HsaINT0039640 @ hg38
Intron Retention
Gene
ENSG00000114270 | COL7A1
Description
collagen type VII alpha 1 chain [Source:HGNC Symbol;Acc:HGNC:2214]
Coordinates
chr3:48590459-48590816:-
Coord C1 exon
chr3:48590673-48590816
Coord A exon
chr3:48590585-48590672
Coord C2 exon
chr3:48590459-48590584
Length
88 bp
Sequences
Splice sites
5' ss Seq
GGGGTGAGT
5' ss Score
7.93
3' ss Seq
CTTCTGTCTGTAACTCCTAGAGC
3' ss Score
7.35
Exon sequences
Seq C1 exon
GGGTTGAGCGGACCCTGGTGCTTCCTGGGAGTCAGACAGCATTCGACTTGGATGACGTTCAGGCTGGGCTTAGCTACACTGTGCGGGTGTCTGCTCGAGTGGGTCCCCGTGAGGGCAGTGCCAGTGTCCTCACTGTCCGCCGGG
Seq A exon
GTGAGTACTGCAGGAGGCTTGTGGAGGACAGCTGCCTGCCTCACTCTGGTCCTGGTTCTGACTTCTGACTTCTGTCTGTAACTCCTAG
Seq C2 exon
AGCCGGAAACTCCACTTGCTGTTCCAGGGCTGCGGGTTGTGGTGTCAGATGCAACGCGAGTGAGGGTGGCCTGGGGACCCGTCCCTGGAGCCAGTGGATTTCGGATTAGCTGGAGCACAGGCAGTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000114270:ENST00000328333:13
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.245 A=NA C2=0.302
Domain overlap (PFAM):
C1:
PF0004116=fn3=PD(51.9=83.7)
A:
NA
C2:
PF0004116=fn3=PU(46.8=86.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal4)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGGGAGTCAGACAGCATTCGA
R:
TTGCATCTGACACCACAACCC
Band lengths:
173-261
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