HsaINT0035169 @ hg19
Intron Retention
Gene
ENSG00000138435 | CHRNA1
Description
cholinergic receptor, nicotinic, alpha 1 (muscle) [Source:HGNC Symbol;Acc:1955]
Coordinates
chr2:175612323-175613547:-
Coord C1 exon
chr2:175613308-175613547
Coord A exon
chr2:175612984-175613307
Coord C2 exon
chr2:175612323-175612983
Length
324 bp
Sequences
Splice sites
5' ss Seq
AATGTAAGC
5' ss Score
6.12
3' ss Seq
AACATTTTCCTCTCTCCCAGGCG
3' ss Score
9.86
Exon sequences
Seq C1 exon
GTTTTTATCGACACTATCCCAAATATCATGTTTTTCTCCACAATGAAAAGACCATCCAGAGAAAAGCAAGACAAAAAGATTTTTACAGAAGACATTGATATCTCTGACATTTCTGGAAAGCCAGGGCCTCCACCCATGGGCTTCCACTCTCCCCTGATCAAACACCCCGAGGTGAAAAGTGCCATCGAGGGCATCAAGTACATCGCAGAGACCATGAAGTCAGACCAGGAGTCTAACAAT
Seq A exon
GTAAGCTTCGTGGCTTGAAATTCATGCCTCTGGGTTTAAATGGTCAAATGTATGAGCACAGGTGGTGAGTCTGACTTAACAAGTAGGTGGCATACAACAGGCAGCTACTGACCTAAGATGAACCCTGGTGACCGCCTCTAGACCACCTTAGTAAGTTATCACTTTGTAAATAATCTATTCAAAAAATAAAGACGATGCCAGCCAAGGGATGGGAGGACTTTGAGATCTACAAATTGAAGGGCCCATAGTTGATGCAAAGCACAAACGTTGTGAGTCCAGAAACCACCTTAGGGAGACTCTGTCTAACATTTTCCTCTCTCCCAG
Seq C2 exon
GCGGCGGCAGAGTGGAAGTACGTTGCAATGGTGATGGACCACATACTCCTCGGAGTCTTCATGCTTGTTTGCATCATCGGAACCCTAGCCGTGTTTGCAGGTCGACTCATTGAATTAAATCAGCAAGGATGAGCAGAAAATGAGCTGAGCTTAGCTCTGCCCTGGAACCTACCAGAGCAGAGAAGGGCAGGAGAGGAAGATTTGTCTACTTGCTCCACTCGCACTTATCAAACGTGTTATATTCCATACTTATTATTGATGATAAGATTTACCTTTATGTAAGTTTATGGCCTTGAAGTGTTTTCATATTGCTTCTCCCTTTAGTTCTGCTGTCTCCCTGAAGAGTGAACCCTCTTTAGTAAATGAAACTAATCACTAAAAAAAGTGTTCATTTCCAGTGTCTGGAAGAGTTTTTGCCAGGATAACCGAGGTTTTCTGTTGCATTGTCATTGCTGTTATATTTATATATTTACTTATTTTGTCTAACCACGAGACCACTAGGGAGTTGCTGATGTTCTAAATGAAGTGTATTCTTTGCTTAAGAGTCAGTTTTGTACCTACTAAGAAAACCCCATCTACCAGTCCTAAAGAGATAAGGCATTTGATTTGGAGAGAGAGGAAGCAGTAGAAATGAAATAAACTAAAATGCAAACTGCATCAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000138435-CHRNA1:NM_000079:8
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0293211=Neur_chan_memb=PD(31.9=57.5),PF0293211=Neur_chan_memb=PU(56.0=52.5)
A:
NA
C2:
PF0293211=Neur_chan_memb=PD(3.0=6.8),PF0293211=Neur_chan_memb=PD(93.9=70.5)
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:
ACCCATGGGCTTCCACTCTC
R:
ACGTTTGATAAGTGCGAGTGGA
Band lengths:
344-668
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)