HsaINT0152829 @ hg19
Intron Retention
Gene
ENSG00000169507 | SLC38A11
Description
solute carrier family 38, member 11 [Source:HGNC Symbol;Acc:26836]
Coordinates
chr2:165771622-165772483:-
Coord C1 exon
chr2:165772413-165772483
Coord A exon
chr2:165771784-165772412
Coord C2 exon
chr2:165771622-165771783
Length
629 bp
Sequences
Splice sites
5' ss Seq
TTGGTGAGT
5' ss Score
9.27
3' ss Seq
TCTTTTTTTTTGTATTGCAGCAT
3' ss Score
10.41
Exon sequences
Seq C1 exon
ACCAAAAACAGAAGACGCTTGGGTATTTGCAAAGCCCAATGCCATTCAAGCGGTCGGGGTTATGTCTTTTG
Seq A exon
GTGAGTATTTGGTTTCAAAGGCCCTTTCTCAATGTGGAGTTCTCTGTTCCATGAAAAAGTGCTGTGTTTCATATTTATGTCTGGATAGCAGATGTCCTAAGTTTTAGACTTCCTATTAGCAGCATATGATCTAGTTTGTGCCAATATAAAATTAGGCTCAAACTTTTCTCACTCATCACTAAAATTTGCTTCAATTTGGAGAAATCTATTTCTCATGCAGAAACTCATTACAGTCATCTTGTTTCTTAACTTGGAAGGCTAGCAAGTGTTATGGACTTCTTCAAACCCTTTATTATGTCCCAAATGGCAAAGGAAGCCACAGGATGAAAACGATGGGAAAAAGATTTCCTTCAGATGGGAAGGGTCATTAGGAAAAGGAAAATGAGAGAGAATGTTGGACTGGCCTGGTTTATATCAAGAGTAACATGAAAAGACCACATAAGCCTGATGTGAATGAATGGTCTCATTTCTAGAACTATTAGAAAAATTATTTTCTGACATATTAATAAAGTTGTATGTTTAAACTTCAGTTCATTGGCATCTAAAGTAGTATATATCTCTGAATTTCAGAACTAAAAAAGAAAACCCTGGTGCTTGATTTAATAATGCTCTTTTTTTTTGTATTGCAG
Seq C2 exon
CATTTATTTGCCACCATAACTCCTTCTTAGTTTACAGTTCTCTAGAAGAACCCACAGTAGCTAAGTGGTCCCGCCTTATCCATATGTCCATCGTGATTTCTGTATTTATCTGTATATTCTTTGCTACATGTGGATACTTGACATTTACTGGCTTCACCCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000169507-SLC38A11:NM_173512:6
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=PU(8.8=40.0)
A:
NA
C2:
PF0149013=Aa_trans=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:
CCAAAAACAGAAGACGCTTGGG
R:
TGGGTGAAGCCAGTAAATGTCA
Band lengths:
230-859
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Genotype-Tissue Expression Project (GTEx)
- Autistic and control brains
Other AS DBs:
FasterDB (Includes CLIP-seq data)
AS-ALPS (AS-induced ALteration of Protein Structure, links to PINs)
APPRIS (Selection of principal isoform)
DEU primates (Only for human)