GgaINT0076872 @ galGal4
Intron Retention
Gene
ENSGALG00000014268 | CHRNA9
Description
Neuronal acetylcholine receptor subunit alpha-9 [Source:UniProtKB/Swiss-Prot;Acc:Q9PTS8]
Coordinates
chr4:68575222-68576562:-
Coord C1 exon
chr4:68576408-68576562
Coord A exon
chr4:68575755-68576407
Coord C2 exon
chr4:68575222-68575754
Length
653 bp
Sequences
Splice sites
5' ss Seq
CAAGTGAGT
5' ss Score
9.1
3' ss Seq
GTTGCTTTTCTGTCTTTTAGGGC
3' ss Score
11.61
Exon sequences
Seq C1 exon
GATGAAAGGAACCAAATTTTGACAGCTTACTTATGGATTCGACAAAGCTGGTATGATGCATACCTCAAATGGGATAAGGATAAATATGATGGATTGGATTCTATCAGAATTCCAAGCAATTTGGTCTGGAGGCCAGATATTGTCCTCTATAACAA
Seq A exon
GTGAGTGAGGCCGGAGAGAATAATCTTGAATGGGCGTAGGGGAAGGGGTAGAAGGAGAAATGACTCATGAAGCCTGAACTTCATTTTACCTTAGCAGGGAATGTATTTGTTGTCTTAATATTTATTATTGATCGTCCCTAAAGCCATAGATAAGATAGTTTGACAATTGATCCAGCTACACAGCAGAGCTGCTATGAATTTCTTGGTTGCACTGAGTTCTGAACATTGTCAGTCTTAAATACTTTCTGCAGAGGCTGCCAAAGAGCTCTGAAAGATGGTGCCTACAGAAAGGTGGTATGCAAAGGCTCTGTATCTTGTCTGCTCTCTTGGCCAGTAACGAACAGCAGATTACCATGATTTTTGAATGAATCTGGTATTTCACTGCCTCCTGTTTGAGGTCAAGTTTGAAGAAGCGATGGCCAAGAAATACAGTATAATTTAGTTGCATTGATGTTTGGCACTAATAGGGACCAGTACTTGTAAATAATATAAAGTAATATAGTAAGTTTCTGGTAAAAATCAATCTGAATAAATAACACGTTTTCAGAACCATGCTTTTAATGTTGTGAAGCCAGGATCTCCCTCCAGCTTTCCCCAGCCCATGCACTAAATTGCTCCATATCAATCTTGACTGTTGCTTTTCTGTCTTTTAG
Seq C2 exon
GGCTGATGATGACTTTTCAGAACCCGTTAATACTAATGTTGTGTTGAGATATGATGGAAAAATCACTTGGGATGCACCTGCTATCACAAAAAGCTCGTGTGTAGTGGATGTATCTTATTTTCCTTTTGACAGCCAGCAGTGCAACCTTACGTTTGGTTCCTGGACCTATAATGGTAATCAGGTAGACATCATCAATTCTCTCGATAGTGGTGACCTTTCTGACTTTGTAGAAGACGTGGAATGGGAGATTCATGGTATGCCGGCGGTTAAGAATGTAATCACTTACGGCTGCTGCTCCGAGCCTTATCCAGATGTAACGTTCACGCTGATTTTGAAAAGGAAGTCATCTTTCTACATATTTAATCTTCTGCTTCCTTGCATTTTGATCTCTTTCCTCGCTCCACTGGGATTTTATCTCCCCGCAGACTCTGGAGAAAAAGTGTCTCTAGGTGTTACAGTTCTTCTTGCTCTGACTGTGTTCCAGCTGATGGTTGCAGAGATTATGCCTCCCTCTGAAAACGTACCTCTGATAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000014268:ENSGALT00000023080:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0293118=Neur_chan_LBD=FE(24.6=100)
A:
NA
C2:
PF0293118=Neur_chan_LBD=PD(55.6=64.2),PF0293211=Neur_chan_memb=PU(23.8=31.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AAGCAATTTGGTCTGGAGGCC
R:
CATCTGGATAAGGCTCGGAGC
Band lengths:
356-1009
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]