DreINT0078047 @ danRer10
Intron Retention
Gene
ENSDARG00000037154 | hivep3b
Description
human immunodeficiency virus type I enhancer binding protein 3b [Source:ZFIN;Acc:ZDB-GENE-100922-42]
Coordinates
chr16:34383860-34384507:-
Coord C1 exon
chr16:34384156-34384507
Coord A exon
chr16:34384006-34384155
Coord C2 exon
chr16:34383860-34384005
Length
150 bp
Sequences
Splice sites
5' ss Seq
GAGGTAATG
5' ss Score
8.73
3' ss Seq
CCTCTCTGTCTGGAGTGTAGGTA
3' ss Score
3.19
Exon sequences
Seq C1 exon
GGAGGAGGAAAGGGAAGAGGCAGAACACCGGTATGCTCCAAGGGTAGCTAGTCCAGTGAGAATCGTGGATCCTTCATATCCTAGTTTGCATACAACAACATCTGTCAGTTGGTGCTACCTAAATTATACAAAGCCCAACCCATCTACACATAGAGATTCAACATCAGTCTATTCCTCATGGAGTGTTAGCATGCATAACCCCAATATACCTGGTTTGTCCACCAAAATATTACTATCTCTGTTGCGCTCAAAACAAAAACATAGTGCTGAAACATACACAATGGCTACAGCTCCACCACCAACCATTGACAAGCTGGTTTCTACAGACAGCAAGGAGACCAGTGCATCAGAG
Seq A exon
GTAATGATCTCTGTAATTTTACATTTGTAAAATAAGTATGCATATTTAAGACTTTTTTATGTTTATTCTACCATGTATCTATCATGTGTTTTGTAAGTTGTGTAAATGTATTACAGTGTTGGTAAATTAGCCTCTCTGTCTGGAGTGTAG
Seq C2 exon
GTACATGCCTCACCACCCAGCACCCCCGTCAAAGTAAAAGAGGAACCAACAAGTGAAAGTAGGGACAAAGATAAGGAGAGTGCTGATGACATGCCAGCTACCTCGACTCAAAATGAGGCAGTACGTGTTTGCATTTTTGAGGGCGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000037154:ENSDART00000142223:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.602 A=NA C2=0.776
Domain overlap (PFAM):
C1:
NO
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:
TCTCTGTTGCGCTCAAAACAA
R:
TGCAAACACGTACTGCCTCAT
Band lengths:
250-400
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]