HsaINT0035175 @ hg19
Intron Retention
Gene
ENSG00000129749 | CHRNA10
Description
cholinergic receptor, nicotinic, alpha 10 (neuronal) [Source:HGNC Symbol;Acc:13800]
Coordinates
chr11:3686817-3688994:-
Coord C1 exon
chr11:3688462-3688994
Coord A exon
chr11:3687795-3688461
Coord C2 exon
chr11:3686817-3687794
Length
667 bp
Sequences
Splice sites
5' ss Seq
TCGGTGAGC
5' ss Score
9.1
3' ss Seq
GCTTTCTCTCTCTCTTGCAGGGA
3' ss Score
13.54
Exon sequences
Seq C1 exon
AGCCGACGCGCAGCCTCCAGGTTCCGCCAGCACCAACGTGGTCCTGCGCCACGATGGCGCCGTGCGCTGGGACGCGCCGGCCATCACGCGCAGCTCGTGCCGCGTGGATGTAGCAGCCTTCCCGTTCGACGCCCAGCACTGCGGCCTGACGTTCGGCTCCTGGACTCACGGCGGGCACCAACTGGATGTGCGGCCGCGCGGCGCTGCAGCCAGCCTGGCGGACTTCGTGGAGAACGTGGAGTGGCGCGTGCTGGGCATGCCGGCGCGGCGGCGCGTGCTCACCTACGGCTGCTGCTCCGAGCCCTACCCCGACGTCACCTTCACGCTGCTGCTGCGCCGCCGCGCCGCCGCCTACGTGTGCAACCTGCTGCTGCCCTGCGTGCTCATCTCGCTGCTTGCGCCGCTCGCCTTCCACCTGCCTGCCGACTCAGGCGAGAAGGTGTCGCTGGGCGTCACCGTGCTGCTGGCGCTCACCGTCTTCCAGTTGCTGCTGGCCGAGAGCATGCCACCGGCCGAGAGCGTGCCGCTCATCG
Seq A exon
GTGAGCAGCGGGGGCGCGGGGGGACCTGACGATGCGCTGGGGTCCCCCCAGGGCGGGGCCGCGACAGGGCCTGGGTCTGCGGAACGGCCCCACTGCAGAAAGTGAGAGGGGGGCGTCCTGGGAACGTGCCCTCATTTTAAGACTGAGGGGAAAGGATTAGCTCCTTCCAGGGAGAACACCCCTCACGACTTGGCCCTTGATGATGGAACATCAGTATCCCCAGATCCTAATGATAGGCAAAATCTGTCGACTGCTTGCTGTGTGCCAGGCACTCCCCTAAGCACTTGACCTTTATTAACTCAGGTAAGCATCACCACAAACCTAGGAAGTAGGTCCTCTGGGTATCCCATTTGTACAAAAAGGATTCGTATCTTGCCCCAGCTCATGCCCGTCGTTATTTGAGAGCGGGACTGTCCTGGATTGTGTATGAGTGCAGCCTCCAGCAGTGACGGGAGCAATTAGAGAGCAGTAGCTTCCGATGACCCACGTGTAGGAATGAAGGATGGGGAGAACTCGGCCCTTACCTCCTTCCTGCTTCCATCCATGGGGCTTGGAGGGTCTGGAGAGCTTCATGGTGGGCTTATTTCCATTTGTGCAGAGGTGGCTGGGAAGCTCAGGAACCACAGGCTTTTGTTTTGAGTCAATTGGCTTTCTCTCTCTCTTGCAG
Seq C2 exon
GGAAGTACTACATGGCCACTATGACCATGGTCACATTCTCAACAGCACTCACCATCCTTATCATGAACCTGCATTACTGTGGTCCCAGTGTCCGCCCAGTGCCAGCCTGGGCTAGGGCCCTCCTGCTGGGACACCTGGCACGGGGCCTGTGCGTGCGGGAAAGAGGGGAGCCCTGTGGGCAGTCCAGGCCACCTGAGTTATCTCCTAGCCCCCAGTCGCCTGAAGGAGGGGCTGGCCCCCCAGCGGGCCCTTGCCACGAGCCACGATGTCTGTGCCGCCAGGAAGCCCTACTGCACCACGTAGCCACCATTGCCAATACCTTCCGCAGCCACCGAGCTGCCCAGCGCTGCCATGAGGACTGGAAGCGCCTGGCCCGTGTGATGGACCGCTTCTTCCTGGCCATCTTCTTCTCCATGGCCCTGGTCATGAGCCTCCTGGTGCTGGTGCAGGCCCTGTGAGGGCTGGGACTAAGTCACAGGGATCTGCTGCAGCCACAGCTCCTCCAGAAAGGGACAGCCACGGCCAAGTGGTTGCTGGTCTTTGGGCCAGCCAGTCTCTCCCCACTGCTCCTAAGATCCTGAGACACTTGACTTCACAATCCACAAGGGAGCACTCATTGTCTACACACCCTAACTAAAGGAAGTCCAGAGCCTGCCACTCCCCTAATTCCAAAAAAAAGAGGAACTCTACAAAGGCCAAGATCACAGAGTACAGTCTTGGAGGGACAGAATTGTTTGTGCTGGGTATTGGAGCTCTCAGTGGGGAGCACATGGGTTATAATGAGAAACTGAACTGTACTGCTGCATTTCCTGTCTTCCTTCCTAGGTGGCTGCTTTGCAGGGCTTTGGCTGTTACCTTTCCCTGCTGAGGGGCTCAGGGAAAAGGGTCGGGGATTCTCAGTCGAGTTTCCAGAGCAGGAGGCCCTACAGACATTTGGCCCCAAATCCCTGACTCAATAAAGTAAGCGTGTACCTAGCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000129749-CHRNA10:NM_020402:4
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.011 A=NA C2=0.138
Domain overlap (PFAM):
C1:
PF0293118=Neur_chan_LBD=PD(55.6=64.2),PF0293211=Neur_chan_memb=PU(36.8=31.3)
A:
NA
C2:
PF0293211=Neur_chan_memb=PD(62.5=62.1),PF0293211=Neur_chan_memb=WD(100=47.1)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTCACCGTCTTCCAGTTGCTG
R:
TTCCTGGCGGCACAGACATC
Band lengths:
348-1015
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Genotype-Tissue Expression Project (GTEx)
- 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)