HsaINT0035261 @ hg19
Intron Retention
Gene
ENSG00000196811 | CHRNG
Description
cholinergic receptor, nicotinic, gamma (muscle) [Source:HGNC Symbol;Acc:1967]
Coordinates
chr2:233409482-233411038:+
Coord C1 exon
chr2:233409482-233409612
Coord A exon
chr2:233409613-233410252
Coord C2 exon
chr2:233410253-233411038
Length
640 bp
Sequences
Splice sites
5' ss Seq
AATGTAAGC
5' ss Score
6.12
3' ss Seq
CACCTGCCTCCCACCCTCAGGGG
3' ss Score
10.08
Exon sequences
Seq C1 exon
AGAAAGGCCCGGAGTTAGGGCTGAGCCAGTTCTGTGGCAGCCTGAAGCAGGCTGCCCCAGCCATCCAGGCCTGTGTGGAAGCCTGCAACCTCATTGCCTGTGCCCGGCACCAGCAGAGTCACTTTGACAAT
Seq A exon
GTAAGCTGAGTCAGGGTGGGGTGGAGGTGGAGTGAGTACCTGGGCTTGGAACCGTGATAGAGACAGGATGAGTGGGGTTGCCAAGATAGGGCAGTGGGATGGAAAAACATGAGGCCGGGTGCAGTGGGTCACACCTGTAATCCCAGTACTTTGGGAGGCCGAGGCGAGTGGATCACCTGAGGTCAGGAGTTTGAGACCAGCCTGGCCAACATGGCAAAACCCTATCTCTACCAAAAATACCAAAAATACCAAAAATTAGCTGGGTGTGGTGGCGGGCACCTGTATTCCCAGCTACTCAGGAGGCTGAGGCAGGAGAATTGCTTGAACCTGGGAGGCGGAGGTTGCAGTGAGCCAAGCCAAGATCGCACCACTGCACTCTGGCCTGGGTGAAAGAGTGAGACGTGAGACTCCGTCTCAAAAAAAAAAAAAAGGAAAGAAAGAAAGAAAAAGGAACAGGGGCAGGGGGGGCACCTCAGGGCCAGGGGGCCATGGAATTAGCCACCAGTTGGGACCCGGACATAGGTAAGAAGGGCCCCAGGAAATGGAGACATGGGCCTGCTGGAAGCCCAAGGATGAGAACAGGACCCAGGGAAGACCTGGTGCCGCCGCTGGTTATCCCACACCTGCCTCCCACCCTCAG
Seq C2 exon
GGGAATGAGGAGTGGTTCCTGGTGGGCCGAGTGCTGGACCGCGTCTGCTTCCTGGCCATGCTCTCGCTCTTCATCTGTGGCACAGCTGGCATCTTCCTCATGGCCCACTACAACCGGGTGCCGGCCCTGCCATTCCCTGGAGATCCACGCCCCTACCTGCCCTCACCAGACTGAGCCAACCAACCACTGTGGGGCATGTGGGAGTCACACACGTGGGTCACACTGAGTCTTATCAGCCACGTTCTCCTACTGAGGTCCTAAGTGTGCTCTTTGGGAAGTGCCCTTCAGGACTGTGTGAGCCAAACAGCCCTGAGAAAAGCTGGGGAAACAGTCTGAGCTGGAGTCCGAGAGTGGTTGGGGGTGGGCCGTGGCTAGTGTCCTGCTGCAGTCAGCACACACGTGGGATTGGCTAGCTCATCCTGGCACCAGCCACCCCTCCACTCAGTGCACTCCCCTCACTTAGGCAAAGCATTATTCATTCCCATCAGTCTGAAGCCCGAAGGACTGTTTTGTATAATACCTTCGGACTTGGGACTGGCTCCCCTTTTACAAGTTCTCCCTGAAAGAGGGCAGTCACAAGAGGTGTGAAGAGTAGCAGCCGATGCTCTCTCCAAAGCAGGGCAGCAGCCCATACCAGCTGGCATCTCCCCCCCGTGCCTTCTGGGTACAATAAGCACCCAATTCTCAACAGCCCCAGTGGCCTTTCCATTCATGTGCATTTTTCTGCCACTGACCACAAGACGATTTCCTGAGTTTTGTAATCCTCTTTTTTTTTTTTTTTTTTTT
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000196811-CHRNG:NM_005199:11
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=0.053
Domain overlap (PFAM):
C1:
PF0293211=Neur_chan_memb=FE(17.6=100)
A:
NA
C2:
PF0293211=Neur_chan_memb=PD(12.7=53.4)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCACCAGCAGAGTCACTTTGA
R:
CCAGCTTTTCTCAGGGCTGTT
Band lengths:
348-988
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)