HsaINT0039716 @ hg19
Intron Retention
Gene
ENSG00000114270 | COL7A1
Description
collagen, type VII, alpha 1 [Source:HGNC Symbol;Acc:2214]
Coordinates
chr3:48610749-48610990:-
Coord C1 exon
chr3:48610946-48610990
Coord A exon
chr3:48610782-48610945
Coord C2 exon
chr3:48610749-48610781
Length
164 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGT
5' ss Score
10.47
3' ss Seq
AGTCTCTGGGTTGTTTGCAGGGG
3' ss Score
6.67
Exon sequences
Seq C1 exon
GGTCTTGCTGGCCCTGCAGGACCCCAAGGACCTTCTGGCCTGAAG
Seq A exon
GTGAGTCTAGGTGTGTGGATAGGAGGAGGAGGCTCCTTCAAGCTGTGTCCATGCCTGGGGTAGTGTGCGCCAACCTCCTGGGCTGTCATCTCCTGCAATGAGGATGAGCTCCAGGAGCCCTGGCCACGTGGGCTCTGCTCATGCAGTCTCTGGGTTGTTTGCAG
Seq C2 exon
GGGGAGCCTGGAGAGACAGGACCTCCAGGACGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000114270-COL7A1:NM_000094:82
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(20.3=100),PF0139113=Collagen=PU(6.5=33.3)
A:
NA
C2:
PF0139113=Collagen=FE(14.5=100),PF0139113=Collagen=FE(13.0=100)
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:
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)