MmuINT0139189 @ mm9
Intron Retention
Gene
ENSMUSG00000040188 | Scamp2
Description
secretory carrier membrane protein 2 [Source:MGI Symbol;Acc:MGI:1346518]
Coordinates
chr9:57427240-57428719:+
Coord C1 exon
chr9:57427240-57427357
Coord A exon
chr9:57427358-57428590
Coord C2 exon
chr9:57428591-57428719
Length
1233 bp
Sequences
Splice sites
5' ss Seq
ATGGTAACA
5' ss Score
4.87
3' ss Seq
CTGAACCCTTTTTTACACAGTGC
3' ss Score
6.6
Exon sequences
Seq C1 exon
GCTGTTGCAGCTGCGGCCCAGGCAGGCTTGCTTCGACAGCAGGAAGAACTAGACAGGAAAGCTGCCGAGCTGGAACGCAAGGAGCGAGAGTTGCAGAACACTGCAGCGAATTTGCATG
Seq A exon
GTAACAGAGACTTTTGGGGTCTAGCCTGCTCTACCTGGCACAAGGGGTACTCTGAACCACCTTCATGGGGGATCTTGCAAAGCTTTTGATTTTGGAAGCATGTTGGTTTGGGGAGCTCAACATAGTGACAATAACTGTAACCCCAACACTAGAGGCAGAGGCAGAAGGATTACTCCAAGTGCCAGGCCAGCCGAGGTTATAATATAGTAAGACAACATCGGGGAAAAAAAGAAAGGAAGGAAGGGAGAGTGCTGGTTCTGGGGTAGAAAGAAGGAAGGCAGAAGTTAAAAGATCAGCAGAGTGGGCCTGACAGATATAAGTTATGTCTGCATTCCTTCCCAGCTCAGAAATTCTTTGATTCCCTGGGCCCACAGTCCCATGGTGTTGCAAAAAACTCCTTCCCAGAGAGAGACCTAAACAAGCTCCCAGTGACAAGATGAGGCACAGTTCCACCAAAGTTTACTCTGTGGAACTGGTTCCTTACAGAGCATGTGTGAGAGGTTACTACAGGAGGGTGGGTGCTCCTCCCCCAACGTTCTGTCCCTGGAAAGTCATATCCAGCAGGGAGGAGGACTTCCCTGTGGTGGCATACATGGGGCCCTCTTCCCTATATGGTCTAGCCGCTCCCCAAGGCTATGTACAACAAAAGCAGAATTACATAGAACTTAGAGTAGGGAGTGGCTGGATGTTTAGATGAGAGTCTCCAGCTCCTCAACACAAGCCTAGCTGGGACTATACTTTTGCAAGAGCGTGCAGTTGAACTCCCCAAGATGGTGGTTGCCTGACTTTTACATGGTTATGATGACAACTCTGGTTATCCTGCTTAAGAGCTGGTCATTAATAAAAATACCTTTTTAAGCCAGTATGCTAGCTCACACCTTTAATCCCAGCACTCAAGAGATAGAAGCAGGCAGATCTCTGTGAGTTTAAGGACAGTCTGGTCTACATTCAATAATAGCCAGGGCTACCTCATAGTCTTGAAAGAAACAAACACGTCATTTAGTACATTTAGCGCCCTCTATTACCCAGAGTAGTTGGGACACGTTATCTTGGAGCAGACCTGTGGGTATCTCTCTGGATTCCTCGTGTTCTCACTTCATGTTCCTTGAAGGCCCCTGAAACTTCTGAACTCTGCTTCTAGGGACTTCTCTGCAAGCTCTGTTTTGCCTATAAACTGGGTGGCTGTGTGCTTGCTTCCGTGCCACTGATGAGGCTGAACCCTTTTTTACACAG
Seq C2 exon
TGCGAGACAACAACTGGCCGCCACTCCCCTCATGGTGCCCTGTGAAACCCTGCTTCTATCAGGACTTCTCCACGGAGATCCCTGCTGACTACCAGCGGATTTGCAAGATGCTTTACTATCTCTGGATGT
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000040188-Scamp2:NM_022813:4
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.512 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF120723=DUF3552=PU(86.7=97.5)
A:
NA
C2:
PF120723=DUF3552=PD(11.1=11.4),PF041448=SCAMP=PU(23.5=95.5)
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:
GCAGGCTTGCTTCGACAG
R:
TCCAGAGATAGTAAAGCATCTTGC
Band lengths:
223-1456
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: