MmuINT0146357 @ mm9
Intron Retention
Gene
ENSMUSG00000017664 | Slc35c2
Description
solute carrier family 35, member C2 [Source:MGI Symbol;Acc:MGI:2385166]
Coordinates
chr2:165102952-165103916:-
Coord C1 exon
chr2:165103741-165103916
Coord A exon
chr2:165103082-165103740
Coord C2 exon
chr2:165102952-165103081
Length
659 bp
Sequences
Splice sites
5' ss Seq
AAGGTACAC
5' ss Score
7.56
3' ss Seq
TGGTCTGCCTTTACCCACAGGAA
3' ss Score
11.1
Exon sequences
Seq C1 exon
GTCTCCACTTGTCCACCTCTGAGAAGATCTTCCGCTTCCAGGACACAGGGCTGCTCCTGTGGGTGCTTGGGAGCCTCCTCCTCGGTGGGATTCTGGCCTTCGGTTTGGGCTTCTCCGAGTTCCTCCTGGTCTCCAGAACGTCAAGCCTCACACTCTCCATCGCTGGCATCTTTAAG
Seq A exon
GTACACACTGGGCAGCCACCCCAGACCTGCCCTGGAAGGAGCCCCCTGAGGGATGCAGGATGTGATGTCATTGTCCCCTGTGGAGCTGAGCCAGTGTCACTTCTCACCAGCACGTAGCTCTGAGGACGCAGGCCAGGCCTCACACCGCCAGGCCTGCAGTGGGCCTACCTTGGGCCTGACTGGCAGCTTGAGTTACATGGCAGTAGCCTGGAGCACTGAATGCTGATCTGTGCAGAGTCCCAGCACTGAGGGCTGGGTGCACAGGTCATGTCTATGGAGGAGCCTGGTCAGGTAGACCCCATGCCGGAGCAGTGACACCCAAAGCAAACATTTGGGTGTTAAGCATCTTCTAGCTCTGATGAGGAGAGACCTGTCTTAACGCCATGCTGAGAGCTGTCCATCTGTGGGTGCCTAGCAACAGCCGACTCCCTTACTGTTGGGGGCACGTGTGCCGCAGTCTGGGGGTTGGTTGGCATTCAGTTTTTGCTGAGAGGCATGCATCTCAGTAACAACAGGTCTGCAGGCTGGTGGTCTGGGTACAGAGGTCCCCACCTCTGCCTGTCACACCAAGTGGTCTGGCTTTGGCCTCAGTGTACACAGAGCCCCGCCTTCCTGGCCACAGAGTCAGCTTCTGACCCATGGTCTGCCTTTACCCACAG
Seq C2 exon
GAAGTCTGCACCCTGCTGTTGGCAGCTCACCTGCTGGGCGACCAGATCAGCCTCCTGAACTGGCTGGGCTTTGCCCTCTGCCTCTCTGGCATCTCCCTGCATGTGGCCCTCAAGGCTCTACATTCCAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000017664-Slc35c2:NM_144893:9
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:
PF0315111=TPT=FE(38.4=100)
A:
NA
C2:
PF0315111=TPT=PD(23.2=79.5)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TCTCCACTTGTCCACCTCTGA
R:
TGGAATGTAGAGCCTTGAGGG
Band lengths:
302-961
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: