HsaINT0039627 @ hg38
Intron Retention
Gene
ENSG00000114270 | COL7A1
Description
collagen type VII alpha 1 chain [Source:HGNC Symbol;Acc:HGNC:2214]
Coordinates
chr3:48567574-48567763:-
Coord C1 exon
chr3:48567710-48567763
Coord A exon
chr3:48567637-48567709
Coord C2 exon
chr3:48567574-48567636
Length
73 bp
Sequences
Splice sites
5' ss Seq
ATGGTGAGT
5' ss Score
10.13
3' ss Seq
TCATGTCTTTTTTTCTCCAGGGG
3' ss Score
10.28
Exon sequences
Seq C1 exon
GGAGAAGCTGGTCCCCCAGGCCGCCCCGGGCTGGCAGGACACAAAGGAGAGATG
Seq A exon
GTGAGTGTGGGCACGCTCAGAATGAGGGGGCCACGGGTGGACGGGGGCCAAGTTCATGTCTTTTTTTCTCCAG
Seq C2 exon
GGGGAGCCTGGTGTGCCGGGCCAGTCGGGGGCCCCTGGCAAGGAGGGCCTGATCGGTCCCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000114270:ENST00000328333:107
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(21.8=100)
A:
NA
C2:
PF0139113=Collagen=FE(25.6=100),PF0139113=Collagen=PU(16.7=66.7)
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:
GGAGAAGCTGGTCCCCCA
R:
GACCGATCAGGCCCTCCTT
Band lengths:
112-185
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