HsaINT0039654 @ hg19
Intron Retention
Gene
ENSG00000114270 | COL7A1
Description
collagen, type VII, alpha 1 [Source:HGNC Symbol;Acc:2214]
Coordinates
chr3:48623507-48623911:-
Coord C1 exon
chr3:48623765-48623911
Coord A exon
chr3:48623680-48623764
Coord C2 exon
chr3:48623507-48623679
Length
85 bp
Sequences
Splice sites
5' ss Seq
CTGGTAAGG
5' ss Score
9.68
3' ss Seq
GCCACTGGACCCCACCTTAGGGC
3' ss Score
4.4
Exon sequences
Seq C1 exon
GCACAGCCGTGGTCACAGCTCACAGATACATGTTGGCACCAGATGCTCCTGGGCGCCGCCAGCACGTACCAGGGGTGATGGTTCTGCTAGTGGATGAACCCTTGAGAGGTGACATATTCAGCCCCATCCGTGAGGCCCAGGCTTCTG
Seq A exon
GTAAGGAGTAGGCTGATGGGGAAGGGGTCTGGGAATAGGGGTGGCCCTGAAAAGGCTATCATGCAGCCACTGGACCCCACCTTAG
Seq C2 exon
GGCTTAATGTGGTGATGTTGGGAATGGCTGGAGCGGACCCAGAGCAGCTGCGTCGCTTGGCGCCGGGTATGGACTCTGTCCAGACCTTCTTCGCCGTGGATGATGGGCCAAGCCTGGACCAGGCAGTCAGTGGTCTGGCCACAGCCCTGTGTCAGGCATCCTTCACTACTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000114270-COL7A1:NM_000094:26
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.080 A=NA C2=0.655
Domain overlap (PFAM):
C1:
PF0009223=VWA=FE(27.8=100)
A:
NA
C2:
PF0009223=VWA=PD(25.6=77.6)
Main Inclusion Isoform:
NA
Other Inclusion 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:
AGGGGTGATGGTTCTGCTAGT
R:
CATCATCCACGGCGAAGAAGG
Band lengths:
182-267
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
Other AS DBs:
FasterDB (Includes CLIP-seq data)
AS-ALPS (AS-induced ALteration of Protein Structure, links to PINs)
APPRIS (Selection of principal isoform)
DEU primates (Only for human)