HsaINT0039687 @ hg38
Intron Retention
Gene
ENSG00000114270 | COL7A1
Description
collagen type VII alpha 1 chain [Source:HGNC Symbol;Acc:HGNC:2214]
Coordinates
chr3:48579785-48580057:-
Coord C1 exon
chr3:48580031-48580057
Coord A exon
chr3:48579815-48580030
Coord C2 exon
chr3:48579785-48579814
Length
216 bp
Sequences
Splice sites
5' ss Seq
CTGGTAAGG
5' ss Score
9.68
3' ss Seq
ACTGGTCATTCCCCCCACAGGTA
3' ss Score
11.88
Exon sequences
Seq C1 exon
GGTCCCCCAGGACCCCCGGGACGGCTG
Seq A exon
GTAAGGGCTGCGCTGGGTCTGGTCCTCTGTCATTGTTCTCACTTGCCCCTTTGGCTCCACATCATGTCCCCTCATTCCTTCCACTAACTCCCACTTCCCCCACTGTCCCTCTGAAACCTCCGCGGATCCCTGGAGCCCCTCACAGACCCTGTATCCCCTCGCCAACTCCTCTTCCCCTTGTTGAGCCATTCTTCTCACTGGTCATTCCCCCCACAG
Seq C2 exon
GTAGACACAGGACCTGGAGCCAGAGAGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000114270:ENST00000328333:56
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=FE(12.1=100)
A:
NA
C2:
PF0139113=Collagen=PD(10.6=70.0),PF0139113=Collagen=PU(7.9=50.0)
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:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
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