HsaINT0039670 @ hg38
Intron Retention
Gene
ENSG00000114270 | COL7A1
Description
collagen type VII alpha 1 chain [Source:HGNC Symbol;Acc:HGNC:2214]
Coordinates
chr3:48583393-48583615:-
Coord C1 exon
chr3:48583556-48583615
Coord A exon
chr3:48583429-48583555
Coord C2 exon
chr3:48583393-48583428
Length
127 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGT
5' ss Score
10.67
3' ss Seq
CCCAAATTCATCCCTTCCAGGGC
3' ss Score
8.04
Exon sequences
Seq C1 exon
GGTGACTCTGAGGATGGAGCTCCAGGCCTCCCAGGACAACCTGGGTCTCCGGGTGAGCAG
Seq A exon
GTGAGTGGAGGGGCCAGGGATTCTGAATATGGTGGGCACAGCTCCAGCCCCTACCTCAATCATCAACCACTGCTCCATCCTCATGCCCAAACCCAAATCTCTGAACCCCCAAATTCATCCCTTCCAG
Seq C2 exon
GGCCCACGGGGACCTCCTGGAGCTATTGGCCCCAAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000114270:ENST00000328333:40
Average complexity
IR
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=PD(7.1=20.0),PF0139113=Collagen=PU(32.1=90.0)
A:
NA
C2:
PF0139113=Collagen=FE(19.6=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping 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:
GGTGACTCTGAGGATGGAGCT
R:
GCCAATAGCTCCAGGAGGTCC
Band lengths:
90-217
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