HsaINT0039719 @ hg38
Intron Retention
Gene
ENSG00000114270 | COL7A1
Description
collagen type VII alpha 1 chain [Source:HGNC Symbol;Acc:HGNC:2214]
Coordinates
chr3:48572862-48573056:-
Coord C1 exon
chr3:48573021-48573056
Coord A exon
chr3:48572943-48573020
Coord C2 exon
chr3:48572862-48572942
Length
78 bp
Sequences
Splice sites
5' ss Seq
GTGGTGAGT
5' ss Score
8.95
3' ss Seq
ACAGAGCTCTTCCCTCTCAGGGG
3' ss Score
5.65
Exon sequences
Seq C1 exon
GGTCCACAGGGGTCTCCAGGTTTGCCTGGACAAGTG
Seq A exon
GTGAGTTCTGGGGGTCAAGGGTTGGGCTCCAGGGGTCAAGGGTCGACAGGCAGCCCTGACAGAGCTCTTCCCTCTCAG
Seq C2 exon
GGGGAGACAGGGAAGCCGGGAGCCCCAGGTCGAGATGGTGCCAGTGGAAAAGATGGAGACAGAGGGAGCCCTGGTGTGCCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000114270:ENST00000328333:85
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=FE(14.7=100),PF0139113=Collagen=PU(10.0=66.7)
A:
NA
C2:
PF0139113=Collagen=FE(33.8=100),PF0139113=Collagen=PU(30.8=74.1)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCACAGGGGTCTCCAGGTTT
R:
CACACCAGGGCTCCCTCTG
Band lengths:
111-189
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