GgaINT0010162 @ galGal4
Intron Retention
Gene
ENSGALG00000005801 | CHRNA4
Description
Neuronal acetylcholine receptor subunit alpha-4 [Source:UniProtKB/Swiss-Prot;Acc:P09482]
Coordinates
chr20:9218845-9225476:-
Coord C1 exon
chr20:9224102-9225476
Coord A exon
chr20:9218997-9224101
Coord C2 exon
chr20:9218845-9218996
Length
5105 bp
Sequences
Splice sites
5' ss Seq
TCAGTAAGT
5' ss Score
9.14
3' ss Seq
TTTCATCTCTGTGTTGCCAGGTG
3' ss Score
9.49
Exon sequences
Seq C1 exon
TGCTGATGGTGACTTTGCAGTCACCCACCTGACCAAAGCCCACCTCTTCTATGATGGGAGAATTAAATGGATGCCACCTGCCATCTACAAAAGCTCCTGCAGCATCGATGTTACCTTCTTCCCCTTTGATCAGCAAAACTGTAAAATGAAATTTGGCTCTTGGACATATGACAAAGCTAAGATAGACTTGGTGAGCATGCATAGCCATGTGGACCAACTGGACTACTGGGAAAGCGGGGAGTGGGTCATCATTAATGCCGTGGGCAATTACAACAGCAAGAAATATGAATGCTGCACAGAGATCTACCCTGATATAACTTACTCCTTCATTATCCGGAGGCTGCCGCTGTTCTACACAATCAATTTGATCATTCCCTGCCTGCTTATCTCCTGCTTGACTGTCCTGGTCTTCTACCTACCCTCTGAGTGCGGAGAGAAGATAACCTTGTGCATCTCTGTGCTGCTATCCCTCACGGTGTTCCTGCTGCTCATCACAGAGATCATCCCTTCTACCTCCCTGGTCATCCCCCTGATAGGAGAGTATCTGCTCTTCACCATGATATTTGTCACCTTGTCTATCATCATCACTGTCTTTGTGCTCAACGTACACCACCGTTCACCACGTACCCACACGATGCCTGACTGGGTGAGGAGGGTCTTCCTTGACATAGTCCCACGTCTCCTCTTCATGAAGCGGCCCTCCACAGTGAAAGACAATTGCAAGAAGCTTATTGAATCTATGCACAAACTAACCAACTCACCAAGGCTTTGGTCTGAGACCGACATGGAGCCCAACTTCACTACCTCATCCTCCCCCAGCCCCCAGAGTAATGAACCTTCACCCACATCTTCCTTCTGTGCCCACCTTGAGGAGCCAGCCAAACCTATGTGCAAATCCCCTTCTGGACAGTACTCAATGCTGCACCCTGAGCCCCCACAGGTGACGTGTTCCTCTCCGAAGCCCTCCTGCCACCCCCTGAGTGACACCCAGACCACATCTATCTCAAAAGGCAGATCGCTCAGTGTTCAGCAGATGTACAGCCCCAATAAGACAGAGGAAGGGAGCATCCGCTGTAGGTCCCGAAGCATCCAGTACTGTTACCTGCAGGAGGACTCTTCCCAGACCAATGGCCACTCTAGTGCCTCTCCAGCGTCGCAGCGCTGCCACCTCAATGAAGAGCAGCCCCAGCACAAGCCCCACCAGTGCAAGTGTAAGTGCAGAAAGGGAGAGGCAGCTGGCACACCGACTCAAGGAAGCAAGAGCCACAGCAACAAAGGAGAACACCTCGTGCTGATGTCCCCAGCCCTGAAGCTGGCGGTGGAAGGGGTCCACTACATTGCAGACCACCTGCGAGCAGAAGATGCAGATTTCTCA
Seq A exon
