HsaINT0096232 @ hg38
Intron Retention
Gene
ENSG00000123384 | LRP1
Description
LDL receptor related protein 1 [Source:HGNC Symbol;Acc:HGNC:6692]
Coordinates
chr12:57195271-57195780:+
Coord C1 exon
chr12:57195271-57195399
Coord A exon
chr12:57195400-57195657
Coord C2 exon
chr12:57195658-57195780
Length
258 bp
Sequences
Splice sites
5' ss Seq
GCTGTGAGT
5' ss Score
7.39
3' ss Seq
GTGTCCACCTCTGTCCACAGTGT
3' ss Score
9.66
Exon sequences
Seq C1 exon
AAGGCAAGACGTGCGGCCCCTCCTCCTTCTCCTGCCCTGGCACCCACGTGTGCGTCCCCGAGCGCTGGCTCTGTGACGGTGACAAAGACTGTGCTGATGGTGCAGACGAGAGCATCGCAGCTGGTTGCT
Seq A exon
GTGAGTGGCGGGGCCACGTGGAGCGGGTGGACAGCAAATGGCCACAGTCTCACTTTGCAGATGGGGAAGCCGGGGTGCAGGAGAGGAAATGCCTCAGCGGGGTCCACTGGGGGCGGAGCCATAGCTGTAGCCCAGGTGTCCAGACTCCTCATCCAGTGCCCTGCCCACTCTACCAGGAGAACCACAGGAGGTTAGAGTGAGGGACGGTCGGCCGCTGGCCAGGCAGGGCTGAAGGGCTGTGTCCACCTCTGTCCACAG
Seq C2 exon
TGTACAACAGCACTTGTGACGACCGTGAGTTCATGTGCCAGAACCGCCAGTGCATCCCCAAGCACTTCGTGTGTGACCACGACCGTGACTGTGCAGATGGCTCTGATGAGTCCCCCGAGTGTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000123384:ENST00000243077:52
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=93.2)
A:
NA
C2:
PF0005713=Ldl_recept_a=WD(100=90.5)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCCCCTCCTCCTTCTCCTG
R:
ACACTCGGGGGACTCATCAG
Band lengths:
236-494
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains
- Pre-implantation embryo development