DreINT0046719 @ danRer10
Intron Retention
Gene
ENSDARG00000087071 | chrna4a
Description
cholinergic receptor, nicotinic, alpha 4a [Source:ZFIN;Acc:ZDB-GENE-130530-903]
Coordinates
chr6:58514394-58514914:+
Coord C1 exon
chr6:58514394-58514521
Coord A exon
chr6:58514522-58514869
Coord C2 exon
chr6:58514870-58514914
Length
348 bp
Sequences
Splice sites
5' ss Seq
GTGGTATAA
5' ss Score
0.19
3' ss Seq
CTATCTTATATCTTCACCAGGAT
3' ss Score
8.43
Exon sequences
Seq C1 exon
TCCAGGCTGAAGAGCGTCTGCTGAACTCTCTGCTCTCAGCATACAGTAAACTGACCCGTCCGGTTCACAGTGTCTCTGATGTGGTTCACGTTCACTTCGGTCTGTCCATCGCTCAGCTCATCGACGTG
Seq A exon
GTATAATCCGCAAACACCTTCTGAAGAGATTGCAAATCCCAACACCATCATTTATTACAGCCTAGGCTCAGTGTAAATAAATGCCTGAGCCTGCATTATTGCAGAACATTAAAGACGCTACTTGGGGTGTGTTGCATGACACGTTTCAGATGACAAATCCAGTAGAGGGCGCTGTCTACATTTTTGCAAATCTGATATACGTGTATTTTGTTGCATAGCTTTAAGTATGTTTTTGAGAATTTTCAAAACGTTAGACAAAGGTAGACTAATGGTACAGCATGTTTAACAGATTACCAAACCAACCGTTATTGTGATAAACTATAAAACTCTATCTTATATCTTCACCAG
Seq C2 exon
GATGAGAAAAATCAAATGATGACCACTAATGTGTGGGTGAAGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000087071:ENSDART00000153740:2
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=PU(18.9=90.7)
A:
NA
C2:
PF0293118=Neur_chan_LBD=FE(6.8=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
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]