HsaINT0039682 @ hg19
Intron Retention
Gene
ENSG00000114270 | COL7A1
Description
collagen, type VII, alpha 1 [Source:HGNC Symbol;Acc:2214]
Coordinates
chr3:48618555-48618773:-
Coord C1 exon
chr3:48618693-48618773
Coord A exon
chr3:48618591-48618692
Coord C2 exon
chr3:48618555-48618590
Length
102 bp
Sequences
Splice sites
5' ss Seq
GATGTAAGA
5' ss Score
5.46
3' ss Seq
CTGACTCTCATGTTTCACAGGGT
3' ss Score
9.2
Exon sequences
Seq C1 exon
GGTGACTCAGGGCCTCCTGGAGAGAAGGGAGACCCTGGGCGGCCTGGCCCCCCAGGACCTGTTGGCCCCCGAGGACGAGAT
Seq A exon
GTAAGAGGCTGGAGTCGGGGGAGTCATGGCGGGTAAGGGAGTAGGGCTGTTGCCAGCATCATGGGGGTTCTTGGAACCAGGGCTGACTCTCATGTTTCACAG
Seq C2 exon
GGTGAAGTTGGAGAGAAAGGTGACGAGGGTCCTCCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000114270-COL7A1:NM_000094:51
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(37.1=100)
A:
NA
C2:
PF0139113=Collagen=FE(15.7=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:
GGTGACTCAGGGCCTCCT
R:
AGGACCCTCGTCACCTTTCTC
Band lengths:
114-216
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)