GgaINT0076873 @ galGal4
Intron Retention
Gene
ENSGALG00000014268 | CHRNA9
Description
Neuronal acetylcholine receptor subunit alpha-9 [Source:UniProtKB/Swiss-Prot;Acc:Q9PTS8]
Coordinates
chr4:68574227-68575754:-
Coord C1 exon
chr4:68575222-68575754
Coord A exon
chr4:68574778-68575221
Coord C2 exon
chr4:68574227-68574777
Length
444 bp
Sequences
Splice sites
5' ss Seq
TAGGTGAGC
5' ss Score
7.96
3' ss Seq
AATTTTATTCTGTGTTCCAGGCA
3' ss Score
8.82
Exon sequences
Seq C1 exon
GGCTGATGATGACTTTTCAGAACCCGTTAATACTAATGTTGTGTTGAGATATGATGGAAAAATCACTTGGGATGCACCTGCTATCACAAAAAGCTCGTGTGTAGTGGATGTATCTTATTTTCCTTTTGACAGCCAGCAGTGCAACCTTACGTTTGGTTCCTGGACCTATAATGGTAATCAGGTAGACATCATCAATTCTCTCGATAGTGGTGACCTTTCTGACTTTGTAGAAGACGTGGAATGGGAGATTCATGGTATGCCGGCGGTTAAGAATGTAATCACTTACGGCTGCTGCTCCGAGCCTTATCCAGATGTAACGTTCACGCTGATTTTGAAAAGGAAGTCATCTTTCTACATATTTAATCTTCTGCTTCCTTGCATTTTGATCTCTTTCCTCGCTCCACTGGGATTTTATCTCCCCGCAGACTCTGGAGAAAAAGTGTCTCTAGGTGTTACAGTTCTTCTTGCTCTGACTGTGTTCCAGCTGATGGTTGCAGAGATTATGCCTCCCTCTGAAAACGTACCTCTGATAG
Seq A exon
GTGAGCTTTACATGCTTTGTCCTTAAACGCAGCTTACTGAAATCAGGGCTGTATGTCAGGTAGACTGTGTGTCATTTATGGCTTTTGGGAAGATAAATGTTGCTGCATTTGTTTAAAAAAAATAAAATAAAATCAAGTGAAATACTTGAAGTATGCATGGTATTTGTACAGTTAAACTGAAGCTCTTTACATTTACTTTGTATTTCTGTTTATGCTAGCTTTCTCATCAGAATTAGTTCCCACCCACATTATGACTTGCTGTATTTGAGTACCTTCCTTACCCATCTATCACTCTAAGCAGACAGGACCTAGCCTTGGTCTGCTTTCTCTCACTGTCCCTCACTGTCCTTCCCAACCTCTTTGTCACATTGTTATTTCTGCACTGATTTAAAAAAAAAAAAAATGTGGATAGCATCTTTAATATAATTTTATTCTGTGTTCCAG
Seq C2 exon
GCAAGTATTACATAGCAACTATGACCATGATCACAGCCTCCACTGCGCTGACAATCATTATAATGAACGTCCATCACTGTGGCTCAGAAGCAAAGCCTGTCCCACAGTGGGCCAGAGTGGTAATCTTGGACTATATGTCAAAAATTTTTTTTGTTTATGATGTGGGTGAAAATTGTACAAGTCCACGAAGAGAGAAGGAACAAGAACACAGGTTAGAGGGCGGTGACATGTGTCGGGGGGGAGACGGAAAGAGCCACCTTTCCAGTAGAAATGATGACAGTGATCTCAAAGAAAATCTGAATGGAAATTGGAATAAAAGCTTTGGAGTTCATGGTGAAAATGTTAGGGAGAATGTTAATTGCTGTTCCTGTTACAAAATGCTGATTAAAAATATTGAGTATATTGCGAATTGTGTTCGAGACCATAAAGCAAACCGGGCCAAAGGAATTGAGTGGAAAAAGGTGGCAAAGGTGATGGACAGGTTTTTCATGTGGATTTTTTTTATCATGGTGTTTTTTATGAGCGTGCTTATCATTGGGAAAGCAGCTTAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000014268:ENSGALT00000023080:4
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.115
Domain overlap (PFAM):
C1:
PF0293118=Neur_chan_LBD=PD(55.6=64.2),PF0293211=Neur_chan_memb=PU(23.8=31.3)
A:
NA
C2:
PF0293211=Neur_chan_memb=PD(75.7=96.7)
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:
TTATCTCCCCGCAGACTCTGG
R:
CACATGTCACCGCCCTCTAAC
Band lengths:
354-798
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]