HsaINT0039669 @ hg38
Intron Retention
Gene
ENSG00000114270 | COL7A1
Description
collagen type VII alpha 1 chain [Source:HGNC Symbol;Acc:HGNC:2214]
Coordinates
chr3:48593102-48593449:-
Coord C1 exon
chr3:48593356-48593449
Coord A exon
chr3:48593264-48593355
Coord C2 exon
chr3:48593102-48593263
Length
92 bp
Sequences
Splice sites
5' ss Seq
TGGGTAAGG
5' ss Score
9.08
3' ss Seq
CTGATGGGTCGTCACTTCAGGGA
3' ss Score
5.45
Exon sequences
Seq C1 exon
GTCTGCATCCTGATCACAGACGGGAAGTCCCAGGACCTGGTGGACACAGCTGCCCAAAGGCTGAAGGGGCAGGGGGTCAAGCTATTTGCTGTGG
Seq A exon
GTAAGGACCGAGCAGGAGTGACAGGTCAGCTGGGGGGTGGGGGCAGTCAGAGAGCATGTGGGTGACTGAGTCCTGATGGGTCGTCACTTCAG
Seq C2 exon
GGATCAAGAATGCTGACCCTGAGGAGCTGAAGCGAGTTGCCTCACAGCCCACCAGTGACTTCTTCTTCTTCGTCAATGACTTCAGCATCTTGAGGACACTACTGCCCCTCGTTTCCCGGAGAGTGTGCACGACTGCTGGTGGCGTGCCTGTGACCCGACCTC
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000114270:ENST00000328333:4
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.218
Domain overlap (PFAM):
C1:
PF0009223=VWA=FE(17.9=100)
A:
NA
C2:
PF0009223=VWA=PD(20.8=65.5)
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:
GTGGACACAGCTGCCCAAAG
R:
GAAACGAGGGGCAGTAGTGTC
Band lengths:
170-262
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