HsaINT0095626 @ hg19
Intron Retention
Gene
ENSG00000198670 | LPA
Description
lipoprotein, Lp(a) [Source:HGNC Symbol;Acc:6667]
Coordinates
chr6:160968821-160969691:-
Coord C1 exon
chr6:160969510-160969691
Coord A exon
chr6:160968970-160969509
Coord C2 exon
chr6:160968821-160968969
Length
540 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGA
5' ss Score
10.57
3' ss Seq
ATTTTTATTTTTTTCTACAGACT
3' ss Score
9.86
Exon sequences
Seq C1 exon
TGGCCTGACAATGAACTACTGCAGGAATCCAGATGCCGATACAGGCCCTTGGTGTTTTACCATGGACCCCAGCATCAGGTGGGAGTACTGCAACCTGACGCGATGCTCAGACACAGAAGGGACTGTGGTCGCTCCTCCGACTGTCATCCAGGTTCCAAGCCTAGGGCCTCCTTCTGAACAAG
Seq A exon
GTAAGAAGTCTGTGTCTTACCTTGTCTAGCACATACCTCTCTATGTGCTTGGACAACGGGATGAAAAGACATGAAAAACCACACTGATGCAGAAGCCTTTAGTGCTACACGGGAGCTCGAGTGTTGGTTGAGGTTCTGCCATGACCAAGGAAGTCTCAGTGCCGTCCCTGGGAAAGCCAGAGCTGTGATTTTTGGCACAACTTGTGGGAGTAGTGACTTTAGGACTGGCGCAAAACCTCCAGGGTGCTCAACTTAACCACTCACCTTATTCTAAAATGGGTTATTTCAGTGTCCCAGTCAAATTCCTATTCTAACATGCTGTCAACTGTGTGATTATTTCCAAGCCAATAAGCATTTCCAGTAATTTCTTAAAATAGTGTTCATTGCAGTCTTCAGCGTTGTGGCTCCTGAGGGATGTGGCCCCTGATTCTGTCGTCCTAGAGAAGCCTGACATGACTGCATTGATTCTGTATCGTCCTGGGTCTATGTGGCTGCCTGGCTGTCTGTAATCATCTGTTTTATTTTTATTTTTTTCTACAG
Seq C2 exon
ACTGTATGTTTGGGAATGGGAAAGGATACCGGGGCAAGAAGGCAACCACTGTTACTGGGACGCCATGCCAGGAATGGGCTGCCCAGGAGCCCCATAGACACAGCACGTTCATTCCAGGGACAAATAAATGGGCAGGTCTGGAAAAAAAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000198670-LPA:NM_005577:32
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.242 A=NA C2=0.140
Domain overlap (PFAM):
C1:
PF0005113=Kringle=PD(44.9=56.5)
A:
NA
C2:
PF0005113=Kringle=PU(60.0=96.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGCCTGACAATGAACTACTGCA
R:
TTTTTCCAGACCTGCCCATTT
Band lengths:
327-867
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)