HsaINT0039258 @ hg38
Intron Retention
Gene
ENSG00000130635 | COL5A1
Description
collagen type V alpha 1 chain [Source:HGNC Symbol;Acc:HGNC:2209]
Coordinates
chr9:134804975-134805214:+
Coord C1 exon
chr9:134804975-134805064
Coord A exon
chr9:134805065-134805160
Coord C2 exon
chr9:134805161-134805214
Length
96 bp
Sequences
Splice sites
5' ss Seq
GTGGTGAGT
5' ss Score
8.95
3' ss Seq
ACCTTTTCATGGCTTTGCAGGGA
3' ss Score
9.78
Exon sequences
Seq C1 exon
GGTGACCCAGGCCCTGCAGGCCTCCCTGGGAAAGATGGCCCTCCAGGATTACGTGGTTTCCCTGGGGACCGAGGGCTTCCTGGTCCAGTG
Seq A exon
GTGAGTGAGAGGCCAGGCGGGGAATGAAATGGGACAGGTGCAGCCCTGGAGGCCTCTCCCCACGTGCCCTTGACCAACCTTTTCATGGCTTTGCAG
Seq C2 exon
GGAGCTCTTGGACTGAAAGGCAATGAAGGGCCCCCTGGCCCACCAGGCCCTGCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000130635:ENST00000371817:40
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(16.7=36.7),PF0139113=Collagen=PU(43.9=96.7)
A:
NA
C2:
PF0139113=Collagen=FE(17.9=100),PF0139113=Collagen=PU(18.5=94.4)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTGACCCAGGCCCTGCAG
R:
CCAGGGGGCCCTTCATTG
Band lengths:
127-223
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