HsaINT0096544 @ hg19
Intron Retention
Gene
ENSG00000070018 | LRP6
Description
low density lipoprotein receptor-related protein 6 [Source:HGNC Symbol;Acc:6698]
Coordinates
chr12:12283717-12284991:-
Coord C1 exon
chr12:12284755-12284991
Coord A exon
chr12:12283828-12284754
Coord C2 exon
chr12:12283717-12283827
Length
927 bp
Sequences
Splice sites
5' ss Seq
AAGGTATCC
5' ss Score
8.33
3' ss Seq
TATTTATGTTTTTTTTCCAGTGC
3' ss Score
9.35
Exon sequences
Seq C1 exon
AACCTCCAACATGTTCTCCTCAGCAGTTTACTTGTTTCACGGGGGAAATTGACTGTATCCCTGTGGCTTGGCGGTGCGATGGGTTTACTGAATGTGAAGACCACAGTGATGAACTCAATTGTCCTGTATGCTCAGAGTCCCAGTTCCAGTGTGCCAGTGGGCAGTGTATTGATGGTGCCCTCCGATGCAATGGAGATGCAAACTGCCAGGACAAATCAGATGAGAAGAACTGTGAAG
Seq A exon
GTATCCAGAATTCTTCAGTGCCTCAGCATGCAATCCTTTTTTCCCATTCAGTTGTTTAAACTTCAGTATTACTTGGCTTAGTGTCAGTTGGGGTTTTTCAAGTACATATGACTGTATCACTTCTGATCATAGTGCCATGTTCCATATTATTGTTTTAATTCACTCCATATGCATAAGATTTATACAAATTAATAAGCTTTGAAAATTGAGAAATGAAACTAAAATATATTAGGCCTTCAGTATATAAAAATAGTCCCTGTTTCCAATGAGCTCTGAATTAGTGGATTTATTAATTACGCTCTAACATATTTTATATTCTTCACTTTCCCTTACTAACTTTTCCCATGGTAAAAACAACCCAGCCAAGTTCTCTAGAATTCTTTAGTGAAAGAGGGAATTTAATGTAAAGAATAAGCCGGGCGTGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGCGGGCGGATCACGAGGTCAGGAGATAGAGACCATCCTGGCTAACACGGTGAAACCCCATCTCTACTAAAAATACAAAAAAATTAGCCGGGCCTGGTGGCAGACGCCTGTAGTCCCAGCTACTTGGGAGGCTGAGGCAGGAGAATGGCGTGAACCTGGGAAGCAGAGCTTGCAGTGAGCCAATATCGCGCCACTGCACTCCAGCCTGGGCGACAGAGCAAGACTCCGTCTCAAAAAAAAAAAAAAAAAAAAAAAAAAAATGTTAGGAAATTTCCTGCTGGATTTTTTTCTCCTACTCTTTTTTCTCTCTCTCAACCAATGGAACTCCAGAGAATAATATTTAAGTTATAGCTAAAAGTCTAATTTGTTTTTCATTTGTGTTCAGAAGGCACCTTTTGATTCTTGCCAGAGTTTGACTTTACATGATATTAAAAATAAGGAAACTATTTATGTTTTTTTTCCAG
Seq C2 exon
TGCTTTGTTTAATTGATCAGTTCCGCTGTGCCAATGGTCAGTGCATTGGAAAGCACAAGAAGTGTGATCATAATGTGGATTGCAGTGACAAGTCAGATGAACTGGATTGTT
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000070018-LRP6:NM_002336:18
Average complexity
IR-C
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=100.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCTCCAACATGTTCTCCTCAGC
R:
ATCCAGTTCATCTGACTTGTCACTG
Band lengths:
342-1269
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
Other AS DBs:
FasterDB (Includes CLIP-seq data)
AS-ALPS (AS-induced ALteration of Protein Structure, links to PINs)
APPRIS (Selection of principal isoform)
DEU primates (Only for human)