HsaINT0035240 @ hg19
Intron Retention
Gene
ENSG00000135902 | CHRND
Description
cholinergic receptor, nicotinic, delta (muscle) [Source:HGNC Symbol;Acc:1965]
Coordinates
chr2:233398641-233399052:+
Coord C1 exon
chr2:233398641-233398845
Coord A exon
chr2:233398846-233398933
Coord C2 exon
chr2:233398934-233399052
Length
88 bp
Sequences
Splice sites
5' ss Seq
CACGTGGGT
5' ss Score
4.46
3' ss Seq
CTCTGGCCCCTCGTCTGTAGGCC
3' ss Score
8.58
Exon sequences
Seq C1 exon
CTCTTCCTGGAGACCCTGCCGGAGCTCCTGCACATGTCCCGCCCAGCAGAGGATGGACCCAGCCCTGGGGCCCTGGTGCGGAGGAGCAGCTCCCTGGGATACATCTCCAAGGCCGAGGAGTACTTCCTGCTCAAGTCCCGCAGTGACCTCATGTTCGAGAAGCAGTCAGAGCGGCATGGGCTGGCCAGGCGCCTCACCACTGCAC
Seq A exon
GTGGGTCCCCGCTGGTCTTGGTTTTCAGCCCATCTGTGGGAGGTGGGTGGAGGCAGGCCTCACACCCACTCTGGCCCCTCGTCTGTAG
Seq C2 exon
GCCGGCCCCCAGCAAGCTCTGAGCAGGCCCAGCAGGAACTCTTCAATGAGCTGAAGCCAGCTGTGGATGGGGCAAACTTCATTGTTAACCACATGAGGGACCAGAACAATTACAATGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000135902-CHRND:NM_000751:10
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.217 A=NA C2=0.475
Domain overlap (PFAM):
C1:
PF0293211=Neur_chan_memb=FE(30.8=100),PF0000317=7tm_3=PD(6.2=7.2)
A:
NA
C2:
PF0293211=Neur_chan_memb=FE(16.5=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:
CGCAGTGACCTCATGTTCGAG
R:
TGTTCTGGTCCCTCATGTGGT
Band lengths:
175-263
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)