HsaINT0039627 @ hg19
Intron Retention
Gene
ENSG00000114270 | COL7A1
Description
collagen, type VII, alpha 1 [Source:HGNC Symbol;Acc:2214]
Coordinates
chr3:48605007-48605196:-
Coord C1 exon
chr3:48605143-48605196
Coord A exon
chr3:48605070-48605142
Coord C2 exon
chr3:48605007-48605069
Length
73 bp
Sequences
Splice sites
5' ss Seq
ATGGTGAGT
5' ss Score
10.13
3' ss Seq
TCATGTCTTTTTTTCTCCAGGGG
3' ss Score
10.28
Exon sequences
Seq C1 exon
GGAGAAGCTGGTCCCCCAGGCCGCCCCGGGCTGGCAGGACACAAAGGAGAGATG
Seq A exon
GTGAGTGTGGGCACGCTCAGAATGAGGGGGCCACGGGTGGACGGGGGCCAAGTTCATGTCTTTTTTTCTCCAG
Seq C2 exon
GGGGAGCCTGGTGTGCCGGGCCAGTCGGGGGCCCCTGGCAAGGAGGGCCTGATCGGTCCCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000114270-COL7A1:NM_000094:107
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(21.8=100)
A:
NA
C2:
PF0139113=Collagen=FE(25.6=100),PF0139113=Collagen=PU(16.7=66.7)
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:
GGAGAAGCTGGTCCCCCA
R:
GACCGATCAGGCCCTCCTT
Band lengths:
112-185
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)