTGTTTTTTGTTTTTGTTTTTGTTTTTTGTTTTGTTTTTTCTGAGACAGGGTTTCTCTGTGTAGCCCTGTCTTTCCTGGAACTCACTCTGTAGACCAGGCTGGTCTCGAACTCAGAAATCCTCCTGCCTCTGCTTCCCAAGTGCTGGGATTTAAGGTGTGTGCCACCACTGTCCGGCCACTGAGTGGCTTGTGTGAATAGAAAGAGAGGCTTTGTGGTAGTGGAGTAGTGTTCACCATAGATTGGAGGGGAAGGAGACCTGGGAAGGGGTGTCTTGGGTAGCCAAGGCGTGTCAGATTTTGTAGGAAAGCTGGGGAGGACAAGCCTTCTGGCTCAGGGGCTCTGGGAGCATAGGCTATGGAGTATAAGAAGTGTGGCCACTCTGTGGCTCCTCCCTGTGGCAATGAGATGACCCTTGGGATGGCTCCTGGGTTCCCTTTTCCTACATCACAGCCCCACAGCTGGCTTCTTCCTACAG
Seq C2 exon
CGGCTGGATTGCCACCATTTCCTTCTTCGGGACGAACATCGGCTCAGCAGTGGTGATGCTCATTCCCACGGTCATGTTCACAGTTGTGGCCGTCTTTTCCTTCATTGCTCTTAGCATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000040722-Scamp5:NM_020270:5
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:
PF041448=SCAMP=FE(19.2=100)
A:
NA
C2:
PF041448=SCAMP=FE(22.0=100)
Main Inclusion Isoform:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GACAGACAGTTCCTTCAGCTTCA
R:
AAGAGCAATGAAGGAAAAGACGG
Band lengths:
214-796
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: