GgaINT0030250 @ galGal4
Intron Retention
Gene
ENSGALG00000003021 | CHRNA5
Description
neuronal acetylcholine receptor subunit alpha-5 precursor [Source:RefSeq peptide;Acc:NP_989746]
Coordinates
chr10:3130409-3133010:-
Coord C1 exon
chr10:3132179-3133010
Coord A exon
chr10:3130571-3132178
Coord C2 exon
chr10:3130409-3130570
Length
1608 bp
Sequences
Splice sites
5' ss Seq
GAGGTGGGT
5' ss Score
7.07
3' ss Seq
TTATGTTCTTTGTTTTTTAGGTT
3' ss Score
12.34
Exon sequences
Seq C1 exon
TGCAGATGGACGTTTTGAGGGGACGTCTACTAAAACTGTGGTAAAATATGATGGCACCATTGCTTGGACTCCACCAGCAAATTATAAAAGTTCTTGTACTATTGACGTAACCTTCTTTCCCTTTGACCTCCAAAACTGCTCTATGAAATTTGGTTCCTGGACTTACGATGGCTCCCAGGTTGATATAATTTTAGAAGATTATGATGTTGACAAAAGAGACTTTTTTGATAATGGAGAATGGGAAATAGTGACTGCAACAGGGAGCAAAGGAAATAGAACTGATGGATGCTGCTGGTATCCCTTTGTTACATATTCATTTATAATTAGACGTTTACCACTTTTTTACACGTTGTTTCTCATCATTCCTTGTATTGGACTTTCTTTTCTAACTGTCCTCGTCTTCTATCTTCCTTCAAATGAAGGTGAAAAAATTTCCCTTTGCACTTCAGTCCTGGTATCTCTGACTGTTTTTCTTCTTGTCATTGAAGAGATTATTCCATCGTCTTCTAAAGTTATCCCACTTATAGGAGAATACTTGGTGTTTACTATGATATTTGTGACATTGTCCATTGTGATAACTGTCTTTGCTATCAATATTCATCACCGTTCTTCATCTACACACAATGCCATGGCACCTTGGGTTCGCAAGATATTTCTTCACAAACTTCCCAAGCTGCTGTGCATGAGAAGTCATGTAGATAGATACTTTGCTCAGAAGGAGGAAAAAGGAAACATGAGTGGATCAGAATCGTCTAGAAACACCTTGGAAGCAGCTCTAGACTCTATCCGATATATCACAAGGCATGTTATGAAGGAAAATGAAGTTCGTGAG
Seq A exon
GTGGGTGTATTAGTCATATTAAACTCATTTTGTTAAAAGTGGAAATTAAAGAAAAAAAAAAAAAGAACAAGCCAACCAAAACGAAGCACAGCAAGGAGTTCACTATGTGGTCACACTTAATATGTGCTAGGTTTTCTGTTTTTTATATTTCACTGGAAGTCATATATTTGTTTCTGCTGGAAAGAAGTACAGGTATGCTCCAGTACTGAGGTATTTGGTTGGTATAATGCCATACGTGAATTCTTGACGTATTTATGCTTTCTTCTAGAAGTCCATGTTGTTGTTAATCAAATATTTTCAGAGACACATGGCTGTTACAAGAGCACGTACAGTAACTGTTACCTGCAGTGCTGCTGAATGTTGTTTTCAGAATGAAAGAAGTAGGTATTTTTCATTTTAATGTTGTACCTGCAGGCTACCTGAAAAACACATTTGATTTACAATTCCAGAATAATTTCTGCTAAACATTTGTCTTGCACCTTTCAATTCCAGATATAGACAGTTTTAAGCTCCATAATTTATATTAGTTTAAATACAGGTTATCACTATAGATTAATCATTTTGTGCTGAGAACAGACATCAACTGGATGACCTCTTGAGTGATCTCTTCTAGCCCTATTATCATTTCCTTTTGACAACTTTTGATATAATTTAAAGGATATTTCTCAGTCTGTGCATTTGCACACTGAGCTAAATAGATAGTTTTGAGTAAATTGTGAGTTGATTTTCCTTATTAAATTACTTTCTTTGGTTGTACGTGGCAAGAGAGTTGATAGGTGTTTTGTTTTTTGGTTGCTGCAACTCTAAATGTCAGAACTGAACATACAGCTGACTGGGGGTTCACTTACATTTTGTTATTTGGCCTCTGGTGAATGCAGGCTTTGGTTGCAGAAAGAGTTTAGCCCTGGTTGTTGAAAATAAAGTTTATACAGCTGGTGTTGTTGTAGCCTTGCCTCGCAGGACGCAGTAGGTCTGGCAAATGCAGATAGCTCCACTTCAGATGAAAGGTGCTTTTTTGTCAGAGTTTTAATTTGCTCGCGTGATTGTATCAGCTGTACTTGCAAAACTGTGCGTAGACAGAAATAATCCTATCAAAAAGGGAAACAGTCTTAAAAGCACTGTGAGTGTTCTACTCGGTGTGTAATTCCATGCACCAGTAACTTCACAGTTGTCAGATGTGTGTAATGCTAGAGATGCTGTCTGCTGTTAATTGTTTGCAACTTCAGTATCTAGCTTCTGCCTGGGAGTCCTACTCTGTGGTGAGGCTGTGGCATGAATCCTAAATCCTCCAGTATGTTATTAAATTGCATACTGATTTTCTCTCTATATAACTGATGATGTTCAATGCTCATCAGGGTCAACTGCTCCACTAAAATTTAGTATTTGGGCTGCATAGTTTACTGGGCTGCATAGAGAGAAGTGTTTTCCTGCTCTGGGTCACAGTGTGATTTATTAATACATGTATATATTAAAAAGGAGGGGGCTATCAAATTGACCTGACTAGGAGGGGGAGGAAAATGTGAAGTGATTAATCATTGCAGAGTCTGATGCTGTATTTTCACCCACTCTTGCCCATACTGGACAGCTCTTATGTTCTTTGTTTTTTAG
Seq C2 exon
GTTGTTGAAGACTGGAAATTTATTGCTCAGGTGCTTGATCGAATGTTCTTATGGGCCTTTCTTCTGGTTTCAATAATTGGATCACTTGTGTTATTTATTCCTGTTATTCATAAATGGGCAAGTATAATAGTACCTGTGCATATAGGCAGTACAAATACGTAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000003021:ENSGALT00000004776:4
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.007 A=NA C2=0.000
Domain overlap (PFAM):
C1:
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)
A:
NA
C2:
PF0293211=Neur_chan_memb=PD(43.1=57.4)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Human
(hg19)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCATGGCACCTTGGGTTCG
R:
ACTGCCTATATGCACAGGTACT
Band lengths:
356-1964
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]