HsaINT0039722 @ hg19
Intron Retention
Gene
ENSG00000114270 | COL7A1
Description
collagen, type VII, alpha 1 [Source:HGNC Symbol;Acc:2214]
Coordinates
chr3:48609813-48609971:-
Coord C1 exon
chr3:48609936-48609971
Coord A exon
chr3:48609855-48609935
Coord C2 exon
chr3:48609813-48609854
Length
81 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGT
5' ss Score
10.47
3' ss Seq
TGACCTCTCCCCCTTACCAGGGA
3' ss Score
10.19
Exon sequences
Seq C1 exon
GCTGTGGTCGGGCTCCCTGGAGCAAAGGGAGAGAAG
Seq A exon
GTGAGTGTGTGTGGGGCTGCCAGTGAGGGGGGGTCAACTGGTGGGGGCCAAGGAATCCCACTGACCTCTCCCCCTTACCAG
Seq C2 exon
GGAGCCCCTGGAGGCCTTGCTGGAGACCTGGTGGGTGAGCCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000114270-COL7A1:NM_000094:88
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=FE(16.9=100)
A:
NA
C2:
PF0139113=Collagen=PD(12.3=57.1),PF0139113=Collagen=PU(15.5=64.3)
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:
CTGTGGTCGGGCTCCCTG
R:
CCACCAGGTCTCCAGCAAGG
Band lengths:
69-150
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)