HsaINT0039653 @ hg38
Intron Retention
Gene
ENSG00000114270 | COL7A1
Description
collagen type VII alpha 1 chain [Source:HGNC Symbol;Acc:HGNC:2214]
Coordinates
chr3:48586332-48586689:-
Coord C1 exon
chr3:48586563-48586689
Coord A exon
chr3:48586479-48586562
Coord C2 exon
chr3:48586332-48586478
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:ENST00000328333:25
Average complexity
IR
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
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:
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