GgaINT0076870 @ galGal4
Intron Retention
Gene
ENSGALG00000014268 | CHRNA9
Description
Neuronal acetylcholine receptor subunit alpha-9 [Source:UniProtKB/Swiss-Prot;Acc:Q9PTS8]
Coordinates
chr4:68577366-68579148:-
Coord C1 exon
chr4:68578642-68579148
Coord A exon
chr4:68577512-68578641
Coord C2 exon
chr4:68577366-68577511
Length
1130 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGA
5' ss Score
8.68
3' ss Seq
TGAACAAATCTATTATCTAGCTG
3' ss Score
4.01
Exon sequences
Seq C1 exon
TCTATCTATTTTGATGAGGGTTCGTAGGCTTCACTGGGCTGGTTTAGAGCAAGATATTCCTGAATGTAAGGTCAGTAAATCTTGACCCACCAGAGCAATGAAAAATGTCTGATCTGTGAAGAAACATAATCATATGTTTGTAGGGAGTAAAGCAATGGAATACAGTTTTCCTACTGATATCCCATCCGTTTGTTGTCTTGCACAGCATTAGCTTCAAGGAGGCAGCTCTCAGGTTACGGAGAGAGGGAGGGTTCTGCAGAGCCCCAGGCATTGCAGGAACAGAGGCCATCGCTGCAGGACACTGACAGCAGCAGGAGGAGGACTGAGTTGCTTCTAGCTGTACTTTAGTGCCGCAATAACTCATCTTTTGTTACAGTTTTGGATAGTGATAAAAATTGTCATGCTTCTGGGTGAACAGTTTTATTTAAGGTCCAGAAATGAAGAGAAATAACCTGTCATCCTTTTATGTCTCTCTCTGGTTGCTGTTCACAGCCACGATGCTTCAAG
Seq A exon
GTGAGAAAACACTTCTTGGTAGCTAAATATTGCATTGAGGTTTCTTCTACTCATATAGGGGTTGGTGTCCTGATGTGTCGTACTTGGCTGAACTCCAGAAGTCCCCTTCATCTGCGTGTTTTTTTGGCTTTTATTCTTGGTCTTACTGACGTATCGACAAAATGAAGGGTTGTGTATGGTTGTGAACCAGATAGATCTAAACGCTCCTTAGGAAGCTTTTGTGAAGATTTCTTTTTAATCAAGAAGTTTATCTTTGAACTCTGGTTAGCCCAGGAAGTGGCTATGAGTCACCAAAGAGCGGTGCGTTCCAGAATGCTTGCTTCCTACCTTATGCCAGCTGGCATTTGTACAAGCCTTGTGAATGTCACTATCCTTGTCCTTTGCTTGCAAAAATGCATGAGTCTAAAGATAACAGAGACCCTGTCTTGAGAAACTATGGTGCATAAAGTAGTACGGAACTACTTTACGGAACAGCAAAAGTGTTTAAAACCTGAAGTTTTAGTGTTATCCATGGCATGTGGATAGCAAGAAATGCCTCCAAATATATGCTCTGGAATATGTGTTGGTCCAAGGATATGTGTTCATGTTTCATGTAATTGTTAAATTGTGAAGAAAAGCAGCTCAGAATATTTCCAAATGCTTATTAAAAAAAAAAAAAGGGCTGTGGGGGGGGGGGGAATGTAAATTCTGAAAGTATCATGAATCTATCAGTGCTGTGTTTAGGGAGATGTCACAAGTTATTAGCCTGGGAACAGGTTTGACTTCAGGCTTTGCTTGTTGTTTTAGCTTGGCAGGTGTGTTTGAGTCAATAATCTTATATCTTGCATAGGCATGGAGTAAAATAAACGTAATGATGTTCACTTTCAAAAATGGTAAGAATCTCTGGGTACAGAGATTTTGTTGTTTTCTCAAGTAGGTGTGAAAAGCTAGGGCTGACTATTCATTTACTACAGGTGAATGCTGGCTTTATTTGAATAACTTTATCAGGTTCGCTCTGTTTCTGCACTAAACTATAGTTTACAGTATGTGACTGATCAATACAGCAAATGCTATTTGAAGCTATTGGAAGGGGATGGCTCCTGATATTGCTCAGTGCTTAATCTGATGTGCTGAACAAATCTATTATCTAG
Seq C2 exon
CTGTAGAATCAGCCAAAGGGAAATATGCTCAGATGCTGTTCAATGAACTGTTTGAAGACTATTCAAATGCTCTAAGACCAGTGGAAGACACGGATAAAGTGCTGAACGTTACCCTTCAGATAACATTGTCCCAAATTAAAGATATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000014268:ENSGALT00000023080:1
Average complexity
IR
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=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0293118=Neur_chan_LBD=PU(18.8=79.6)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CATTGCAGGAACAGAGGCCAT
R:
ACGTTCAGCACTTTATCCGTGT
Band lengths:
348-1478
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]