DreINT0078049 @ danRer10
Intron Retention
Gene
ENSDARG00000037154 | hivep3b
Description
human immunodeficiency virus type I enhancer binding protein 3b [Source:ZFIN;Acc:ZDB-GENE-100922-42]
Coordinates
chr16:34377119-34377480:-
Coord C1 exon
chr16:34377305-34377480
Coord A exon
chr16:34377215-34377304
Coord C2 exon
chr16:34377119-34377214
Length
90 bp
Sequences
Splice sites
5' ss Seq
AAGGTAGAC
5' ss Score
7.07
3' ss Seq
GACTTGTCTTTTTCTTCAAGGGA
3' ss Score
7.59
Exon sequences
Seq C1 exon
GTATAAGTCAAACGAGGATTATGTGTATGTTCGTGGAAGGGGAAGAGGCAAGTACGTGTGTGGTGAATGTGGGATTCGCTGTAAGAAGCCCAGCATGTTAAAAAAGCACATTCGCACTCATACAGATCTGCGTCCGTATGTCTGCAAGTACTGCAACTTCGCCTTTAAAACCAAAG
Seq A exon
GTAGACATACATTCAAACTCATCCTATCATCTCTTTAAAGGCTCACGTTTCGGTACTGTGTTGATGTTGAGACTTGTCTTTTTCTTCAAG
Seq C2 exon
GGAACCTTACCAAACACATGAAGTCTAAGGCTCATGGTAAGAAATGCCTGGAGATGGGAGCATCCGAGTCCTCTGAGCTGGACCCTGAGGAAGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000037154:ENSDART00000142223:3
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=0.530
Domain overlap (PFAM):
C1:
PF134651=zf-H2C2_2=WD(100=43.3)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGTGAATGTGGGATTCGCTGT
R:
GCTCCCATCTCCAGGCATTTC
Band lengths:
176-266
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]