HsaINT0035242 @ hg19
Intron Retention
Gene
ENSG00000135902 | CHRND
Description
cholinergic receptor, nicotinic, delta (muscle) [Source:HGNC Symbol;Acc:1965]
Coordinates
chr2:233391239-233392155:+
Coord C1 exon
chr2:233391239-233391384
Coord A exon
chr2:233391385-233392110
Coord C2 exon
chr2:233392111-233392155
Length
726 bp
Sequences
Splice sites
5' ss Seq
CTGGTGAGA
5' ss Score
7.54
3' ss Seq
GCCCTACCGTCTAATTACAGAAA
3' ss Score
6.89
Exon sequences
Seq C1 exon
GCAGCTGGGGGCTGAACGAGGAGGAGCGGCTGATCCGGCACCTGTTTCAAGAGAAGGGCTACAACAAGGAGCTCCGGCCCGTGGCACACAAAGAGGAGAGTGTGGACGTTGCCCTGGCCCTCACACTCTCCAACCTCATCTCCCTG
Seq A exon
GTGAGAGGCCCTCCGGTGCTGGGTTGGGAGGGAGGGCAGGGATGGCTTTCCAGTACCAGGATAGCCATGGAGGAAGCTAGAAGCCCCCACCTGGCCTATGGCCACTCCCTTCCTGGGAAACGTGCTGCGGCTGCTCTGTGCCCTGAGAGGCTGCTGTCCTGCCCCTCCAGTGTCAGCTCTGCGGTGTCCCCCAACCACACCCATAGCATGCCCCATCTGTGACACACTTCAGAGGCCACTGGTCCTCTCTGCTCCCTGGCGGCCTACCCACTCCTGACTGCGAGTGATCAGGGCCCAGATGCCACGGTTTCCCTGGGTGCCAATTGACAGTGGGTGAATGTAGGCTGGGTGTGGTGGCTCATGCCTGTAATCCCAGCACTTTGGGAGGCCCAGGTGGGTGGATCACCTGAGGTCAGGAGCTCGAGACCAGCCTGGCCAACATAGTAAAACCTGATCTCTACTAAAAATACAAAAATTAGCCGGGTGTGATGGTGTGGGCCTATAATCCCAGCTACTAGGAAGGCTGAGGCAGGAGAATCGCTTGAACCCAGGAGGCAGAGGTTGCAGGTTGCAGTGAGCCAAGCTCGTGCCACTGCACTCCATCCTGGGCAATTGAGCAAGACCCTGGAAAAAAAAAGAGAGAGAGAGAGAGAGAGAGAGTGGGTGAATGTGTGCGGATAAAAGAATGATATGGCCCTGAAGGATGGCCCTACCGTCTAATTACAG
Seq C2 exon
AAAGAAGTTGAGGAGACCCTCACTACCAATGTGTGGATAGAGCAC
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000135902-CHRND:NM_000751:2
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=0.000
Domain overlap (PFAM):
C1:
PF0293118=Neur_chan_LBD=PU(95.3=83.7),PF0293118=Neur_chan_LBD=PU(2.7=6.1)
A:
NA
C2:
PF0293118=Neur_chan_LBD=FE(16.7=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:
GGGGCTGAACGAGGAGGAG
R:
GTGCTCTATCCACACATTGGT
Band lengths:
184-910
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)