HsaINT0035188 @ hg19
Intron Retention
Gene
ENSG00000101204 | CHRNA4
Description
cholinergic receptor, nicotinic, alpha 4 (neuronal) [Source:HGNC Symbol;Acc:1958]
Coordinates
chr20:61987723-61991051:-
Coord C1 exon
chr20:61990900-61991051
Coord A exon
chr20:61987768-61990899
Coord C2 exon
chr20:61987723-61987767
Length
3132 bp
Sequences
Splice sites
5' ss Seq
GTGGTAGGT
5' ss Score
7.23
3' ss Seq
TTCCTCTCTCGGTGCCCTAGGAT
3' ss Score
9.61
Exon sequences
Seq C1 exon
CCAGCAGCCATGTGGAGACCCGGGCCCACGCCGAGGAGCGGCTCCTGAAGAAACTCTTCTCCGGTTACAACAAGTGGTCCCGACCCGTGGCCAACATCTCGGACGTGGTCCTCGTCCGCTTCGGCCTGTCCATCGCTCAGCTCATTGACGTG
Seq A exon
GTAGGTGAGGGCGTGGCCATCGTGCACTGTGACTGAGGTCGCCCTGCAAGGAGCACAGGGGTCTGGGTGGGCAGAGGGGACACAGCCATCAACACTCCCCGTGGCTGTGAGTGTCCGGCCCGGGCTGGTACGTCAGAACGACAGCCACCAGCTCTGCCCCGCCTGAGCCCCAGCCAAGGGTTGATTCAGAGCGTCCCAGCCAGGCCCTGCCCTTTCCTCCCCCTTGACGTGGGAACACTCCAAGTGGCCAGGTTCTCAGTACAGAGCCCAGGCACCTTCGGAAGCAAAGAACAGCAAAGGCCTTGCTTGGGGGTGGCGGGGCACGCTGTGACCTCGGAGCAACAGGGACAACCGGCCGGGGCAGGGGCCGGGGCAGGAGCAGGCACTGTGGTGTCCCGGCAGCACCCCAACCTTAGCTGGCCCCAGAGGCCCCTCACCCACAGATCTGGAATGTGGGGTTTGGGGGAGTCTTGGGCGAAGTCTGTTTGTCTGAAGATATGTTCTTTCTGGTGGGGGGCCCAAGAAGGCTGCTGGGAGGAAGCCTACTGGTCCAGCCAGGCCCCTGCAGCGTGGGCCAGTGCACATGGAGCCCCAAGGCAGGATAGGAACCAGGAGGCTTCGAGGCTGAGAGAACTGAGCTGCGGGAGGCTCGGCCTTGTGCTCGGTTGAGATGCTTGGTTACCTACCCAGGCCTGAGCCAGACTGTCTGGGGGTCTCGGCGGCCCTGGAGGGGCCGGGTAAGGGGCAGCAGAGACATTTCCACGTTTCCCAGCCAGGCTCAGCCACTCCAAATGGGGTGAGACCATCCCTCAGGGTACCTGGCTGGGTGGGGGTGCATAGCCTGGGGGCTGCCACCATGGAGGAGGGCAGGTTGGGCAGGCCATGGTCTCTGGGAGCTGGCCCACTTGCGAGTGGGCAGCCAATGGCCAGCTGAGCTGCAGGGGCTCGTCTTCCACACTGAAGTCCGCCAGCTCCAGCCCTGCTGCCAAATCCCAGCTCGCTGGTCCAGGGAGGGCACCCCCACATGGGGAGGCATTTGTATGCTGTAGAGGCCCAGCCCACACCTTGCCAGGATGCCAAGCCTGGGTCTGCCGCTGAGGGAGGAGCCACCGGGTTGCGGGAGAATTTCCTCTCTTTGGGAGGCTGGTGCCGTGCGTGTTGGGTAACCCTGGGCCTGGGGCCTGTGAAACGGGGTGAGAGCTGCTTCACTATCCCAGGCTGAGTGGGCCACACCCCAGGGGCTTTTGGGAGGTGTGGGGAGCTGCAGCCACATTCCCGCGGACAGGCTGCTCAGTGGTGGCAGTTGCCCATGCAGGGCAGCGCATGGAGACTCCAGTCAGCCAGCCCCGTCCAGGGTTGGCCACCCAGACCTCCAGCCTCAGTGTCCTGGAGCTGCCCTTGAGTGGCTCCTGTGGAGTGTCCCTGGCGGAGGCCCAGCCAGAAGACAATGCGGGTTGCACAGGCTTGGCAAGCCTGCTGAGGTTTGCAAACACGGCTGCAAAGTGATAGCTGGCAGAGGCGGCCGCTGGCAGCTGCCCAAGGCTCTGGGTCTGCCACCCCCCACCTGGCTGCCTACCTGAGCTTCTCAGGGCTCAATCCATGGCTCCCTACGCCACCACAGAGTCCCCAGTTTGCCCAGGAGACATTGAGGCCTGGAGCACACCCAGAACCAAGACTCCCAGAGCTGCCCACCCCTCTCTCCACCCTGCAGCCGACTAAGGACTTACACGAACATGCACACGTGGGTGCTGACGCTCCTGGGTGCCCAAGGCCGAGGGCCACGTGTGCACGGAAGGGGCTGCCTGATGCTCCTGGGTGCTGGCCTAAGGCTGAGGACCACGTGTATGTGGAAGGGGCTGCCTTGTGTCTGGCCCACTCTGCCCGTCCCACCAGGGGCTGGGGATTCACCTGTGCCCCCTTTGCGGGCTCGGATACTTGTTATAGGTGCCATCACCAGGGTCTGTCCTGGAGGGGAGGGCTTGTGAGCTGCACGTGTGAGCTCAGGCCCCAGGACTGGCTGCAGAGGAGGGTCTGGAAGACCCAGTGCTTTTCCAACCAGCCCAGGCCAGTGCTGAGTGGTGGTGAAATGTGCAGTGTTGACCTGCCCTCCAGCTTCAAGGGCGACTGAGAATGACGGCTGCAAGGGGGTAGGGCACGACACTGGGCAGGAGGGCCAGGCCTGGCCACGTGAAGCTGGTTCTGAGGACCCTGGAGCTTCCTCAGACACACGGGATGAGGTCCTGAGGGGATGAGGTCCTGTGGGGAGATATGGCCCTGCACGGAGACATGGTCTGTGGGGACGTGGTCTGTGGGACGTGGTCCTGTGGGGACATGGTCAGTGGAGATGTGGTCCTGTGGGTTGTGGTCCTGTGGGAATGTGGTCCTGTGGAGACGTGGTCCTGTGGGGACACGGTCCGTGGAGACGTGGTCCTGTGGGAATGTGGTCCTGTGGGGATGTGGTTCTGTGGGGACGTGGTCCGTGGAGATGTGGTCCTGTGGGTTGTGGTCCTGTGGGGACGTGGTTCTGTGGGGATGTGGTCCATGGAGATGTGGTCGGTGGGGACGTGGTCCTGTGGGGATGTGGAAGGAGGTGGGTGGGGTGGGTCGGAAGGGGCTGGGGTGAGTGGCCCAGCTGCACACAGTGACCTTGAGTGACAGGTCCCACCTGCTCAGGTCATGAGGCACAGTCCTGGAGGGGCCACCCTGGCCAGCAGTGGAACCCACTTATGTGCCAGGGGCAGCTTTGCTGGCTGTGTGTGCCCACATGGGGGCCTTGTCTGCAGAGGGGCTGCCCCCAAGGGCCGGGAGGGAGCAAGGCAGGTGGGCAGAAGGAGGCTCCCCATGCCCGCCACACCTGTCCTTAGCTGGGGAAGCCTGTGAGGCCGCCGACTCCTCTCCAGTTTCCTGCTGGAGATGTTTGTGGCCTTGTCCCCACATCCCTAGGTCCCCTCAGAGTCCCCATCCTGGGCTCGGCTGCCTCCAGGGACGGGGCACTCACCCCCTCCACAGGTCGCCCGTCCACCATATCTTGCCCTGGCCGTGTCCTTGTGCCAGTGGCTGTAGATGAGGAAACCTAGGGCCAGAGAAAGACACCAAGGGGTCACTGGCCCCCTTCCTCTCTCGGTGCCCTAG
Seq C2 exon
GATGAGAAGAACCAGATGATGACCACGAACGTATGGGTGAAGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000101204-CHRNA4:NM_000744:2
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.029 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0293118=Neur_chan_LBD=PU(18.8=76.5)
A:
NA
C2:
PF0293118=Neur_chan_LBD=FE(15.0=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:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
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)