HsaINT0039626 @ hg38
Intron Retention
Gene
ENSG00000114270 | COL7A1
Description
collagen type VII alpha 1 chain [Source:HGNC Symbol;Acc:HGNC:2214]
Coordinates
chr3:48567710-48567891:-
Coord C1 exon
chr3:48567838-48567891
Coord A exon
chr3:48567764-48567837
Coord C2 exon
chr3:48567710-48567763
Length
74 bp
Sequences
Splice sites
5' ss Seq
AAGGTACAG
5' ss Score
8.04
3' ss Seq
CCACTGCCTGATGCCTGCAGGGA
3' ss Score
6.63
Exon sequences
Seq C1 exon
GGTGAACGGGGAGTGAAGGGAGCCTGTGGCCTTGATGGAGAGAAGGGAGACAAG
Seq A exon
GTACAGAGGGGATGGGGGCTGGGGGGCTACGTGGCCTGGGGCCTAAGGCTCACCCCACTGCCTGATGCCTGCAG
Seq C2 exon
GGAGAAGCTGGTCCCCCAGGCCGCCCCGGGCTGGCAGGACACAAAGGAGAGATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000114270:ENST00000328333:106
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=PD(16.9=72.2),PF0139113=Collagen=FE(21.8=100)
A:
NA
C2:
PF0139113=Collagen=FE(21.8=100)
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:
TGAACGGGGAGTGAAGGGAG
R:
TCTCTCCTTTGTGTCCTGCCA
Band lengths:
104-178
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