HsaINT0039708 @ hg38
Intron Retention
Gene
ENSG00000114270 | COL7A1
Description
collagen type VII alpha 1 chain [Source:HGNC Symbol;Acc:HGNC:2214]
Coordinates
chr3:48574797-48575126:-
Coord C1 exon
chr3:48575064-48575126
Coord A exon
chr3:48574866-48575063
Coord C2 exon
chr3:48574797-48574865
Length
198 bp
Sequences
Splice sites
5' ss Seq
AAGGTGATC
5' ss Score
4.41
3' ss Seq
CTGTGACCTTGTGTTTGTAGGTG
3' ss Score
9.47
Exon sequences
Seq C1 exon
GGCAGAGATGGCCCTCCTGGACTCCCTGGAACCCCTGGGCCCCCCGGACCCCCTGGCCCCAAG
Seq A exon
GTGATCACCCCATCCCTGCCTTAGTCCTGTGACTAGTGACCAGGAAGCCACCCTTAGCTTGGTCCCCAGAAATATGGTAGTGTGTGCCATAACCCTGGAATTTCTGACCCTATAACCCTCTGTGATCCTGAGATCTGTGATGACTCCCCCATGCCTCTATGACAGAGACATCTCTCCCCTGTGACCTTGTGTTTGTAG
Seq C2 exon
GTGTCTGTGGATGAGCCAGGTCCTGGACTCTCTGGAGAACAGGGACCCCCTGGACTCAAGGGTGCTAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000114270:ENST00000328333:75
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(30.3=100)
A:
NA
C2:
PF0139113=Collagen=PD(7.6=21.7),PF0139113=Collagen=PU(28.3=73.9)
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:
CAGAGATGGCCCTCCTGGAC
R:
CTTAGCACCCTTGAGTCCAGG
Band lengths:
130-328
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