GgaINT0030249 @ galGal4
Intron Retention
Gene
ENSGALG00000003021 | CHRNA5
Description
neuronal acetylcholine receptor subunit alpha-5 precursor [Source:RefSeq peptide;Acc:NP_989746]
Coordinates
chr10:3132179-3134093:-
Coord C1 exon
chr10:3133984-3134093
Coord A exon
chr10:3133011-3133983
Coord C2 exon
chr10:3132179-3133010
Length
973 bp
Sequences
Splice sites
5' ss Seq
CAAGTAAGA
5' ss Score
7.61
3' ss Seq
TATATCTCTTTTTCTTTCAGTGC
3' ss Score
10.97
Exon sequences
Seq C1 exon
GAGTGGATAGATGTAAAATTAAGATGGAACCCTGAAGATTATGCTGGAATAACATCTATTCGTGTCCCATCAGATTCTATTTGGATTCCAGACATTGTGTTATATGACAA
Seq A exon
GTAAGATTTTAATCTCTTTATATAGAATACCTTTTCCTCTTTTTAATGTTACTCTCCAAGCTGCTTGTAGGAGGCTTCTTGAATGGACCGTGTGTGTCCATTTAGTACATTTAGAATTTGCTTCCAAATGCACATTGATTTTGTTGCTACATTAAATGCAAGTTTTATTTTGCTACTGTGTCTTTTTTAGTCTCTTTGAAATGTTTATTTCCATTTCTCATAAACTGTTATTTAGGAGACAACATCTTGCATAGCTTTGGGTACAAGCTAATAATGTAGAGGGTGCGTGCAGCGGGAAGAGAGTGACTAACTCATACTGCTGTAACTCATATTTGGCATGGATTTAAAATGAAATGCACTTAACAGTAAGTTTGTTTTTTCAAGAATTGATGGACCCCAGAGGAAATAAGTTTTGAATGAACCTTTCTGATCAATTCAGGTGCATATGTAACACTTTTTACATTTTCTGGCTTGGTGAGTCAAGAGAGGCTGATTATAATTTCAGGTTTGGAAGTGGAGCACAAGTGGTGTGGTTGTTTTTTTTCCCCAATTATTATGATTTTTCCAGATTTAGAAGTATTTGTGCTGCATTACCATTAGAAACATCAGGGTTTGGTCAGGCTGCTAAAGGTTAGGATTTCTACAATCCCTTGTTTGAATCATCAGGTAAGTTGTACAGATCTTTTAATGGCTTGACAACATTCTTTACTTTTGTGAAGGTAATTAACTGTGTGAGATTCAGGTTAAAAAACAAAACAAAAGCAAACAACAAAAACCACCCCCCCCCAAAAAAAAACAAGCCCATAAACCAACAAACCCCCCAGAAAACCAACCAACTACAAGAAGTAAACTGTGAACACAGCACAATACAAAACTTTGTCAGTGAGAGGGGAGAAGGAAGGAGCAAACAGCTGAAACGACAATAATCTCTTCCTCCATCATAATTGTACGCATATATCTCTTTTTCTTTCAG
Seq C2 exon
TGCAGATGGACGTTTTGAGGGGACGTCTACTAAAACTGTGGTAAAATATGATGGCACCATTGCTTGGACTCCACCAGCAAATTATAAAAGTTCTTGTACTATTGACGTAACCTTCTTTCCCTTTGACCTCCAAAACTGCTCTATGAAATTTGGTTCCTGGACTTACGATGGCTCCCAGGTTGATATAATTTTAGAAGATTATGATGTTGACAAAAGAGACTTTTTTGATAATGGAGAATGGGAAATAGTGACTGCAACAGGGAGCAAAGGAAATAGAACTGATGGATGCTGCTGGTATCCCTTTGTTACATATTCATTTATAATTAGACGTTTACCACTTTTTTACACGTTGTTTCTCATCATTCCTTGTATTGGACTTTCTTTTCTAACTGTCCTCGTCTTCTATCTTCCTTCAAATGAAGGTGAAAAAATTTCCCTTTGCACTTCAGTCCTGGTATCTCTGACTGTTTTTCTTCTTGTCATTGAAGAGATTATTCCATCGTCTTCTAAAGTTATCCCACTTATAGGAGAATACTTGGTGTTTACTATGATATTTGTGACATTGTCCATTGTGATAACTGTCTTTGCTATCAATATTCATCACCGTTCTTCATCTACACACAATGCCATGGCACCTTGGGTTCGCAAGATATTTCTTCACAAACTTCCCAAGCTGCTGTGCATGAGAAGTCATGTAGATAGATACTTTGCTCAGAAGGAGGAAAAAGGAAACATGAGTGGATCAGAATCGTCTAGAAACACCTTGGAAGCAGCTCTAGACTCTATCCGATATATCACAAGGCATGTTATGAAGGAAAATGAAGTTCGTGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000003021:ENSGALT00000004776:3
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=0.007
Domain overlap (PFAM):
C1:
PF0293118=Neur_chan_LBD=FE(17.6=100)
A:
NA
C2:
PF0293118=Neur_chan_LBD=PD(54.9=40.3),PF0293211=Neur_chan_memb=WD(100=48.9),PF0293211=Neur_chan_memb=PU(54.2=14.0)
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:
TGGAACCCTGAAGATTATGCTGG
R:
CTTTGCTCCCTGTTGCAGTCA
Band lengths:
355-1328
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]