HsaINT0039398 @ hg19
Intron Retention
Gene
ENSG00000080573 | COL5A3
Description
collagen, type V, alpha 3 [Source:HGNC Symbol;Acc:14864]
Coordinates
chr19:10078580-10078755:-
Coord C1 exon
chr19:10078702-10078755
Coord A exon
chr19:10078616-10078701
Coord C2 exon
chr19:10078580-10078615
Length
86 bp
Sequences
Splice sites
5' ss Seq
GCGGTGAGT
5' ss Score
10.49
3' ss Seq
TCCCTGTCTGTACCCTACAGGGC
3' ss Score
9.92
Exon sequences
Seq C1 exon
GGTCCCCCTGGTCCCATTGGCTCTCTGGGCCACCCTGGGCCCCCAGGTGTGGCG
Seq A exon
GTGAGTATGCAGGGAATCTTTTGTGGGATGAGGTCACTGTGGTGGTCCAGGCCAGGACCTCAGCTCTCCCTGTCTGTACCCTACAG
Seq C2 exon
GGCCCTCTAGGACAGAAAGGCTCAAAAGGGTCTCCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000080573-COL5A3:NM_015719:60
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PD(11.8=50.0),PF0139113=Collagen=FE(27.0=100)
A:
NA
C2:
PF0139113=Collagen=FE(17.5=100)
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:
GTCCCCCTGGTCCCATTGG
R:
CGGAGACCCTTTTGAGCCTTT
Band lengths:
89-175
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)