DreINT0090867 @ danRer10
Intron Retention
Gene
ENSDARG00000006921 | lrp5
Description
low density lipoprotein receptor-related protein 5 [Source:ZFIN;Acc:ZDB-GENE-050518-2]
Coordinates
chr25:10552989-10553407:-
Coord C1 exon
chr25:10553171-10553407
Coord A exon
chr25:10553100-10553170
Coord C2 exon
chr25:10552989-10553099
Length
71 bp
Sequences
Splice sites
5' ss Seq
AAAGTAGGT
5' ss Score
6.84
3' ss Seq
AACAGCCTCTCTTTTTGCAGCCA
3' ss Score
8.55
Exon sequences
Seq C1 exon
AGCCTCCCACCTGTTCGAGCGAACAGTTTACCTGTGCTACCGGTGAGATTGACTGTATCCCCATGGCGTGGCGCTGTGACGGCATCGCTGAATGTGCAGACAACAGTGACGAGATGAACTGTCCCATCTGCTCCAAACTGCAGTTTCAGTGTGACAAAGGCCAGTGTGTGGACATTCAGGTGCGCTGCAATGGAGAGCCTGACTGCGCAGACGGCTCCGATGAACAGGACTGTGAAA
Seq A exon
GTAGGTCTCGTTTCGCAGAAGCTAGTTGCACTAATGGAAGCCATCTAAACTAACAGCCTCTCTTTTTGCAG
Seq C2 exon
CCATTTGCCTGTCTAATCAGTTCCGTTGCGGCAACAGCCAGTGTATTCTGAAGAAGCAGCAGTGCGACTCCTTCCCAGACTGCACTGATGAATCTGACGAGCGTTTCTGCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000006921:ENSDART00000121724:19
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=48.8),PF0005713=Ldl_recept_a=WD(100=46.2),PF0005713=Ldl_recept_a=PU(0.1=0.0)
A:
NA
C2:
PF0005713=Ldl_recept_a=WD(100=97.4)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGTGTGACAAAGGCCAGTGTG
R:
ATCAGTGCAGTCTGGGAAGGA
Band lengths:
179-250
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]