HsaINT0097612 @ hg19
Intron Retention
Gene
ENSG00000090006 | LTBP4
Description
latent transforming growth factor beta binding protein 4 [Source:HGNC Symbol;Acc:6717]
Coordinates
chr19:41119310-41119944:+
Coord C1 exon
chr19:41119310-41119435
Coord A exon
chr19:41119436-41119821
Coord C2 exon
chr19:41119822-41119944
Length
386 bp
Sequences
Splice sites
5' ss Seq
TCGGTTCGT
5' ss Score
4.07
3' ss Seq
TCGGACGCCCTGTCCCGCAGACG
3' ss Score
7.76
Exon sequences
Seq C1 exon
ACGTGAACGAGTGCCTGGAGGGCGATTTCTGCTTCCCTCACGGCGAGTGCCTCAACACTGACGGCTCCTTTGCCTGTACTTGTGCCCCTGGCTACCGACCCGGACCCCGCGGAGCCTCTTGCCTCG
Seq A exon
GTTCGTACCCGGGCTGATCCTGGCCCCGGAAAGGGTGGGCTTAGGGCAGGAAAAGGCGGGACGGGGAGAAGAGGGCGAAAAGGGGAAAACGAGTTTTTAGCCGGGGTATTCCAGCAGGATCAGGGGGCAGCTGGTGGGAGTCTCGAGGCAGTGAGGGGGGGCGGGGCGTGGAGATGAAAGGGCCGAGTCTGGGTATTTGGACCGTGATTGTAAAGAAGCTGTTCTAAACCCGTCGGGGGGCGGTGTTTGCAGGGAGGGAAGTAGCGTGAGGCAGGTTGGGGAAGGCGTGAGAGGCCTAGGAGAGCCGAGGGGCGGTGGAGGGGTGTGGCCTAGAATGTTAGGCGGAGCGGGAGGTGGGCCGGGCCTTCGGACGCCCTGTCCCGCAG
Seq C2 exon
ACGTTGACGAGTGCAGCGAGGAGGACCTTTGCCAGAGCGGCATCTGTACCAACACCGACGGCTCCTTCGAGTGCATCTGTCCTCCGGGACACCGCGCTGGCCCGGACCTCGCCTCCTGCCTCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000090006-LTBP4:NM_003573:20
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=0.015
Domain overlap (PFAM):
C1:
PF0764510=EGF_CA=WD(100=95.3),PF0764510=EGF_CA=PU(0.1=0.0)
A:
NA
C2:
PF0764510=EGF_CA=WD(100=95.2),PF0764510=EGF_CA=PU(0.1=0.0)
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CGTGAACGAGTGCCTGGAG
R:
GAGGCAGGAGGCGAGGTC
Band lengths:
247-633
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Genotype-Tissue Expression Project (GTEx)
- 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)