HsaINT0096349 @ hg38
Intron Retention
Gene
ENSG00000168702 | LRP1B
Description
LDL receptor related protein 1B [Source:HGNC Symbol;Acc:HGNC:6693]
Coordinates
chr2:140456455-140457651:-
Coord C1 exon
chr2:140457463-140457651
Coord A exon
chr2:140456604-140457462
Coord C2 exon
chr2:140456455-140456603
Length
859 bp
Sequences
Splice sites
5' ss Seq
ATGGTAATT
5' ss Score
6.49
3' ss Seq
TGTTTCTTTCTTATCTTTAGTCT
3' ss Score
8.73
Exon sequences
Seq C1 exon
TCCCTAATCAAGATATTCCAGGGGTGATTGCACTAACATTGTTTGAAGACTACATCTACTGGACTGATGGGAAAACCAAGTCACTCAGCCGTGCCCATAAAACATCGGGAGCAGACAGACTCTCACTGATTTACTCATGGCATGCCATCACAGATATCCAGGTGTATCATTCTTATAGACAACCTGATG
Seq A exon
GTAATTATTCTTTCCATGATTTCCATAAATGCATTAACATCTTTCAGTAACATTCCATTTTTTATTATTTCAAGGTTAAATGTAATTTTATTTTTGATGAAGATTACTAGATTTAATTATTTAGCATCACTTTATGGAAGAATTCAGTCAATATGAAGTACTGCTCTTAAGGCATATGATTAGAAGCTCAATAATAGGACAAAGAATTATGGATTTGTTCAACTCATATTAAGCTAAAATGATAATAATGCATTTAGTCAGATAAGTGAAGACTGTATTCTTGAAATAATTTGTTTACAAAATAGAGGATCCTTAGTTTCTGAAATGCTGAGTAGGAGGAATTATGCTTAAGTAGCTCTAGGGTTTTAAAACTGACAACTCTATCAAGTTTTCTTCAGCATATGTTTAATAGGAATTTCATCTGGCCTTGTGAAATAAAGGTTTGATTATTTTCCTTAAAAAAACCTATCCGGCCTATAAAGCAAAGTCATTACACTAGTAGTTGTAGATCATTGTTTCATTGTTTTATTTTATGTTTGTATTTCTGAACATATGTTTGTCTTCATCCAAAATGCTTCTAGTCTTTGTTTATTTTTCTCATGGACAGTTTTTTTCTACTAAAATTTTTGTTTTGTAGAAATGCACCTTTAAAATTATTGAATGGTAGAATTAATGTCAATGGACAATGAGTAGCATTTGTGACAAAGTAAAATTATATTTATAGTCTTGATGAGTTCTTGAGTACAAAGATTTATTCTAATTCAAGTTATGCAGCTTAAAAGTCCTATCTCTAATCCCATGTTATATTATTAGTCTTGATTATCCTGTTTTGTTGTTGTTGTTTCTTTCTTATCTTTAG
Seq C2 exon
TCTCCAAACATCTCTGCATGATAAATAATGGTGGTTGCAGTCATTTGTGCCTTTTAGCCCCTGGAAAAACCCACACTTGTGCATGTCCCACTAACTTCTATCTGGCAGCTGATAATAGGACTTGCTTATCCAACTGCACAGCCAGCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000168702:ENST00000389484:61
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:
NO
A:
NA
C2:
PF146701=FXa_inhibition=WD(100=74.0),PF0005713=Ldl_recept_a=PU(15.8=12.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TCCCTAATCAAGATATTCCAGGGGT
R:
GCTGGCTGTGCAGTTGGATAA
Band lengths:
335-1194
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