MmuINT0146582 @ mm9
Intron Retention
Gene
ENSMUSG00000061171 | Slc38a11
Description
solute carrier family 38, member 11 [Source:MGI Symbol;Acc:MGI:2443383]
Coordinates
chr2:65172647-65173859:-
Coord C1 exon
chr2:65173789-65173859
Coord A exon
chr2:65172809-65173788
Coord C2 exon
chr2:65172647-65172808
Length
980 bp
Sequences
Splice sites
5' ss Seq
TTGGTGAGT
5' ss Score
9.27
3' ss Seq
GGTTTTCTTTTGTGTTCCAGCGT
3' ss Score
8.46
Exon sequences
Seq C1 exon
ACCAAAGACAGACAATGCTTGGGTGTTTGCAAAGCCCAATGCCATCCAGGCTATTGGGGTGATGTCTTTTG
Seq A exon
GTGAGTACCTGGTTTCAAAACTCTTTGTCAATATGACACATCTGCTCTGTGAAGAGGTTCTGGTCCATGTATAGAGGGTCTTCTACGTTTAGATTCCCCATTAACAGTACACAATCTAGTTCCTGTTGATATAAAATCAAGCTCAAGCCTTGCTCGTCCATTATTAAACTTTCTCATTTGTTACTAAATTTTGCTTCTAATTGGAGAACAGTGTTTCGATGCTGGACATTCATGACAGTAGTTAGCACTCAAGCATATCCCTGGCCAGCCCAAAGGGACCCCCATGACAATGGTAGCAATCAGGCACCTTCCTGGCCATCCCCAAGGGACTGGGCAACAAGTCATATCATCCCTGGCTGCTCAAAGGCAAAACAATTCCCATTGTTGCCCCTGTCACATGTCCTCCTGCGCATGTGTCATGGCCCCAATAAAAAGCCACTTTTTCCCCAACCCCAAACCACTTCATTTTCCTTCCTTCCTTTATGTTCTATCGCCCCTCTCTTTAATAAGCCCCACCCCCTCCACATGAGACCTGTTTCCCGGTGTGATTTTGTCAAACTTGTGTTAGTTCCACCAATGGTTAGTGTGTCTCCTAACTTGGAAGTCCAGTAAATGTCATAGACTTCTATAAAGTCTTGGCAGAAAGGATTTAGGATTTCGCTAGATATTTATAACTCCACTATGTCCCAGCTGCCAAATAAAGCAAGGTACAAATTTTCCTGAAGATAGGAAGAGGAAAAAATGGGAGAGTTGTTGGACAGGTCTGGTTTATGTTGAGAGTTACATGAAGTTACTAGGTAAGCCTTCTGTGAAGTTCCTTGTATGTAGGCCTTACGTTCTGGCTTACTTAGTGCTGTAAATTAATATATGTTCATTTGAGATATTAGATATTCTAAGGCAGTATACATCTCTCACCTTTTCAAAGTAGAAAACACAGTCCTGCTGTTTCCCGAGTAATGAGGTTTTCTTTTGTGTTCCAG
Seq C2 exon
CGTTCATTTGCCACCATAACTGCTTCCTAGTCTATGGTTCTCTCGAAGAGCCCACAGTAGCGAAGTGGCGCCGGATTATCCACACATCCATCTTGGTTTCTGTATTCATCTGTGTGCTCTTTGCAACGTGCGGGTACTTCACTTTTACTGGCTTCACTCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000061171-Slc38a11:NM_177074:8
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:
PF0149013=Aa_trans=FE(8.5=100)
A:
NA
C2:
PF0149013=Aa_trans=FE(19.0=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:
CCAAAGACAGACAATGCTTGGG
R:
TGAGTGAAGCCAGTAAAAGTGAAGT
Band lengths:
230-1210
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: