DreINT0078036 @ danRer10
Intron Retention
Gene
ENSDARG00000103658 | hivep1
Description
human immunodeficiency virus type I enhancer binding protein 1 [Source:ZFIN;Acc:ZDB-GENE-070912-512]
Coordinates
chr19:3448536-3449416:-
Coord C1 exon
chr19:3449241-3449416
Coord A exon
chr19:3448638-3449240
Coord C2 exon
chr19:3448536-3448637
Length
603 bp
Sequences
Splice sites
5' ss Seq
AAGGTGGGT
5' ss Score
8.23
3' ss Seq
TGTTCCCTTTATCCACACAGGGA
3' ss Score
8.73
Exon sequences
Seq C1 exon
ATACAAATCAAACGAGGAGTATGTGTATGTACGGGGCCGCGGAAGAGGAAAATACATCTGTGAGGAATGTGGAATTCGCTGCAAGAAACCTAGCATGCTGCGGAAGCACATCCGTACACATTCAGATATCCGTCCATTTCACTGCACGCACTGCAACTTCTCTTTCAAAACTAAAG
Seq A exon
GTGGGTTCAGTCTCAAACACACTGATTAAAAACTGTGATGCTTACATTTTGTTTTCCTCCTCAATTAGCAAGTATTGAAAGGTTATTTTTGATGGTAACAAATAATGAACTGGATAAAAAGATACTAAATTCGAACTTGATTGTAATCCATAAAAAATTAACCACAATGAATTGTGTACCTCTACACTTGGCCAAAGACTTATGTAATCATGTGTGTAATTTAAAAATGTAAAATTTTCTAAATGAAATGGGTCAGGATTTCATAACAGTTGGGTAATTTTGATCATTTTTAAGGATGGTTGGAAATTATTTCTGTATTAAGTGTTTCTTCTTACCTGCTTTTTTTTTTTTTTTTTTTTTGAAGAATGTGCCTGTTCTCTTTAAAAAGCCAGTATGATTCATCACAGTTGAACTTCCCACGCTGTTCTGCAGAACAGCACACAGTGTCAGACCAGCCCACGTTCCTTTAAGAACTTCTTTATCAGTTACTCACCCATTACATAGAGCTAGTGCTTGGGAACATGTCATGCTTATGTAAACCACTCCCATGCCCTGCATAAGCCTCCCACCTGAGCGACCTCTCTGTTCCCTTTATCCACACAG
Seq C2 exon
GGAACCTTACCAAGCACATGAAGTCCAAAGCCCACAGCAAGAAGTGCATGGAAATGGGAGTCGCTGTGGGTATTATTGAGGACCAGGACGCAGAAGACTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000103658:ENSDART00000172520:6
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.117 A=NA C2=0.829
Domain overlap (PFAM):
C1:
PF065247=NOA36=PU(39.9=98.3),PF134651=zf-H2C2_2=WD(100=43.3)
A:
NA
C2:
PF065247=NOA36=FE(23.0=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:
ATACAAATCAAACGAGGAGTATGTGT
R:
CTGAGTCTTCTGCGTCCTGGT
Band lengths:
278-881
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]