DreINT0153703 @ danRer10
Intron Retention
Gene
ENSDARG00000067673 | snapc4
Description
small nuclear RNA activating complex, polypeptide 4 [Source:ZFIN;Acc:ZDB-GENE-030131-5794]
Coordinates
chr5:50537621-50537961:-
Coord C1 exon
chr5:50537889-50537961
Coord A exon
chr5:50537786-50537888
Coord C2 exon
chr5:50537621-50537785
Length
103 bp
Sequences
Splice sites
5' ss Seq
GATGTAAGT
5' ss Score
9.11
3' ss Seq
TCTTGTTTGTGTTCATATAGTTT
3' ss Score
6.96
Exon sequences
Seq C1 exon
AACCCTGAAAGACGATCAACTGTTGGGTGATCTGCAAGACGATCATGACTGGGATAAAATATCAAATATCGAT
Seq A exon
GTAAGTTATGTAGCATTTTTATTGATACCTAGCAGATGAAGTCCTGTACTTTCTGCAGTTTCTCATTTTAGAATCATAAAAAGTCTTGTTTGTGTTCATATAG
Seq C2 exon
TTTGAAGGTTTGCGTCAGGCCGATGATTTGAAGAGGTTCTGGCAGAACTTTTTGCACCCGTCCATTAACAAATCGGTGTGGAAGCAAGACGAGATTTATAAACTACAAGCAGTCGCAGAAGAGTTCAAGATGTGCCATTGGGATAAAATCGCAGAGGCTCTTGGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000067673:ENSDART00000141424:7
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:
NO
A:
NA
C2:
PF139211=Myb_DNA-bind_6=PU(46.7=50.9)
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:
ACCCTGAAAGACGATCAACTGT
R:
CCCAAGAGCCTCTGCGATTTT
Band lengths:
237-340
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]