DreINT0106670 @ danRer10
Intron Retention
Gene
ENSDARG00000007654 | nsfa
Description
N-ethylmaleimide-sensitive factor a [Source:ZFIN;Acc:ZDB-GENE-030616-37]
Coordinates
chr3:34654444-34654737:-
Coord C1 exon
chr3:34654698-34654737
Coord A exon
chr3:34654611-34654697
Coord C2 exon
chr3:34654444-34654610
Length
87 bp
Sequences
Splice sites
5' ss Seq
AAGGTGTGT
5' ss Score
6.64
3' ss Seq
TTTTATTCCCACCATTTCAGTGT
3' ss Score
8.96
Exon sequences
Seq C1 exon
AGGAAATGGGCAGGCCTGTCCATTGGGCAAGAAATAGAAG
Seq A exon
GTGTGTATATTATTCCTGGAGAACATTTAGAACACAGTTCAATTCAGCACACAATTCAAATCACTGATTTTATTCCCACCATTTCAG
Seq C2 exon
TGTCAAACTACAACTTTGACAAGTCCAGGCAGTGCATTGGTGCCATGACCATTGAGATTGACTTCCTGCAGAAGAAGAGCACAGACTCCAGCCCTTACGACTCAGACAAAATGGCTGCTGAGTTCATCCAGCATTTTAACAATCAGAGCTTCTCCGTGGGGCAGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000007654:ENSDART00000103043:4
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0235913=CDC48_N=FE(15.9=100)
A:
NA
C2:
PF0235913=CDC48_N=PD(7.3=10.7),PF0293312=CDC48_2=PU(32.9=42.9)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGAAATGGGCAGGCCTGTC
R:
ATGCTGGATGAACTCAGCAGC
Band lengths:
173-260
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]