MmuINT0146573 @ mm10
Intron Retention
Gene
ENSMUSG00000061171 | Slc38a11
Description
solute carrier family 38, member 11 [Source:MGI Symbol;Acc:MGI:2443383]
Coordinates
chr2:65363347-65364034:-
Coord C1 exon
chr2:65363881-65364034
Coord A exon
chr2:65363468-65363880
Coord C2 exon
chr2:65363347-65363467
Length
413 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAAA
5' ss Score
8.59
3' ss Seq
TATTTTATCTATTAAAATAGAGA
3' ss Score
3.9
Exon sequences
Seq C1 exon
GCACCGGCTCCTTCCATCTCGCTGGCGAACTTAAGCGGGCAAAACCTGCAGGGGAGTTTGGCCTGGTGGGAGCCTGCTTCCCAGCCTCAGAACCTGCCCTTGCGCAGATGCAGACATGAGCTATCAGCAGCCACAGCTGAGCGGTCCTCTGCAG
Seq A exon
GTAAAACTGGCAACAAGGGCAAGAGCTCAACATCCTCCTTAAGTTTAATGCTGGGGTCTTGGTTTGGCAAAAAGGGATAGATCTGACTTAATCTGACCTACACCGATTTGGCAAACACTTTTCAATAACACCAATAACCTCTTTAATTTCATAAAACCGTGTGGTTGACTCCTAACAGACTCTGGAGTTGGGTCAAAGCAGTTGGGCAGCCTCAACATGGAGACTTGTGAAGACTTAAGGATAGACTTTAAGTTCTTTTGGATTGCTGGCCATTCTTGTTTTCCCTCCTTATTGATGTATTATTAACACTATAGGCATAACTTGATGTCATTACTATGTTTGAATCCTGCGTTGCTTATTTATCTGACTTTTTTTTCGAACTAGTAAAATCGTTATTTTATCTATTAAAATAG
Seq C2 exon
AGAGAGACAGACTCGAGTGACAGAGAAAGCCTGATCTCCGGACATGAACACGGAGGGAAATCTAGTCAGTCTGCCGCTGTTTTCAATGTAGTCAATTCTGTTATAGGATCTGGGATAATAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000061171:ENSMUST00000152324:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.615 A=NA C2=0.294
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0149013=Aa_trans=PU(12.0=51.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCACCGGCTCCTTCCATCTC
R:
ATCCCAGATCCTATAACAGAATTGAC
Band lengths:
270-683
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- Ribosome-engaged transcriptomes of neuronal types
- Neural differentiation time course
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types