GgaINT0030094 @ galGal4
Intron Retention
Gene
ENSGALG00000003014 | CHRNA3
Description
Neuronal acetylcholine receptor subunit alpha-3 [Source:UniProtKB/Swiss-Prot;Acc:P09481]
Coordinates
chr10:3124662-3127129:+
Coord C1 exon
chr10:3124662-3124771
Coord A exon
chr10:3124772-3126117
Coord C2 exon
chr10:3126118-3127129
Length
1346 bp
Sequences
Splice sites
5' ss Seq
CAAGTAAGA
5' ss Score
7.61
3' ss Seq
TATTTTCATTTGCTTTGCAGTGC
3' ss Score
8.01
Exon sequences
Seq C1 exon
ATCTGGAATGATTACAAGCTTCGGTGGAATCCAGTGGATTATGGAGGTGCTGAATTCATCCGTGTGCCCTCTGGCCAGATCTGGAAGCCAGATATTGTATTATATAACAA
Seq A exon
GTAAGACACCCACATATCTGTCTTAATTCAGTTGTAATAGTTCTAAGCTAAAAGAAGGTAGATCTGTGCAAGATGGAAGTAAGAAATGCTTTGCTGTGGTGGCAGTGAGGTGCTGGAGCAGGTTTCCCAGAGAAAGTGTGTGTGCCCCATCCTTGGATGTGCTCCAGGCCAGGCTGAATGGGGCTGTGAGCAACCTGACCCAGTGAAAGCTATCTGAGCCCCATGGCAAGGGATTGGAACTAGATGGTCTTTAAGGTCCATTCCAAGCCAAACCACTCTGTGATTCTACAGGAAGAACTGCTGCTGATTTTTTTTAAAACTAATAAATACCAACAAATTCAGTGAACTTGCTAAAAAAGCCTACTTTCCAGTATCCCATCTCTCTGGTACTTACATGCCATCTACATCAGCATCACTGGCCATGACCCAAGCACTACTAACCTGAAGGTGCAAGCGCTGGGGGGGCAGGCCAAAGTGAGGTTTACTTTTTCCCTTCACAAGACCCTGATTTTACTACTGTTTTTAACACTGCTGACAAGGGAAATGACAGTAAGTTCCCATGGACTGCAGTTCTCTTGTCTGAAACACACAAACAAGCTAGTTCTAACTTTCTAGCCACTAAACTCATAATTTGACACCTTTCCTGTAGCAGCACTGACATACAAAAGTAACATCTAAAATATGACTGTGAAGAGCCAAACCATAATTAAATGGATCCCTCTGCTCTTCAGGGAAGCAGTTCTCAGTCTAACGTGTTTAACTACAGAGATCCAAAGCTTAAGCCTGTGGAAGAGCAGCGATAGTGCTACTTTTCTAACTGCAACCATGAAAATGAAAATGACGTTTTCAGTTTTACTTTTTGTATAAAAAAATATAATGGTCGCATGGATCTTATTATGATTGACGGGACCAGGAGAGAGATACAAAACTTTACAAAAGCCTCACCGAATACATAATTCAGGCAAAGGTGCACCCCAACCCTACTTACTGCCTTCATGGTCCGCAGAAGAGGTGGAGATATCAGTACTGCAGATATCCTCTGATCGGCCCTTGGGTTCTGACATGCTTGATCTCACACTTGCTGCTTTGTATACTGACTGCACTATCTGATTACTGTAAAAGAGAATTTTATTTTATTTTTTTCAAATTCTCCAAATCCTCAAAATCTATGAAGCTGTTTATTTCATTTTAGCTGTGATAATTTATGGCAACCAGACAGTCCTGCATATTGACACAGAGCTGAATTGCATATGTAATTGCTGGCTTCCACAAACTATATTAAAGATGTAAAGTGAGTTATAACCTGGATCGGTTGCATCCTGATGTTATTTTCATTTGCTTTGCAG
Seq C2 exon
TGCAGTTGGGGATTTCCAGGTTGATGACAAGACAAAGGCCCTACTGAAGTACACGGGTGATGTGACCTGGATACCCCCAGCTATATTTAAAAGCTCATGTAAAATAGATGTGACCTACTTCCCATTTGACTATCAGAACTGCACCATGAAGTTTGGTTCCTGGTCTTATGATAAAGCCAAAATTGACTTGGTTTTAATTGGCTCTACAATGAACCTGAAAGATTACTGGGAGAGTGGAGAATGGGCCATTATTAAAGCTCCCGGGTATAAACATGACATTAAATATAACTGCTGTGAAGAGATCTACACAGACATCACATACTCTCTTTACATTAGACGCTTACCTTTATTTTACACTATCAACATGATTATTCCATGTCTGCTGATCTCTTTTCTGACTGTATTAGTTTTCTATTTGCCCTCAGACTGTGGTGAAAAGGTGACTCTCTGTATATCAGTCCTTCTGTCTTTAACGGTGTTTCTTCTTGTTATCACTGAAACCATACCTTCTACTTCCCTGGTGATCCCACTTATTGGGGAATACCTCCTTTTCACTATGATATTTGTAACTCTGTCCATTGTCATTACGGTATTTGTACTTAACGTGCACTACAGAACACCCAAGACACACACCATGCCTGTGTGGGTGAGAACTATCTTCTTGAACTTACTTCCCAGGATCATGTTTATGACAAGGCCGACCAGTGATGAAGAGAATAATCAGAAGCCAAAGCCATTTTACACTTCTGAGTTTTCAAACTTAAATTGCTTCAACAGCTCTGAAATCAAATGCTGCAAAGATGGCTTTGTATGTCAAGACATGGCATGCAGCTGCTGCCAGTACCAGCGAATGAAGTTTTCCGATTTCAGTGGCAATCTCACAAGAAGTTCCAGCTCTGAATCTGTAGATCCTCTGTTTTCATTTTCAGTTCTGTCACCAGAAATGAGAGATGCTATTGAAAGTGTTAAATACATTGCAGAAAATATGAAAATGCAGAACGAAGCAAAAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000003014:ENSGALT00000004759:4
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=0.020
Domain overlap (PFAM):
C1:
PF0293118=Neur_chan_LBD=FE(17.4=100)
A:
NA
C2:
PF0293118=Neur_chan_LBD=PD(55.6=34.0),PF0293211=Neur_chan_memb=PU(86.7=63.6)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ACAAGCTTCGGTGGAATCCAG
R:
CCCATTCTCCACTCTCCCAGT
Band lengths:
342-1688
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]