HsaINT0035173 @ hg19
Intron Retention
Gene
ENSG00000129749 | CHRNA10
Description
cholinergic receptor, nicotinic, alpha 10 (neuronal) [Source:HGNC Symbol;Acc:13800]
Coordinates
chr11:3690426-3691171:-
Coord C1 exon
chr11:3691026-3691171
Coord A exon
chr11:3690581-3691025
Coord C2 exon
chr11:3690426-3690580
Length
445 bp
Sequences
Splice sites
5' ss Seq
ATGGTGCGT
5' ss Score
8.27
3' ss Seq
CCATTCCCTGCCCCCACTAGGAT
3' ss Score
8.27
Exon sequences
Seq C1 exon
AGTGCCTGGGAGCTGAGGGCCGGCTGGCTCTCAAGCTGTTCCGTGACCTCTTTGCCAACTACACAAGTGCCCTGAGACCTGTGGCAGACACAGACCAGACTCTGAATGTGACCCTGGAGGTGACACTGTCCCAGATCATCGACATG
Seq A exon
GTGCGTTGTGGTGGTGGTACAGCTGTGGAGTCTTACCTGTCACAGTGTCAAGAAATGAAGGGGTGAGAGACTGGGATTATTCTCCATGGAATTTCTTTTCTGTAAATGTTAATATTAACAAAGGTAGCAGTTACAAACTGTTGGGTACTGACTGTTGGGTACTGAGTATTGGGTGCCTACCTCGTGCCCAATATTTTGTTCACCTGAACTTACTGAATCCCTGCTAAGCAGGGATTCTCACCCCATATTCCTGCTGAGGAAACAGGGGCAGAAAAGAGAAGAGCCCACTAAGGTCACATGGCAAGGTCAGGTCTGGGTGGGAACTGGACGGTATGGACAAGTCAGGTTTGTGGGTGCTGACCAGAGCCCTGCAGGGGAGTGTGCACAGACAGGGCAGGATATGCATATACATGTCCACATCTCTGCCATTCCCTGCCCCCACTAG
Seq C2 exon
GATGAACGGAACCAGGTGCTGACCCTGTATCTGTGGATACGGCAGGAGTGGACAGATGCCTACCTACGATGGGACCCCAATGCCTATGGTGGCCTGGATGCCATCCGCATCCCCAGCAGTCTTGTGTGGCGGCCAGACATCGTACTCTATAACAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000129749-CHRNA10:NM_020402:2
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
No protein impact description available
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0293118=Neur_chan_LBD=PU(18.8=79.6)
A:
NA
C2:
PF0293118=Neur_chan_LBD=FE(24.6=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGTGCCTGGGAGCTGAGG
R:
TAGAGTACGATGTCTGGCCGC
Band lengths:
295-740
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
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)