DreINT0090485 @ danRer10
Intron Retention
Gene
ENSDARG00000029146 | lrp1ab
Description
low density lipoprotein receptor-related protein 1Ab [Source:ZFIN;Acc:ZDB-GENE-030131-7126]
Coordinates
chr23:25568530-25568906:-
Coord C1 exon
chr23:25568784-25568906
Coord A exon
chr23:25568671-25568783
Coord C2 exon
chr23:25568530-25568670
Length
113 bp
Sequences
Splice sites
5' ss Seq
GTGGTAAGC
5' ss Score
8.15
3' ss Seq
TCTATTCTTTTACAATGTAGAAT
3' ss Score
6.22
Exon sequences
Seq C1 exon
TGTTTAACAAGACCTGTGATGACACTGAGTTCCAGTGTCAGAATTCTCAGTGTATTCCCAAAAACTTCATGTGTGATCATGACATTGACTGTCGCGATGGCTCTGACGAGTCGCCAGAGTGTG
Seq A exon
GTAAGCATGTGGTGTAGACTTGGTGCTTTTTAAAATTATTATTGGTCATGTTTACTGTACCAGCAAAGTGATCGCAGAGTGTGTCAAATGTTGTCTATTCTTTTACAATGTAG
Seq C2 exon
AATATCCTACCTGTGGGCCAAATGATTTCCACTGTGCAAATGGCCAGTGCCTGAAGCAGAAAAACTGGGCATGTGATGGAGAGTTTGACTGTAGAGACCAATCAGACGAAGCACCCAAAAACTTGCAATGCACAGACACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000029146:ENSDART00000088208:53
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:
PF0005713=Ldl_recept_a=WD(100=90.5)
A:
NA
C2:
PF0005713=Ldl_recept_a=WD(100=87.5)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCTGTGATGACACTGAGTTCCA
R:
GCATTGCAAGTTTTTGGGTGC
Band lengths:
242-355
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]