HsaINT0039635 @ hg38
Intron Retention
Gene
ENSG00000114270 | COL7A1
Description
collagen type VII alpha 1 chain [Source:HGNC Symbol;Acc:HGNC:2214]
Coordinates
chr3:48565410-48565668:-
Coord C1 exon
chr3:48565636-48565668
Coord A exon
chr3:48565497-48565635
Coord C2 exon
chr3:48565410-48565496
Length
139 bp
Sequences
Splice sites
5' ss Seq
CACGTGAGT
5' ss Score
9.3
3' ss Seq
GCCCCTGCTCTTGGCTCCAGGAC
3' ss Score
9.4
Exon sequences
Seq C1 exon
CCTGCCAGGGCCAGTTCATCGCATCTGGATCAC
Seq A exon
GTGAGTAGTTTTCTACTCCCAGAACTTTCTTCACCCCAGGCCCTGCCCTGCCTATCAACTGGGGTCCTCTCAGGGGGGTTGGCTGGGATGGCTGCCCATGGTGACTTCAGGGCCCTGAGGCCCCTGCTCTTGGCTCCAG
Seq C2 exon
GACCCCTCCCTAGTTATGCTGCAGACACTGCCGGCTCCCAGCTCCATGCTGTGCCTGTGCTCCGCGTCTCTCATGCAGAGGAGGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000114270:ENST00000328333:114
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.583 A=NA C2=0.967
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
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:
CAGGGCCAGTTCATCGCATC
R:
TCTGCATGAGAGACGCGGAG
Band lengths:
107-246
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