MmuINT0146573 @ mm9
Intron Retention
Gene
ENSMUSG00000061171 | Slc38a11
Description
solute carrier family 38, member 11 [Source:MGI Symbol;Acc:MGI:2443383]
Coordinates
chr2:65201404-65202083:-
Coord C1 exon
chr2:65201938-65202083
Coord A exon
chr2:65201525-65201937
Coord C2 exon
chr2:65201404-65201524
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
TCCTTCCATCTCGCTGGCGAACTTAAGCGGGCAAAACCTGCAGGGGAGTTTGGCCTGGTGGGAGCCTGCTTCCCAGCCTCAGAACCTGCCCTTGCGCAGATGCAGACATGAGCTATCAGCAGCCACAGCTGAGCGGTCCTCTGCAG
Seq A exon
GTAAAACTGGCAACAAGGGCAAGAGCTCAACATCCTCCTTAAGTTTAATGCTGGGGTCTTGGTTTGGCAAAAAGGGATAGATCTGACTTAATCTGACCTACACCGATTTGGCAAACACTTTTCAATAACACCAATAACCTCTTTAATTTCATAAAACCGTGTGGTTGACTCCTAACAGACTCTGGAGTTGGGTCAAAGCAGTTGGGCAGCCTCAACATGGAGACTTGTGAAGACTTAAGGATAGACTTTAAGTTCTTTTGGATTGCTGGCCATTCTTGTTTTCCCTCCTTATTGATGTATTATTAACACTATAGGCATAACTTGATGTCATTACTATGTTTGAATCCTGCGTTGCTTATTTATCTGACTTTTTTTTCGAACTAGTAAAATCGTTATTTTATCTATTAAAATAG
Seq C2 exon
AGAGAGACAGACTCGAGTGACAGAGAAAGCCTGATCTCCGGACATGAACACGGAGGGAAATCTAGTCAGTCTGCCGCTGTTTTCAATGTAGTCAATTCTGTTATAGGATCTGGGATAATAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000061171-Slc38a11:NM_177074:1
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.592 A=NA C2=0.321
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0149013=Aa_trans=PU(22.9=53.7)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TCCTTCCATCTCGCTGGCG
R:
ATCCCAGATCCTATAACAGAATTGAC
Band lengths:
262-675
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: