HsaINT0039653 @ hg19
Intron Retention
Gene
ENSG00000114270 | COL7A1
Description
collagen, type VII, alpha 1 [Source:HGNC Symbol;Acc:2214]
Coordinates
chr3:48623765-48624122:-
Coord C1 exon
chr3:48623996-48624122
Coord A exon
chr3:48623912-48623995
Coord C2 exon
chr3:48623765-48623911
Length
84 bp
Sequences
Splice sites
5' ss Seq
TGGGTGAGG
5' ss Score
6.74
3' ss Seq
TGACATGTCCTTCCTTCCAGGCA
3' ss Score
10.72
Exon sequences
Seq C1 exon
GTTGGCCTGCTGTCTTACAGTCATCGGCCCTCCCCACTGTTCCCACTGAATGGCTCCCATGACCTTGGCATTATCTTGCAAAGGATCCGTGACATGCCCTACATGGACCCAAGTGGGAACAACCTGG
Seq A exon
GTGAGGACTGCAGCAGGCATGGACTCCTGGGGCTATCCACTGGGAGCTTGGTGCCCCAGGGTTCTGACATGTCCTTCCTTCCAG
Seq C2 exon
GCACAGCCGTGGTCACAGCTCACAGATACATGTTGGCACCAGATGCTCCTGGGCGCCGCCAGCACGTACCAGGGGTGATGGTTCTGCTAGTGGATGAACCCTTGAGAGGTGACATATTCAGCCCCATCCGTGAGGCCCAGGCTTCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000114270-COL7A1:NM_000094:25
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.047 A=NA C2=0.080
Domain overlap (PFAM):
C1:
PF0009223=VWA=FE(23.9=100)
A:
NA
C2:
PF0009223=VWA=FE(27.8=100)
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:
CACTGAATGGCTCCCATGACC
R:
ACTAGCAGAACCATCACCCCT
Band lengths:
175-259
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)