HsaINT0035239 @ hg19
Intron Retention
Gene
ENSG00000135902 | CHRND
Description
cholinergic receptor, nicotinic, delta (muscle) [Source:HGNC Symbol;Acc:1965]
Coordinates
chr2:233390922-233391384:+
Coord C1 exon
chr2:233390922-233390977
Coord A exon
chr2:233390978-233391238
Coord C2 exon
chr2:233391239-233391384
Length
261 bp
Sequences
Splice sites
5' ss Seq
GTGGTAAGG
5' ss Score
8.37
3' ss Seq
TTGTCGCTGACCCTCCCCAGGCA
3' ss Score
6.62
Exon sequences
Seq C1 exon
TGGGATGGAGGGGCCAGTGCTGACACTGGGGCTGCTGGCTGCCCTGGCGGTGTGTG
Seq A exon
GTAAGGGAAGACACCCTCCCCACCCTGGGGTCCCCCGTGATGCTTACCCAGGCCCCACACCGCATGGCTCCTCACTCACTCCACTCCCACTCTGCCATCTCTCCCTGTGGGGGGCCGCCTTCTGGGGTCCCCACTCCCAGGGAGTGGTTGGGTTCCCCCCTGCTCATCCCAACCTCATGGTCCAGCAGGACCTCAGGGCAGCTTCCTTCCTGAGTCCCCTGCCCAGGGCCCCATTCAGTCCTTGTCGCTGACCCTCCCCAG
Seq C2 exon
GCAGCTGGGGGCTGAACGAGGAGGAGCGGCTGATCCGGCACCTGTTTCAAGAGAAGGGCTACAACAAGGAGCTCCGGCCCGTGGCACACAAAGAGGAGAGTGTGGACGTTGCCCTGGCCCTCACACTCTCCAACCTCATCTCCCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000135902-CHRND:NM_000751:1
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0293118=Neur_chan_LBD=PU(95.3=83.7),PF0293118=Neur_chan_LBD=PU(2.7=6.1)
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:
GGAGGGGCCAGTGCTGAC
R:
CAGGGAGATGAGGTTGGAGAGT
Band lengths:
196-457
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)