DreINT0131055 @ danRer10
Intron Retention
Gene
ENSDARG00000077093 | scaf4a
Description
SR-related CTD-associated factor 4a [Source:ZFIN;Acc:ZDB-GENE-030131-9003]
Coordinates
chr10:25744431-25744737:-
Coord C1 exon
chr10:25744637-25744737
Coord A exon
chr10:25744545-25744636
Coord C2 exon
chr10:25744431-25744544
Length
92 bp
Sequences
Splice sites
5' ss Seq
AATGTATGT
5' ss Score
5.87
3' ss Seq
TGTTTATTTGATTTTGATAGATG
3' ss Score
6.33
Exon sequences
Seq C1 exon
TGTGCAGCACAACTCTATGGGTGGGTCAGCTGGATAAGAGGACACAGCAGCAGGACGTGGCCTCTATACTAGAGGAGTTTGGCCAGATAGATTCAATTAAT
Seq A exon
GTATGTTCTGGATTATTATTGTACGTTCTGTTGAATGTGTAGCTCATAGCTTTCTAACCTAATGCCATGTGTTGTTTATTTGATTTTGATAG
Seq C2 exon
ATGATTCCTCCACGAGGTTGTGCCTACATCGTCATGATTCATCGTCAAGATGCCTATCGAGCCCTGCAAAAACTAAGCAGAGGTCCATACAAAGTCAACCAGAAAGCCATTAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000077093:ENSDART00000140483:13
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.059 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0007617=RRM_1=PU(41.8=82.4)
A:
NA
C2:
PF0007617=RRM_1=FE(55.2=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGCACAACTCTATGGGTGGGT
R:
GCTTAGTTTTTGCAGGGCTCG
Band lengths:
174-266
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]