DreINT0131064 @ danRer10
Intron Retention
Gene
ENSDARG00000077093 | scaf4a
Description
SR-related CTD-associated factor 4a [Source:ZFIN;Acc:ZDB-GENE-030131-9003]
Coordinates
chr10:25750634-25751019:-
Coord C1 exon
chr10:25750858-25751019
Coord A exon
chr10:25750764-25750857
Coord C2 exon
chr10:25750634-25750763
Length
94 bp
Sequences
Splice sites
5' ss Seq
CGGGTGAGA
5' ss Score
7.62
3' ss Seq
TCATGTGTTTTTTTTTTCAGAGT
3' ss Score
11.15
Exon sequences
Seq C1 exon
TGCAAACCGGAGTACAAAGTTCCCGGTCTCTATGTGGTGGATTCCATTGTGAGACAGTCACGGCATCAGTTTGGAGCAGATAAAGATGTGTTTGGACCCAGGTTTACTAAAAACATCACTGGGACATTTGAGAATCTATGCTTGTGTCCCACTGAAGATCGG
Seq A exon
GTGAGAGTATTTAAATATAAAGACTATAAAAGATTTATTTAGTTGTGTCATTGTATGACTAATGATTTGAATATTCATGTGTTTTTTTTTTCAG
Seq C2 exon
AGTAAGATAGTACGAGTGCTCAACCTGTGGCAGAAGAATGGAGTGTTTAAGATCGAGGTCATTCAGCCTCTGTTGGACATGGCTGCTGGGTCCAGCAGCTCCTCAGGCTTGGACAATGGCCCAGATGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000077093:ENSDART00000140483:4
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=0.258
Domain overlap (PFAM):
C1:
PF048188=CTD_bind=PU(72.7=88.9)
A:
NA
C2:
PF048188=CTD_bind=PD(24.2=36.4)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCCGGTCTCTATGTGGTGGAT
R:
CCACAGGTTGAGCACTCGTAC
Band lengths:
171-265
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]