HsaINT0039682 @ hg38
Intron Retention
Gene
ENSG00000114270 | COL7A1
Description
collagen type VII alpha 1 chain [Source:HGNC Symbol;Acc:HGNC:2214]
Coordinates
chr3:48581122-48581340:-
Coord C1 exon
chr3:48581260-48581340
Coord A exon
chr3:48581158-48581259
Coord C2 exon
chr3:48581122-48581157
Length
102 bp
Sequences
Splice sites
5' ss Seq
GATGTAAGA
5' ss Score
5.46
3' ss Seq
CTGACTCTCATGTTTCACAGGGT
3' ss Score
9.2
Exon sequences
Seq C1 exon
GGTGACTCAGGGCCTCCTGGAGAGAAGGGAGACCCTGGGCGGCCTGGCCCCCCAGGACCTGTTGGCCCCCGAGGACGAGAT
Seq A exon
GTAAGAGGCTGGAGTCGGGGGAGTCATGGCGGGTAAGGGAGTAGGGCTGTTGCCAGCATCATGGGGGTTCTTGGAACCAGGGCTGACTCTCATGTTTCACAG
Seq C2 exon
GGTGAAGTTGGAGAGAAAGGTGACGAGGGTCCTCCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000114270:ENST00000328333:51
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(7.5=18.5),PF0139113=Collagen=FE(47.3=100),PF0139113=Collagen=FE(29.5=100)
A:
NA
C2:
PF0139113=Collagen=PD(1.8=8.3),PF0139113=Collagen=FE(12.5=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:
GGTGACTCAGGGCCTCCT
R:
AGGACCCTCGTCACCTTTCTC
Band lengths:
114-216
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