DreINT0090832 @ danRer10
Intron Retention
Gene
ENSDARG00000007906 | lrp2b
Description
low density lipoprotein receptor-related protein 2b [Source:ZFIN;Acc:ZDB-GENE-111115-1]
Coordinates
chr12:16146507-16146874:+
Coord C1 exon
chr12:16146507-16146635
Coord A exon
chr12:16146636-16146742
Coord C2 exon
chr12:16146743-16146874
Length
107 bp
Sequences
Splice sites
5' ss Seq
GCAGTAAGC
5' ss Score
5.06
3' ss Seq
TGATGAGCTCATCTTTTCAGATT
3' ss Score
6.53
Exon sequences
Seq C1 exon
GCCAAGAACCCACTCTCGCCCCCTGCACACCAAATGAGTTTAAATGCTCAAATGGCCACTGTGTTCCTCTGCCTTACGTGTGCGACCACAATAACAACTGTGGAGACCTAACTGATGAGCTGGGCTGCA
Seq A exon
GTAAGCCAACAAATACCCTATTTCATCATTATTTTTCTTAAAATAGAACTCTAAAGTAACTGCATTAGATTTCGTCTGTCAGGTTGCTGATGAGCTCATCTTTTCAG
Seq C2 exon
ATTTTGGCCATGATCGCAACTGTGATGAGAAGTTATGCAAGCATGAGTGTACAAACCTGAATGGCACTGGCTTTATCTGTTCTTGTCGTCCTGGCTATGCAGTAGATCCTGATAACACCTTTCTTTGCAACG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000007906:ENSDART00000152550:63
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=PD(0.1=0.0),PF0005713=Ldl_recept_a=WD(100=84.1)
A:
NA
C2:
PF146701=FXa_inhibition=WD(100=88.9),PF0764510=EGF_CA=PU(0.1=0.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCCCTGCACACCAAATGAGTT
R:
CGTTGCAAAGAAAGGTGTTATCAGG
Band lengths:
242-349
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]