MmuINT0139211 @ mm10
Intron Retention
Gene
ENSMUSG00000040722 | Scamp5
Description
secretory carrier membrane protein 5 [Source:MGI Symbol;Acc:MGI:1928948]
Coordinates
chr9:57446072-57447233:-
Coord C1 exon
chr9:57447077-57447233
Coord A exon
chr9:57446174-57447076
Coord C2 exon
chr9:57446072-57446173
Length
903 bp
Sequences
Splice sites
5' ss Seq
CAAGTAAGT
5' ss Score
10.08
3' ss Seq
AACCATCTTCTCTGCCATAGGAC
3' ss Score
9.46
Exon sequences
Seq C1 exon
TGAACAGCGTCACGCTGGCCGTGAACCTGGTGGGCTGTCTCGCGTGGCTGATCGGAGGCGGGGGAGCCACCAACTTTGGCCTGGCCTTTCTCTGGCTCATCCTCTTCACACCTTGCTCCTACGTCTGCTGGTTTCGGCCCATTTACAAGGCCTTCAA
Seq A exon
GTAAGTGGTTGGTGCCGACCCCAGCTCCTACCCCTATTTCCCTCTGACTGCTGTTCCACACTCTTATCTTCTGTTTCCCTTGGGATTCCTGGGAGTTCCTGGCTGGGTTGAGAGGGTTGGGAGTGGGACCTTCCTTAGTTCCTTCCTTCTTCAGTTTTCCCTTCTTGTTAAGTTTTGCCTATGGGGCTGTCTTGGTGGAGCTGTCCATCCTTGTACCAGTGGGGAATGACTGGTTTGGTACCAAGAAAACCCTTTATTCACGTGTCAGTGGAAGTGGCCATCTAAGACCCATGGATGCTATTCATGGGCCAATGATGCCATCCAAGCCTGTGCCAAAGGGAATACCTATCTATGTATTGATGGGGTGCCAGGGAGTGTCTATCCAGTGCCAACTGGGATTTCCATTTTTTGTGCCATTAGAGCTGCAAGACAGCAACAAAGCTGTCTTGGTGCCAGCAGAATATACATTTCAGTGCCATGGAGCCTTAAATCTCTTTATCGACAGGACTCACCATCTATGTGCCAATTAGCTACTGTTTGGTGTCAGTAAGGTCTCTTTTCTATGCCACCGAGACTTGCTGTTTCTGAGTCTATAGAGCCACCCACCCCCATTCCAGTTCCTTGATAATGGAGCTGCTTGCTTTTCCCACAACAGAGCCAAGTATCGCTATGCCAGTAGGGCCGTTAATCTATGTGCTACGGATGGACGGTCCTTTTATGGGGGCAGCCCTTTCTTGCACACAGGCCTAGCTCATCTCTGAATGAAGGCCATCCTTTTTACATTCTCATTCAAAGCACACTTGTGTTGTTTGCTCGTCCTTTTGCCCAGAGGAGCTTTGGGAGCTCGAGTGCAGGGAAGCCCAGTGCCTCTGCCCAGGTGACAAACCATCTTCTCTGCCATAG
Seq C2 exon
GACAGACAGTTCCTTCAGCTTCATGGCATTCTTCTTCACCTTCATGGCTCAGCTGGTCATCAGCATCATCCAGGCTGTGGGAATTCCAGGCTGGGGTGTCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000040722:ENSMUST00000046587:4
Average complexity
IR
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(29.4=100)
A:
NA
C2:
PF041448=SCAMP=FE(19.2=100)
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:
GCTGGCCGTGAACCTGGT
R:
CAGACACCCCAGCCTGGAATT
Band lengths:
246-1149
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