HsaINT0039639 @ hg19
Intron Retention
Gene
ENSG00000114270 | COL7A1
Description
collagen, type VII, alpha 1 [Source:HGNC Symbol;Acc:2214]
Coordinates
chr3:48628106-48629025:-
Coord C1 exon
chr3:48628897-48629025
Coord A exon
chr3:48628250-48628896
Coord C2 exon
chr3:48628106-48628249
Length
647 bp
Sequences
Splice sites
5' ss Seq
AGGGTGAGG
5' ss Score
7.13
3' ss Seq
TACCCTGACTTCTCTCTTAGGGG
3' ss Score
8.84
Exon sequences
Seq C1 exon
GACCAGAGCTGCCTGTGAGCCCTGTAACAGACCTGCAAGCCACCGAGCTGCCCGGGCAGCGGGTGCGAGTGTCCTGGAGCCCAGTCCCTGGTGCCACCCAGTACCGCATCATTGTGCGCAGCACCCAGG
Seq A exon
GTGAGGTGGACGCAGCCAGCACCCCCACCACACACACTGAAGTTCCAGCCTGAGGGGTCTGAGTGTACCTCCAGCCCTCTCCTTCCACACCTGGGTCCCTATAGTCTCCTCCCTGTCTCGTTATCCATCTGCTTCCCAAGATGGCACTGAGCCCTGAACTGTCAACAGGGTGTGTCTGCCCCTACCCTACCCCAACCAATCTCCTCCCTGCCCCACACCCCATCCACGGCTTTCACCTCTGCACAGCCACAAGCTCAATCACCTGTCTTTCTGTTACCCTAGTGGTGACCACTGTACACCAACCTCTCATTGCATGTCCCCATCCAGCACTGACCTCTGCCATCCCACATCAGTGTCTGTCAATGGCTCATCAGTTCTCACTGCAGTCCACTGACTCCTGTCATCCTACATGCTAAGATCCCACAGACTCCTGTCCTCCAGTGTCCCTGACCATCACTGGCCCCTTTCATCCTATGTCCTTGTCTTGCACTCACTTTTTTCAGCCATATCCCAGCTCTCTGGTCCCCACCACCCCACATCCCCACCCCCATGGCCCTTCTCACTCTGCGTCCCTGTCCATCACTGCCATCGTCCCACATCCCTGTCTCTTTCTGACCCCTGCCCACCTACCCTGACTTCTCTCTTAG
Seq C2 exon
GGGTTGAGCGGACCCTGGTGCTTCCTGGGAGTCAGACAGCATTCGACTTGGATGACGTTCAGGCTGGGCTTAGCTACACTGTGCGGGTGTCTGCTCGAGTGGGTCCCCGTGAGGGCAGTGCCAGTGTCCTCACTGTCCGCCGGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000114270-COL7A1:NM_000094:12
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.364 A=NA C2=0.245
Domain overlap (PFAM):
C1:
PF0004116=fn3=PU(46.8=84.1)
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:
GACCAGAGCTGCCTGTGAG
R:
CGGCGGACAGTGAGGACA
Band lengths:
271-918
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)