DreINT0131077 @ danRer10
Intron Retention
Gene
ENSDARG00000018854 | scaf4b
Description
SR-related CTD-associated factor 4b [Source:ZFIN;Acc:ZDB-GENE-050506-42]
Coordinates
chr15:42338667-42338970:+
Coord C1 exon
chr15:42338667-42338711
Coord A exon
chr15:42338712-42338808
Coord C2 exon
chr15:42338809-42338970
Length
97 bp
Sequences
Splice sites
5' ss Seq
AGGGTATGT
5' ss Score
8.34
3' ss Seq
GCTGTCGTTTTCCCCTTCAGTGT
3' ss Score
10.14
Exon sequences
Seq C1 exon
CTGTATAAGCATGTTGTTCAAATTGTGGAGAAGTTCATCAAGAGG
Seq A exon
GTATGTAATAAACTATATATGTACAACAGCTTATCTTATACTAAAAATCTCAGTTATGAGAAGATAAAGACTAAATTGCTGTCGTTTTCCCCTTCAG
Seq C2 exon
TGTAAACCAGATCTTAAGGTTCCAGGTCTCTACGTGGTCGACTCCATTATCAGACAGTCCCGTCATCAGTTTGGCGCAGACAAAGATTTGTTTGGTCCGAGGTTTCTGAAAAACTTCACTGTAACTTTTCAGAATCTTTTCGAGTGTCCAGAAGATGACAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000018854:ENSDART00000099234:3
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:
PF048188=CTD_bind=PU(72.7=88.9)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGTGGAGAAGTTCATCAAGAGG
R:
TGTCATCTTCTGGACACTCGA
Band lengths:
182-279
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]