HsaINT0039658 @ hg38
Intron Retention
Gene
ENSG00000114270 | COL7A1
Description
collagen type VII alpha 1 chain [Source:HGNC Symbol;Acc:HGNC:2214]
Coordinates
chr3:48593356-48593696:-
Coord C1 exon
chr3:48593537-48593696
Coord A exon
chr3:48593450-48593536
Coord C2 exon
chr3:48593356-48593449
Length
87 bp
Sequences
Splice sites
5' ss Seq
AAGGTGATC
5' ss Score
4.41
3' ss Seq
GACCCCTGCACCTGTCCCAGGTC
3' ss Score
6.1
Exon sequences
Seq C1 exon
GACAGAGTTCGGCCTGGATGCACTTGGCTCTGGGGGTGATGTGATCCGCGCCATCCGTGAGCTTAGCTACAAGGGGGGCAACACTCGCACAGGGGCTGCAATTCTCCATGTGGCTGACCATGTCTTCCTGCCCCAGCTGGCCCGACCTGGTGTCCCCAAG
Seq A exon
GTGATCCCTACCCCTACCATGCCTCCCAAGATGACCCCAAATGAAGTGTCCAGGGGAACCGTGATTTGACCCCTGCACCTGTCCCAG
Seq C2 exon
GTCTGCATCCTGATCACAGACGGGAAGTCCCAGGACCTGGTGGACACAGCTGCCCAAAGGCTGAAGGGGCAGGGGGTCAAGCTATTTGCTGTGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000114270:ENST00000328333:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0009223=VWA=FE(30.6=100)
A:
NA
C2:
PF0009223=VWA=FE(17.9=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:
CTGGATGCACTTGGCTCTGG
R:
CCGTCTGTGATCAGGATGCAG
Band lengths:
170-257
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