HsaINT0039641 @ hg19
Intron Retention
Gene
ENSG00000114270 | COL7A1
Description
collagen, type VII, alpha 1 [Source:HGNC Symbol;Acc:2214]
Coordinates
chr3:48627646-48628017:-
Coord C1 exon
chr3:48627892-48628017
Coord A exon
chr3:48627790-48627891
Coord C2 exon
chr3:48627646-48627789
Length
102 bp
Sequences
Splice sites
5' ss Seq
GTGGTCAGT
5' ss Score
4.85
3' ss Seq
GCATTTCCCTCTGACCTCAGGTC
3' ss Score
8.91
Exon sequences
Seq C1 exon
AGCCGGAAACTCCACTTGCTGTTCCAGGGCTGCGGGTTGTGGTGTCAGATGCAACGCGAGTGAGGGTGGCCTGGGGACCCGTCCCTGGAGCCAGTGGATTTCGGATTAGCTGGAGCACAGGCAGTG
Seq A exon
GTCAGTGTGGGGTGTGTGGGGGGACTGCCAAAGGGACCAATGAGGGTATGGGTGCCAGAGGGGACAGGCAGGAGCCATGCCAGCATTTCCCTCTGACCTCAG
Seq C2 exon
GTCCGGAGTCCAGCCAGACACTGCCCCCAGACTCTACTGCCACAGACATCACAGGGCTGCAGCCTGGAACCACCTACCAGGTGGCTGTGTCGGTACTGCGAGGCAGAGAGGAGGGCCCTGCTGCAGTCATCGTGGCTCGAACGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000114270-COL7A1:NM_000094:14
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.302 A=NA C2=0.694
Domain overlap (PFAM):
C1:
PF0004116=fn3=PU(46.8=86.0)
A:
NA
C2:
PF0004116=fn3=PD(51.9=83.7)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCGGAAACTCCACTTGCTGTT
R:
CACGATGACTGCAGCAGGG
Band lengths:
258-360
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)