HsaINT0039713 @ hg19
Intron Retention
Gene
ENSG00000114270 | COL7A1
Description
collagen, type VII, alpha 1 [Source:HGNC Symbol;Acc:2214]
Coordinates
chr3:48629535-48629900:-
Coord C1 exon
chr3:48629784-48629900
Coord A exon
chr3:48629682-48629783
Coord C2 exon
chr3:48629535-48629681
Length
102 bp
Sequences
Splice sites
5' ss Seq
GTGGTGAGT
5' ss Score
8.95
3' ss Seq
CCTTGGTGTCCCCCATGCAGGTG
3' ss Score
10.25
Exon sequences
Seq C1 exon
CTGCCCTAGAAGGGCCGGAACTGACCATCCAGAATACCACAGCCCACAGCCTCCTGGTGGCCTGGCGGAGTGTGCCAGGTGCCACTGGCTACCGTGTGACATGGCGGGTCCTCAGTG
Seq A exon
GTGAGTGAGAGATGTGGGCTGAGGGGAGTCCCCGCGCCTCAGACAAGGCTGTAGAGTCCTGAGTCTGCAAGGCCCACTGGCCCCTTGGTGTCCCCCATGCAG
Seq C2 exon
GTGGGCCCACACAGCAGCAGGAGCTGGGCCCTGGGCAGGGTTCAGTGTTGCTGCGTGACTTGGAGCCTGGCACGGACTATGAGGTGACCGTGAGCACCCTATTTGGCCGCAGTGTGGGGCCCGCCACTTCCCTGATGGCTCGCACTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000114270-COL7A1:NM_000094:8
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.225 A=NA C2=0.440
Domain overlap (PFAM):
C1:
PF0004116=fn3=PU(44.2=85.0)
A:
NA
C2:
PF0004116=fn3=PD(54.5=84.0)
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:
CCTAGAAGGGCCGGAACTGA
R:
GCGAGCCATCAGGGAAGTG
Band lengths:
256-358
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
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)