MmuINT0042014 @ mm9
Intron Retention
Gene
ENSMUSG00000026853 | Crat
Description
carnitine acetyltransferase [Source:MGI Symbol;Acc:MGI:109501]
Coordinates
chr2:30260048-30260593:-
Coord C1 exon
chr2:30260458-30260593
Coord A exon
chr2:30260111-30260457
Coord C2 exon
chr2:30260048-30260110
Length
347 bp
Sequences
Splice sites
5' ss Seq
CCGGTGAGA
5' ss Score
8.72
3' ss Seq
CCTGTCCCCCTCTCCCCCAGGAG
3' ss Score
11.63
Exon sequences
Seq C1 exon
GATCTATGGGCAGGCGTGTGCCACGTATGAAAGTGCCTCTCTGCGCATGTTTCACCTGGGCCGCACTGACACCATCCGCTCAGCCTCCATAGACTCGCTGGCCTTTGTCAAAGGCATGGGTGACTCCACAGTGCCG
Seq A exon
GTGAGAGGGCTAGAGCAAGGGTGTGTAGACTGAGCTTAGGCCTCTCCTTCCTTTCCTGTTGACTCTCTGCAAATGGATTGTACCTCTATGGTATTTCAGCCCCACTGTGGGCAAAGGGAACTTAACAGAAGATGGAGCCATGAATTTAGTTCTAAGCTTTCTGGCAAAACCATGTATCCGTAAGAGACAAGCCAGTCTCCGTCCACTCATGCAAGTGAGTGCTAGGCTCCAGAGAATGAGGGGATGGGAATGCAGTACTCGCTGTGGTGCCGGGTACAGAGCGAGCTGCTAAGGTGGAAAGGGAGAGGGAGGACAGGGCTTCAGCTTCCTGTCCCCCTCTCCCCCAG
Seq C2 exon
GAGCAGCAGAAGGTGGAGCTGCTCCGGAAGGCTGTGCAGGCCCACCGAGCCTACACTGACCGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026853-Crat:NM_007760:11
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.011 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0075515=Carn_acyltransf=FE(33.8=100)
A:
NA
C2:
PF0075515=Carn_acyltransf=FE(15.8=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GATCTATGGGCAGGCGTGTG
R:
CGGTCAGTGTAGGCTCGGT
Band lengths:
198-545
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: