MmuINT0139188 @ mm9
Intron Retention
Gene
ENSMUSG00000040188 | Scamp2
Description
secretory carrier membrane protein 2 [Source:MGI Symbol;Acc:MGI:1346518]
Coordinates
chr9:57425446-57427357:+
Coord C1 exon
chr9:57425446-57425544
Coord A exon
chr9:57425545-57427239
Coord C2 exon
chr9:57427240-57427357
Length
1695 bp
Sequences
Splice sites
5' ss Seq
CAGGTACTG
5' ss Score
9.04
3' ss Seq
CCTGCTCCTGTTCTCTCTAGGCT
3' ss Score
11.35
Exon sequences
Seq C1 exon
ACAAATGCAGCGACAACAGTTCCTGCCACACAAGCTCCTGGGCCCTCCCAGCCAGCAGTTCTCCAGCCCTCAGTGGAACCAGCACAGCCAACGCCCCAG
Seq A exon
GTACTGCTCAGGAGTCCTTTGGCCTCTCCTGTGCAGGTGGGAATCACCCAGGTCCATAGTTGAACCTGCGTTGGGGGCAGGGAAAGGGCCTTCATCCCCCAGGCTGCTTGTAAGATTCTTTGGATCACACTACAGCCCTACTCCTCCTACCCAACCCCCAGCCCCTGGAATAAGCTCTACTCACCAGGCTGGGACCCCTGGTGTCTGCAGAGAACCCCTGTCCTGTTGCACCACTCCAGGTCCTTCCTGGGGCACAGAATCTGCCTGGGTATTTGTTTGTTTGTTTGTGGTGCTGCAAATGAAGTCCAAGGCCTTACAAATACTCTGTCACCAAGCTACATCCCTGGCCCCTCTCTTTTTTAACCTCATTTATTCCTGCCTTCTATCCTATTTGCTTTAGTCCCTTCACTGAGTCTAGTGAACCTTGTCTGCTTGTGCCTAACGCTGACCTCTGTCACCCTCCCCACCCCACCTCCTGACCCCAGGCTTCTCACTGTCTTGGTGAGCATGGCCCACAGTGGAGTTGTGTATTGCAGCTCCCGGTTAGACAGGCCAGCAAGTTTCTGCCTGCCCGATTCCTGGCAGCGGGTGAGCCCTCAGAGAGGCAGACGCTACTAGGAGGAGATAGTATTTCCAGGGACAGCCACAAGCGCAAGCCTTCGAAGGTATGCCCAGTGTAGATGAGCAAGATGAGGGTGGGCTGGGCACCTGGAACCTACCCAGGCTGGGTCCTAGAACCCTGCGAGGTGAGACACTCCCTGTGTGTGGGGTGACTTTATGTTCAGCAGGTATGATGGGATGCAGGGACCCGGCCTCTGTTCCACCCACAGCATAGGGAGATGAGGCTAGGACCAGTTCTAATCCCAGTGCCTGAAGTTCATCTCCCAGGGAGGCAAACTTCACTCTCTGGCGAACTGCTTTTCTGAAATGTGTGCATATGCATACATATGCCTAGTTGTCATTCTGTGAGATGGCCACTCCTGCTCCCCAAAAGAGGACCATAGTCTTGTTCTTCAGGAGGAAGATGGGGCCAAACAGGGGTGACAGCCTAGCTCTGCTCAGCCTCACCCAAGAATCCCTGAACTGCCATTGACAGGCTCTGCCCTTCTGCAGAGGTGACAAAGCTTGGCTGCTTCGTGCCATGAAGGTCAGGCAGGGAAGGGCCACACACCACGGACTGTCCCCAGACATTGTTCAGGAGGGCCTGGGATGCAGCTCCTGGCAGAGTGGAGAGGGAGGTTGCTTTGCTGAGGCTCTGGTGCTGTGGCCTGCCTCGATCTCCTCTGTGCTTTCTGCTGGCAGCCTAGCGTTGTTTCTACTTTGCACACACGCTCAGTTCTTCCCTCTAGCTTCAAGTCTCTGGCTTTCCCGCTTCAGGTTGGGCTCCTGTGCTTTTACCAAAGGACAATACAATTCAGTAGCCTGGACTTCGCCATGGCTGAGCCATGGGAGGTTGGGGAGGGAGTGGAGAGCCCTGCAAGGACTGAGGGGTCAAAGGTGGTGTAAGGGTAGTAGGCAATGGGTCACCTAGGCACTCCCATGGTATTCCTTAATGCTCAAGACACTTTCTTGGGCAGGACTGCCTCAGACCACCTGCTAGCTCTTCCTGCCTGGGTGAAGTGCCTGTGCTGGCCTGCCTGGGCTCACACTGTCTCTTTCTCATTGCTGGCTGTGCCCTGCTCCTGTTCTCTCTAG
Seq C2 exon
GCTGTTGCAGCTGCGGCCCAGGCAGGCTTGCTTCGACAGCAGGAAGAACTAGACAGGAAAGCTGCCGAGCTGGAACGCAAGGAGCGAGAGTTGCAGAACACTGCAGCGAATTTGCATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000040188-Scamp2:NM_022813:3
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=0.512
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF120723=DUF3552=PU(86.7=97.5)
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:
CAAATGCAGCGACAACAGTTCC
R:
TGCAAATTCGCTGCAGTGTTC
Band lengths:
214-1909
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: