HsaINT0039280 @ hg19
Intron Retention
Gene
ENSG00000130635 | COL5A1
Description
collagen, type V, alpha 1 [Source:HGNC Symbol;Acc:2209]
Coordinates
chr9:137714844-137715315:+
Coord C1 exon
chr9:137714844-137714879
Coord A exon
chr9:137714880-137715261
Coord C2 exon
chr9:137715262-137715315
Length
382 bp
Sequences
Splice sites
5' ss Seq
TCGGTAAGT
5' ss Score
11.78
3' ss Seq
ATTCTTTTCTTTCTCCCCAGGGT
3' ss Score
11.84
Exon sequences
Seq C1 exon
GGTCCGCCTGGTCCAAAAGGTGCTAAGGGCTCCTCG
Seq A exon
GTAAGTAACATGCTGCCCAGCCAGGCCAATGCCTGGAAGGTAGGGGAGGGCGACGGGTCCCCTGGCACGGGAACAAACTACCCAGACAACCGTCCTAGCTCAGGCCCTGCTGCTCACGATCCTCCCATCTTTCTACACTGACCCATGGCGGACTGAGGCAGGTGGGCTGCTCGCCGCCTGCCCTAGGAAGGGCTCCATCCCTCTCTGTTCTCATCTCAAGGATCCAGGAGGGTACAGGGGTCTCTGCCATTCTCTTCTCTGCTGTGGCTGATAGGGCCACCTCCCCCACATAGGTCTCCAGGGACCATTCTAGAGCTGAAGGTGGATTCAAAGTCCCCTCATACCTCTGTGACCAAGGGTTGATTCTTTTCTTTCTCCCCAG
Seq C2 exon
GGTCCAACTGGCCCGAAGGGTGAGGCAGGCCACCCAGGACCCCCAGGCCCCCCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000130635-COL5A1:NM_000093:60
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=FE(17.5=100)
A:
NA
C2:
PF0139113=Collagen=FE(27.0=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:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
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)