DreINT0103787 @ danRer10
Intron Retention
Gene
ENSDARG00000035505 | nelfb
Description
negative elongation factor complex member B [Source:ZFIN;Acc:ZDB-GENE-040426-765]
Coordinates
chr5:28952667-28952983:-
Coord C1 exon
chr5:28952888-28952983
Coord A exon
chr5:28952810-28952887
Coord C2 exon
chr5:28952667-28952809
Length
78 bp
Sequences
Splice sites
5' ss Seq
ATGGTAAGA
5' ss Score
9.48
3' ss Seq
TGGGTCTTGCTTGCCTTCAGGAT
3' ss Score
9.6
Exon sequences
Seq C1 exon
GACAGTCCTGACCTTCTCCTCCTGCTGCGGATGCTCTCTCTGGGGCAGGGCGCCTGGGACATGATCGACAGTCAGGTTTTCAAAGAGCCTCGAATG
Seq A exon
GTAAGATCAGCCCTCAACAGTCTAATGTTTGAAATGGATTTGTCCGGTTTACACAAGGTGGGTCTTGCTTGCCTTCAG
Seq C2 exon
GATCTGGAGGTGGTGACACGCTTTCTGCCTGCCATGATGTCGATAGTGGTGGACGACTACACGTTTACTGTAGAGCAGAAACTGCCGAGCGAAGAGAAGACTTCTCTCGCATACCCCAGCACCCTGCCTGAAACCTTCTCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000035505:ENSDART00000133949:8
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.033
Domain overlap (PFAM):
C1:
PF062098=COBRA1=FE(6.6=100)
A:
PF062098=COBRA1=FE(6.8=100)
C2:
PF062098=COBRA1=FE(10.0=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:
GGGACATGATCGACAGTCAGG
R:
GAGAAGGTTTCAGGCAGGGTG
Band lengths:
181-259
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]