HsaINT0039680 @ hg38
Intron Retention
Gene
ENSG00000114270 | COL7A1
Description
collagen type VII alpha 1 chain [Source:HGNC Symbol;Acc:HGNC:2214]
Coordinates
chr3:48592775-48593263:-
Coord C1 exon
chr3:48593102-48593263
Coord A exon
chr3:48592939-48593101
Coord C2 exon
chr3:48592775-48592938
Length
163 bp
Sequences
Splice sites
5' ss Seq
CTCGTGAGT
5' ss Score
8.41
3' ss Seq
CCCTGATCCCGCATTCCCAGCGG
3' ss Score
4.63
Exon sequences
Seq C1 exon
GGATCAAGAATGCTGACCCTGAGGAGCTGAAGCGAGTTGCCTCACAGCCCACCAGTGACTTCTTCTTCTTCGTCAATGACTTCAGCATCTTGAGGACACTACTGCCCCTCGTTTCCCGGAGAGTGTGCACGACTGCTGGTGGCGTGCCTGTGACCCGACCTC
Seq A exon
GTGAGTTCCTGCCCACACGGTGTACCCTGACCTAGACCCCGGACCCCAATCCCCACTTGGCAGTGCTGATTCCATCCTATGTGCTCCTGACCCCGACCCCAACTCTGCATCATACATGCCCACCCCAATCCTCCTGCCTGATCCCCTGATCCCGCATTCCCAG
Seq C2 exon
CGGATGACTCGACCTCTGCTCCACGAGACCTGGTGCTGTCTGAGCCAAGCAGCCAATCCTTGAGAGTACAGTGGACAGCGGCCAGTGGCCCTGTGACTGGCTACAAGGTCCAGTACACTCCTCTGACGGGGCTGGGACAGCCACTGCCGAGTGAGCGGCAGGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000114270:ENST00000328333:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.218 A=NA C2=0.455
Domain overlap (PFAM):
C1:
PF0009223=VWA=PD(20.8=65.5)
A:
NA
C2:
PF0004116=fn3=PU(57.0=89.1)
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:
AGCCCACCAGTGACTTCTTCT
R:
CCGTCAGAGGAGTGTACTGGA
Band lengths:
246-409
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