HsaINT0085418 @ hg19
Intron Retention
Gene
ENSG00000088247 | KHSRP
Description
KH-type splicing regulatory protein [Source:HGNC Symbol;Acc:6316]
Coordinates
chr19:6417750-6418090:-
Coord C1 exon
chr19:6417992-6418090
Coord A exon
chr19:6417853-6417991
Coord C2 exon
chr19:6417750-6417852
Length
139 bp
Sequences
Splice sites
5' ss Seq
GATGTGAGT
5' ss Score
7.77
3' ss Seq
GCTGCTGCCTCCCTCCCCAGGTG
3' ss Score
11.62
Exon sequences
Seq C1 exon
CAAGCCTGTGAGATGGTGATGGACATCCTCCGGGAACGTGACCAAGGCGGCTTTGGGGACCGGAATGAGTACGGATCTCGGATTGGCGGAGGCATCGAT
Seq A exon
GTGAGTGTGGGCCCTGCCTTCACCCCCCTCTCCCCCGCCAGTGGAGGGAGGGGCCGGGGTGAGTGGCTCCTTGTGGCCAGTGGGCAGCAGAGGGCAGCAGAGCTGCGGGCCGAGCTGACGCTGCTGCCTCCCTCCCCAG
Seq C2 exon
GTGCCAGTGCCCAGGCATTCTGTTGGCGTGGTCATTGGCCGGAGTGGAGAGATGATCAAGAAGATCCAGAATGATGCTGGCGTGCGGATACAGTTCAAGCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000088247-KHSRP:NM_003685:10
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.596 A=NA C2=0.324
Domain overlap (PFAM):
C1:
PF0001324=KH_1=PD(7.7=15.2),PF0001324=KH_1=PU(3.2=6.1)
A:
NA
C2:
PF0001324=KH_1=FE(54.0=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CAAGCCTGTGAGATGGTGATGG
R:
CTTGCTTGAACTGTATCCGCAC
Band lengths:
202-341
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains
- Pre-implantation embryo development
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)