GgaINT0046842 @ galGal4
Intron Retention
Gene
ENSGALG00000009301 | CHRNA1
Description
Acetylcholine receptor subunit alpha [Source:UniProtKB/Swiss-Prot;Acc:P09479]
Coordinates
chr7:16306890-16307937:+
Coord C1 exon
chr7:16306890-16307085
Coord A exon
chr7:16307086-16307699
Coord C2 exon
chr7:16307700-16307937
Length
614 bp
Sequences
Splice sites
5' ss Seq
CCGGTGAGC
5' ss Score
8.69
3' ss Seq
GTGGGTTTATTTGCTGTCAGGAG
3' ss Score
3.52
Exon sequences
Seq C1 exon
TGCAGATGGCGATTTTGCCATTGTTAAATACACCAAGGTCCTTCTGGAACACACAGGAAAAATCACCTGGACGCCTCCTGCTATCTTTAAAAGTTACTGTGAAATTATAGTCACGTACTTCCCATTCGATCAGCAGAACTGTAGCATGAAGCTGGGAACGTGGACGTATGACGGTACAATGGTGGTTATCAACCCG
Seq A exon
GTGAGCAATGGTTTGGTAATTGGGAAAACAGCAGAGCCTTGGGTATATTTTTAGGGACTTCTCCGGTTTAAAAGGAATATAATCTTGGTTTGACTGAAAAACAAGGCACTACCAGTTTAATATAAAAGCCCCATTCGTAGGTGTTGTACAAAATTGCCCAGTTTGACTTGTGGAGTTCTGCATGCAGTTCCTTCCCATGCTCCTGCTTCCCCAGTCCTTCTGCCTCCCTATCCTCTTTACAGCCTCATGCCACTGCTTCTGGTGCTGCCCATTCTGCTTTTGTTCTCCTTCGTGGGGGTGATTTTTCTCTGCTTATGACTTAGTTTACATTCTGCCTCCTCAGGTATGTCTCCTATCTGTAAATATTTAAGTGGTCTTTCCCATTAGCAGACTATCCCGAACTCCTGCAAAATATTTAGTTGAACACTGTGCAAAGGATGATGTTCTAAGGCAAAATCACATAATAAGAATGGATGTTTGAGTCACAAAAATGCACAAAGCACCTGAATTATTCGAAATTCTGTTCCTGAGAGACCACATCATGTGGGTTTGTTCAGAACGTCTAGAATTTATAATATGTTGGTCCGTGGTGTTGTGGGTTTATTTGCTGTCAG
Seq C2 exon
GAGAGCGATCGCCCCGACCTGAGTAACTTCATGGAGAGCGGTGAGTGGGTGATGAAGGACTACCGTGGCTGGAAGCACTGGGTTTACTACGCCTGCTGCCCTGACACCCCCTACCTGGACATCACATACCACTTCCTCATGCAGCGCCTGCCTCTCTACTTCATCGTCAACGTCATCATCCCCTGCCTGCTCTTCTCCTTTCTGACCGGGTTTGTTTTTTATCTACCCACAGATTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000009301:ENSGALT00000015138:5
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(31.2=100)
A:
NA
C2:
PF0293118=Neur_chan_LBD=PD(24.0=62.5),PF0293211=Neur_chan_memb=PU(21.0=27.5)
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:
GGAAAAATCACCTGGACGCCT
R:
GAAAGGAGAAGAGCAGGCAGG
Band lengths:
343-957
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]