HsaINT0039665 @ hg38
Intron Retention
Gene
ENSG00000114270 | COL7A1
Description
collagen type VII alpha 1 chain [Source:HGNC Symbol;Acc:HGNC:2214]
Coordinates
chr3:48584035-48584375:-
Coord C1 exon
chr3:48584298-48584375
Coord A exon
chr3:48584062-48584297
Coord C2 exon
chr3:48584035-48584061
Length
236 bp
Sequences
Splice sites
5' ss Seq
AAGGTGACA
5' ss Score
5.19
3' ss Seq
GGTCGTCATCTGTTTTCTAGGGT
3' ss Score
8.46
Exon sequences
Seq C1 exon
GGCCCCCCTGGACCTCGTGGACCACTGGGGGACCCAGGACCCCGTGGCCCCCCAGGGCTTCCTGGAACAGCCATGAAG
Seq A exon
GTGACAGCCTCATGAGTGCCATGTGATGCAGAGACCTGGTGACCCCATTTGAACCCACATAACCCCTGCCAGTTACTCTGGCCCTTGTGACCCTTTGATTACCCCCATCCTCACCATGACGCCTCAGTTCTCCCAAAATCCTTGAAATCCAATTGGACCCCATGACCCTCATCACTCCTGGTATCTTTGGGAGTGAGGTGTGGCCCAGGGTCATGGGGTCGTCATCTGTTTTCTAG
Seq C2 exon
GGTGACAAAGGCGATCGTGGGGAGCGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000114270:ENST00000328333:36
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(42.4=100),PF0139113=Collagen=PU(3.6=7.7)
A:
NA
C2:
PF0139113=Collagen=FE(13.6=100),PF0139113=Collagen=FE(14.3=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:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Genotype-Tissue Expression Project (GTEx)
- Autistic and control brains
- Pre-implantation embryo development