HsaINT0039398 @ hg38
Intron Retention
Gene
ENSG00000080573 | COL5A3
Description
collagen type V alpha 3 chain [Source:HGNC Symbol;Acc:HGNC:14864]
Coordinates
chr19:9967904-9968079:-
Coord C1 exon
chr19:9968026-9968079
Coord A exon
chr19:9967940-9968025
Coord C2 exon
chr19:9967904-9967939
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:ENST00000264828:60
Average complexity
IR
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
Chicken
(galGal3)
No conservation detected
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