HsaINT0039655 @ hg38
Intron Retention
Gene
ENSG00000114270 | COL7A1
Description
collagen type VII alpha 1 chain [Source:HGNC Symbol;Acc:HGNC:2214]
Coordinates
chr3:48585940-48586246:-
Coord C1 exon
chr3:48586074-48586246
Coord A exon
chr3:48585976-48586073
Coord C2 exon
chr3:48585940-48585975
Length
98 bp
Sequences
Splice sites
5' ss Seq
CAGGTTTGG
5' ss Score
5.63
3' ss Seq
AAGAGACCCTATGTCCGCAGCCC
3' ss Score
4.05
Exon sequences
Seq C1 exon
GGCTTAATGTGGTGATGTTGGGAATGGCTGGAGCGGACCCAGAGCAGCTGCGTCGCTTGGCGCCGGGTATGGACTCTGTCCAGACCTTCTTCGCCGTGGATGATGGGCCAAGCCTGGACCAGGCAGTCAGTGGTCTGGCCACAGCCCTGTGTCAGGCATCCTTCACTACTCAG
Seq A exon
GTTTGGAAGAGGCCTCTGGGGGACTGGGTGGTAGAATATAAGGGGTCTGGGGGTTCTTGGTAGAAATGTTCAACCTCAAAGAGACCCTATGTCCGCAG
Seq C2 exon
CCCCGGCCAGAGCCCTGCCCAGTGTATTGTCCAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000114270:ENST00000328333:27
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.655 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0009223=VWA=PD(25.6=77.6)
A:
NA
C2:
PF0139113=Collagen=PU(3.3=16.7)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GAATGGCTGGAGCGGACC
R:
GACAATACACTGGGCAGGGC
Band lengths:
183-281
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