HsaINT0035177 @ hg19
Intron Retention
Gene
ENSG00000120903 | CHRNA2
Description
cholinergic receptor, nicotinic, alpha 2 (neuronal) [Source:HGNC Symbol;Acc:1956]
Coordinates
chr8:27327278-27328711:-
Coord C1 exon
chr8:27328503-27328711
Coord A exon
chr8:27327499-27328502
Coord C2 exon
chr8:27327278-27327498
Length
1004 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGT
5' ss Score
10.67
3' ss Seq
TGGCTCTGATTTGATGGCAGGTG
3' ss Score
5.64
Exon sequences
Seq C1 exon
GTTCGGTGGTGAGAGGAAGCCTCGCAGAATCCAGCAGAATCCTCACAGAATCCAGCAGCAGCTCTGCTGGGGACATGGTCCATGGTGCAACCCACAGCAAAGCCCTGACCTGACCTCCTGATGCTCAGGAGAAGCCATGGGCCCCTCCTGTCCTGTGTTCCTGTCCTTCACAAAGCTCAGCCTGTGGTGGCTCCTTCTGACCCCAGCAG
Seq A exon
GTGAGTGTTTGTCACCTGTCATTGTAAGACTTCATCTCATGCCTGTGGGCTCACAAATTGTAGGAAGGAGTCTGCAGGTGGATGTGTTGCAACCGTCAAAGCTGCAGGGGACTTCAGAGGCCATCAGCCAGGTGGCTGTTTCCACTGGCAGAGGTGGAGGGGCAGTCACAGCTCTGACGTTAGCATCTGTGTCACCTTAAATGTCCCCAAGCTTCAATGTCCTCAGCTGCAAAACGCAAATAGTGTTGTGTACCTCCCAGGCCTATTGTGAGGATTAAACGCAAGTTTGTGACCAGAATCTGGGATACAGGAGGCACTCGGGACACAGCGCTTTCTGTCCCAGATGGTGCTGACACGTTTTTCTGGGATTTGGAGCTGTAGTTCTCGACTCGCTCGGACAGCAGAGCCCTGAAGGGGTGAAGCTGTTTGCTGAACACAGTGAAAACTGACATGAGCGATGCCATAGAAACATTTTGAAAAGTTTTGTTTATCTGATAGGAAGTGGCAAATGCCCATGGTTTAAGAAAAAATTGGGGAGGTTCCCAAAGCGGTCCATTTCCCTGTTAGCATTAATGGTTCATCGGACAAGTGGGTGGGAACGGGAGACTGCTTACCCTGGCCAGGCTTACTGCAATGCCAGAGCCCTTCTCCCTGCAGCCCCGCCACGTAGACCAGGCGTCTCTTCCACTTCCCTGTCCACCTGGCACTCCTCCATATGGGGCTGAATCTTGTCTCTAGATTCGTTTCCCCTCTTCCCTGCCTCTGCCCCTGCCCCTCGCCACCTGCAGCACTAGTTCTCACTCTTTTCTTCTCTAACATCACAAAACAGCTGACCTTTCCTGAGCTCCGACCCCGCAGCCTGCTCATGCTGTGCTCAGCTCTGATAGACATTATCATCTGCCATCTTCAACAATGTTTTGAGATAGGTTCTGGATAAGCATCTCCATTTTACAGATGAGCAAACTGAGGCTCAGTGAGGCTGAGTGGCTCTGATTTGATGGCAG
Seq C2 exon
GTGGAGAGGAAGCTAAGCGCCCACCTCCCAGGGCTCCTGGAGACCCACTCTCCTCTCCCAGTCCCACGGCATTGCCGCAGGGAGGCTCGCATACCGAGACTGAGGACCGGCTCTTCAAACACCTCTTCCGGGGCTACAACCGCTGGGCGCGCCCGGTGCCCAACACTTCAGACGTGGTGATTGTGCGCTTTGGACTGTCCATCGCTCAGCTCATCGATGTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000120903-CHRNA2:NM_000742:2
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=0.429
Domain overlap (PFAM):
C1:
PF0315410=Atrophin-1=PU(5.4=12.0)
A:
NA
C2:
PF0315410=Atrophin-1=PD(93.2=74.3),PF0293118=Neur_chan_LBD=PU(18.8=52.7)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCTCACAGAATCCAGCAGCAG
R:
CACCACGTCTGAAGTGTTGGG
Band lengths:
348-1352
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)