HsaINT0036318 @ hg19
Intron Retention
Gene
ENSG00000169583 | CLIC3
Description
chloride intracellular channel 3 [Source:HGNC Symbol;Acc:2064]
Coordinates
chr9:139889894-139890209:-
Coord C1 exon
chr9:139890100-139890209
Coord A exon
chr9:139890020-139890099
Coord C2 exon
chr9:139889894-139890019
Length
80 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGG
5' ss Score
10.07
3' ss Seq
CACCCCGCTGCTGCCCGCAGGTC
3' ss Score
9.99
Exon sequences
Seq C1 exon
GCGAGTGAGGACGGGGAGAGCGTGGGTCACTGCCCCTCCTGCCAGCGGCTCTTCATGGTCCTGCTCCTCAAGGGCGTACCTTTCACCCTCACCACGGTGGACACGCGCAG
Seq A exon
GTGAGGCCCCATCCTGTGGACCCCCGCCTGGCCTCGCACACTGGTGGGCCGGCCTCCTCCCACCCCGCTGCTGCCCGCAG
Seq C2 exon
GTCCCCGGACGTGCTGAAGGACTTCGCCCCCGGCTCGCAGCTGCCCATCCTGCTCTATGACAGCGACGCCAAGACAGACACGCTGCAGATCGAGGACTTTCTGGAGGAGACGCTGGGGCCGCCCGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000169583-CLIC3:NM_004669:2
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=0.005
Domain overlap (PFAM):
C1:
PF134171=GST_N_3=PU(41.1=81.1)
A:
NA
C2:
PF134171=GST_N_3=FE(57.5=100),PF134101=GST_C_2=PU(11.2=34.9)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TCTTCATGGTCCTGCTCCTCA
R:
GCGTCTCCTCCAGAAAGTCCT
Band lengths:
174-254
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)