GTAAGTATGTTAACTTGGCCTCTTTGGGTAAGCTGAAAATAATCTGAAAGAAACCTCACCAAACGTGAGGGCTGTCAGGCTGTACTCATCATCATGGGTCCTGGACACACTGGCACTATAGATGGAGTCATAGGATTATAGAATCATAAAGGTTGGAAAAGCCCACTAGGATCAACAAGTCCAACCATCAACCCATCCCCACTATGCCCACTATGCCATGTACCCTGGATAGAGCTAGAGAGCTTGTCCCAGGGATCTTATCAGGCCAAGGGTCTGGCACAACCTGGGCATGTTCAGGGCTGCTCTCAAACAATAGGGTTCTTCAGCAGAAAAGTGGAGCTGTTGGTCAAGTAGGACTAGTTGTAGAAAAGAACAGTCATCTTCCCCTCAACTCTTTTCAAATTTTGGGGTGGATAGAAGGGTTTTTAATTTATTTTGCTTCTTAGGGGATCAAAATGTAGCTAGGAGAAAAGATAAATCCTTTGGTATTTCAAACCTGAACCGTTTCAAAACACCTTTAATTGCAGGTAAGGATGTGATTTTAATTGAGGCTAGAGGGCTCCTTGCAAGAGTGATTCTGCCTTTGCCTGCTATAGGAAACAGCCAGAGAAGGAGCCAGCATGATTTGTTGTTGTCCCATTCCTGTAAACAATATCAGCAAGTGCATTTTGACGTTGGTTGCCCCAGCATTGCCCTAACATCCCTGCCTTGGTAGTTCAGCAGTTCACAGCACTGCTGTGGGATCACATCAATGGCTCTGAAACGTGCCTTCAGTTTCCTGCAGATAAAAGCCAATGAGATAGCACAGGAACAGAATCCTGCCAGGAAGCATCTTGACCCTTCCTGGGCTGAGATTGGGAAAGAAAATAGAAAAGCAGTCATCTCTGTGGGAACACAGCAGAATTCTTTATAGCGAAGCCTCTGACAGACAGGTAATTTGCACTGTGATTTCTCTTCAGCGATGACTGTGGTTACTGAGCCTGGGAAGGCAAATGCCTGAAATAGGCTGTGGCTGTGGGAAGTGTGCCATAGCGTGGGGATGCTGCAGGGTATGTTTAGCCATGTGTGACGCCATTCCTCATTAGTGGACTTCCAGTGGAGCACCACTTGGCTCAGTCTGCGGGAAGGTGGGTGGACAGACAGACTTCGTGCTTACTCTGAAGGGGTAAATATGGCTACAGATAGAGAAAGTAGAGGCTGAAAGGTTGTTGTTTTTTTTTAATGGAGATGGTGATGCACATACAAATGCCACATCCTTTTATATCTCATAGCTCTTCCCTTACAATACTATAGTTACAGTATGCCAGCTAATTATGGTCACAGACACAAGCTTCTTGCTAAAGAAAACAGGATCTAGTTTTTCTTAGAGGTATCAGTCAGCAAAGATACCTTTCTGACAGTTCTTACAGTTCGATTGTCACCAGATTTACAGTCAAAGGAAGTCGTAGTGCTTTTAGGCAAGACTTCCTGGGCTTGAAGAGTGTCTTTATATTTGCATTTTTCATAGCACAGAGCACTTAGCAGCAGCAACAAAGGATTAAGTGCTACTGTCCATTTATGTACTCTTTGGTACCACAGTTTTAGAGGCCTCTCTTCTTTAATGTATTTCACTTCACAACATCCCTTTGAGGAAGCGGCTGTTTATTCCTCGTTTTGAGGAGTGACAGCCAAAGCACAGAGACGAGTTGACCTGCACAAGGTCACAGAACAAATCTCTGGCAAAGAAGGCTGTGAACCCCCACCTTCATTAGCTGACAGCTCTCTTTCCTGGGCTAAAACATTTCACCGTCACATTAAGGCTGTGGGAATTAAACTCTGCTCTCTCCAGCTAGTAATAATCATGAATAAACCCATGGAAGGCAATTGATTTTAACTCACATATTTCCCCGTGGTGCAAATGAAAAAAATATTGCATCAGTAATACTTCTCATTTCAACTGATTCTCTCCCTGCTAAGCCTGTTGATGTCAACAAGAACTGAGTCGATGAATACCGTGGGTTGTTTCCTCTTAATCCATCACTGCTTCTTTCTTCAAGAAAGAACACTGGAACAGGTTGCCCAAGGAGGCTGTGGATGCCCCCATCCCTGGAGGCATTCAAGGCCAGGCTGGATGTGGCTCTGGGCAGCCTGGTTTAGTGGTTGGCGACCCTGCACATAGCAGGGGGTTGAAATGAGATGATCATTGTGGTCCTTTTCAAACCAGACCATTCTATGATGTTATGATTCAAAATGAGCTTTCTTCCACTCTCTGCTATTCTTCCCCCTTCCCTCTCCCTGTTTCCCTCTTGAAATGAAACAATTATCCCAAGGAGAAATATATTTAGAGCACTAAACATCAAAAGCAGAAGAAAAGGAAGAATTCTTTGAGCTCTAAACAGCCCTCCATGGCGAGCAAAGGCACCACATGCACATCCAGCAGTGAGTGGACACTGTCAATGCACCAGGCTCCCTGGTATTGAAAATTACTGCAAGGAACAGAGCTGATCTAATAAAACAAGAATTTACTATGGAAAAAAAGATATCGGTACTCAGAAATTTGCTTTCATCTTAGAATCAAATTGTGGCATTTCTGCCAGGGATGGAAGCCTCCCCCCAAACCCATCAGCAGACAGCTCTGTGCAGGAGCAGCCCTTGGGACACAGCTCACTGCCTCTCAGGTCATATTTTCTGAGCCATGGACCTTTGCAGGATGGGGACAAAGCTTCTTTTAAACTTCCTCTTTTTTTCTAAAGCACCATTGCCACAGGGGCAGTGTTTCTAAATTAAAAGTAAACAGCTCATTTAATTAAGTGCTTCAGCAAAGAGAAAATGGGAAATGCAGGAGGGCAGTTGTTTGCTACAGAAACTTATCTGCGACCAAACCGGCACAACAAGACACTGGGGAAAAGGCAAGACTGAATTGTCCCAGTGTGTGATAGGAATGCCATTAGAAATTAATTACAGGCTGAGAAGTAAAACGAGCCGCATGTCTCACACCAGTCAAAATAAGCAGACACCGACAGCACCGTCTGCAAAGCCTCATTGTCCTCGTGACTGCGTGCATCTCAGGGCTACTCTAATAGGAAGCCCATGAAGACAGCTTAAAAAATGAAATGGGAGAGAGAAAATAGCTGAGGGGGAGGGAACACGGGATAATCTCACTGGTTTATTTTTAACAAAGTACAATAAAACCACTTGGGACTCCTCTAATCTGTGTTACAGGCTCTGGCTCCTGAGCATCAGATGGCACTTGGAGGTCCCCAAGGCACCTCCACCCCAGCCGTGGGGCTCATGCCCTGCTCTGCTGCTGGGGTGGACCAGGGAAGAGCCAGAGAGCCCCTGACCTTGCAGGAATTTGGGGGTGGTCAGCTGGTTGCAGCCCCTGATCCTTTCCCGAGAAGAGTTTTGAGTGAGCCTCTTAAAAACTAATCAGGACACAGCTCAGGAGTTGGGGCAGCAGATGCTGGCAGCTGCATGGATGCTGTCAGAGAGGCCTCTGTGGATCACACTCTACGTGAGATGCTGGAGAGTTTCAATCATGGGGAAATGCTACAGAGCAGTCAGAAAACAAAACAGAACCCCAAACCATTTTTTTTCCCTCTCCTCTCTTGCTCTGAAGCTGGATATTGATTTTGCAAACATCCAATGTGCTCCCAGCCGTCATTTTCAAGTTGGGCCCACTGTTTATGTATCAACCATTTTGTCTGAAAGCAAATTTCAGCTGAACTTTTCAAGCTGTTCCTCTCCATTCTCCTTTCCTTTCCTCCAAGATAAACTCATTTCTTTCATTTCTTGTATTCAAGTGGTCAACCACTCACTTCTCTTAGCATAAAGACTCAAAAAAAACCCCACTTATATTGCCATAATGGGGAAGTATTTATCTCAATCAACCTTTCCAGATTGACATCAGATGGAGAATTTCAGTTTTTCTTTACACATTGCCTCTTCACGAGATGCTAAACCTCTAAATACAGTCATCCTGAGCTTGCTGAGTGGCCTTCTCACCAGGAATTCTAACCTTCAGAGACTCACTCCAACTCTCAGCAAATGATGAATAGATCAGAAAACCTGTCTGACAAAAGGGAGCTATCCACAGCGACTTCATCCGTGGGACGAGAGGATAGCATTTGATTTCAAGGGTTATTATTGTAATGATAGAACAATCATTTCCTCCAAGAAAGTAAGCCAACTTTTAATTAATCTTTTTAACCTGGCTGATGAACAGTAAAAACCTCTGTTTGCACCCACTGGTGGGTGCAGGAAAGCAGCCCTCAGCAAAGCACACCCTCAGCTTTGCTGCCTCCTACTCCATGCAACACACTCCTGATTTGCTACAGTCACAACCACAGAAGAGGCAGGAGCAAGCTCCTGCTGAGAGGTTTTCCCTAAGGATCAGGGCAGCCTGCCAGGTTTCAGCCCGAAGCGCAAGGCGACATCAGGGCTATTAATCATCAAGCAGTATATTGTGGGGAATTCTAATGGGTGCAGCCGTATCAAATAAAGCTTCACCATCTGATCAGTCCTCTTCCTGGGAAAGAAATTAATAACAGCAATGTAATGAAAGAGGTTTTCATATGTATGTGGTTTCTTACTTGATGAAATAGACATTTACAACAGGTCTTGCCTGATGGTGCTAATAAGAACCAGACTTCCCTAGAGAGGAATTGCTGGAAAATCATCCCACAGAAAGACAAAAGTGGAGAAAAAGCAGGATGAGGCAAACCACTTCTTTCATTTGCTGGTTCGTTTTCACTGCTCACTCAGCCAAAGCTGTAATTCCCTTCACAGAATGCATTTGGCTTCATTAATCTGTAAACAAATCTGTTTACCAGCATGAAGAAACAGGCAATTTCTTTCCCCCTTCAACTTGAATCGTGGTCTCATTTACACACCCTGTTACAGCTGTTGCTCGTGGAAACTGGGATCGTGAGTGTGCATACACACTTAATTATCCACAGACGTATCATCCCCGGGGAGCTCTGAACAGGGTTTGTGGTTGGGGATGTCTCCCATGCAAGTGATGAGTAAAAATTGCCATCATGTTTAGAATAAAGCACAAAGAAGTCTTCATACACTTTAATCTCAATTAAGTATTACTAACTGGCCTTTCATCTCTGTGTTGCCAG
Seq C2 exon
GTGAAGGAAGACTGGAAGTACGTAGCAATGGTCATTGACCGGATCTTTCTCTGGATGTTCATCATCGTGTGTTTGCTGGGGACCGTTGGGCTCTTCCTCCCGCCGTGGCTGGCAGGAATGATCTAAGCACAGCCACAGAGTGAGGAAACACA
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000005801:ENSGALT00000009316:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.248 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0293118=Neur_chan_LBD=PD(55.6=25.1),PF0293211=Neur_chan_memb=PU(91.1=73.2),PF113173=DUF3119=WD(100=20.5)
A:
NA
C2:
PF0293211=Neur_chan_memb=PD(8.4=73.8)
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:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]