HsaINT0149191 @ hg19
Intron Retention
Gene
ENSG00000125731 | SH2D3A
Description
SH2 domain containing 3A [Source:HGNC Symbol;Acc:16885]
Coordinates
chr19:6754262-6754742:-
Coord C1 exon
chr19:6754627-6754742
Coord A exon
chr19:6754437-6754626
Coord C2 exon
chr19:6754262-6754436
Length
190 bp
Sequences
Splice sites
5' ss Seq
GAGGTGAGC
5' ss Score
8.7
3' ss Seq
CTTGCCCTCCACCTCTGCAGGCA
3' ss Score
9.79
Exon sequences
Seq C1 exon
GCCACAGGCCTCCTGGGAGTGACCAGAGATCAGCGGGGCAACATGGGAGTCTCATCTGGCCTGGAGCTGCTCACTCTTCCCCATGGACACCACTTGAGGTTGGAACTGCTGGAGAG
Seq A exon
GTGAGCCAGCAGCTTGTAATCTTGGTTGGGGGAGGCCAATTCCCCCCACTTCCCAAGATCTCCAAACAGCTCCCCACTCATGGTTCCCCAGGGAAGAAGGGAGATGGGGCAATGCCACCTCCTGTCCCCCCTCACCCCTGCATTACAAACCTCCCCACTTCCCCCAGACCCTTGCCCTCCACCTCTGCAG
Seq C2 exon
GCATCAGACACTGGCGCTGGCCGGGGCGCTGGCGGTGCTGGGCTGCTCGGGGCCGCTGGAGGAGCGCGCAGCCGCACTGAGGGGACTGGTAGAGCTGGCGCTGGCGCTGCGGCCAGGGGCGGCGGGGGACCTGCCCGGGCTGGCTGCAGTCATGGGCGCCCTGCTCATGCCCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000125731-SH2D3A:NM_005490:6
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.115 A=NA C2=0.040
Domain overlap (PFAM):
C1:
PF0061714=RasGEF=PU(7.5=23.1)
A:
NA
C2:
PF0061714=RasGEF=FE(48.3=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Rat
(rn6)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGGGAGTGACCAGAGATCAGC
R:
CATGACTGCAGCCAGCCC
Band lengths:
257-447
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)