MmuINT0139197 @ mm9
Intron Retention
Gene
ENSMUSG00000028049 | Scamp3
Description
secretory carrier membrane protein 3 [Source:MGI Symbol;Acc:MGI:1346346]
Coordinates
chr3:88983239-88984302:+
Coord C1 exon
chr3:88983239-88983359
Coord A exon
chr3:88983360-88984173
Coord C2 exon
chr3:88984174-88984302
Length
814 bp
Sequences
Splice sites
5' ss Seq
GCAGTAAGT
5' ss Score
9.07
3' ss Seq
CCTGGTTTTGTGCCTTACAGCTC
3' ss Score
9.82
Exon sequences
Seq C1 exon
GCCTCAGCTGCAGCGGCCACTGCTGAGCTGCTGAAGAAGCAGGAGGAACTCAACCGCAAGGCAGAGGAGTTGGACCGCCGGGAGCGAGAACTGCAGCATGTCGCCCTGGGTGGTGCAGGCA
Seq A exon
GTAAGTGAGGCCTGGTTAGGGTGACAGATTAGAAGGAGCATGGGGTCCTCAGTCACACTGTTAAATTCGAGTTTAGTTATAGTTGACACTTCTTAGCCATGGGCTCACAACAGAATGGGTTGTTTTTAAAAGGCTCCTTTATAATATTTTTATTTTATGCGTATGAGTGTTTTGCCTGCACGTATATCAGCACAGCATATGTATGTCGTGTCCATGGAGACCAGAAGAGGGCCACAGATGCCCTGGGGCTGCAGTTACAGGCTGCTGTAAGCCCACATGTGGGTCCTGGGAACCAGCTCTGGGCCTCTGCAAGAGCAGCAAATGTTTCTGATCACTGAGCCTTCTCTGTAGCCCTTTGGGCGGTAGACACCCTTGGGGTGTCTCAGCCCCAACCCACTGATACGCACTCCAACCATTGAGACTTTAGAGTGAACACTTCAGGTTCCTATTTTCTAGAATGTTCTTCTCAATTTACAAAGTGAGGAATTGTGAGGGCTGAATAAAATCAACCTGGGCAAGGTTCTTGGGAGCCTCAGATGTTTCGAGTAGTAACTCTTTGCTTACTGTTGCTTCTTTGTTGTTCTTTGTTTTGTCTTCAAAGAGTCTTGTGTAGACCAGGCTGGGCTGGGCCTCTCTGACCTCCTGCCTCAGCCTCCACAGTGTGGGACTGCAGGCATGCATCCCATGCCTGCTGCTGTCCACTATTTGCCTCTTTTTACCTGGGATTGAGAAGACAGGAGTGGAGGAAGAGGTGAGTGTGGCTCTGATTGACTTGCATTGATATTTGATGTTTTCCTGGTTTTGTGCCTTACAG
Seq C2 exon
CTCGACAGAACAACTGGCCTCCCCTACCGTCTTTTTGCCCTGTAAAGCCTTGCTTTTTCCAAGACATCTCTATGGAGATACCCCAAGAATTTCAGAAGACGGTGTCCACCATGTACTACCTCTGGATGT
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000028049-Scamp3:NM_011886:4
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.715 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF049918=LicD=FE(36.4=100)
A:
NA
C2:
PF049918=LicD=PD(35.5=88.6),PF041448=SCAMP=PU(23.6=95.5)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CACTGCTGAGCTGCTGAAGAA
R:
TCCAGAGGTAGTACATGGTGGAC
Band lengths:
230-1044
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: