HsaINT0039623 @ hg38
Intron Retention
Gene
ENSG00000114270 | COL7A1
Description
collagen type VII alpha 1 chain [Source:HGNC Symbol;Acc:HGNC:2214]
Coordinates
chr3:48568499-48568855:-
Coord C1 exon
chr3:48568784-48568855
Coord A exon
chr3:48568535-48568783
Coord C2 exon
chr3:48568499-48568534
Length
249 bp
Sequences
Splice sites
5' ss Seq
CAGGCAAGT
5' ss Score
3.1
3' ss Seq
CCCATCTGTGTTTCTCACAGGGT
3' ss Score
10.68
Exon sequences
Seq C1 exon
GGCAGCAAGGGAGAGCCTGGTGACAAGGGCTCAGCCGGGTTGCCAGGACTGCGTGGACTCCTGGGACCCCAG
Seq A exon
GCAAGTTCTGCCCCAGGCCCAGGCCCAGGCCCAGGTCCAGAGCCAGCATCACACACACACATATCCTGGGGGTCCTCTTAAGTGCTGGGGGTTCTGGCTCCCTTGCTGCCGGCCCCATGTGTGTTCACCCGGGATCTGTGTGTGGCCTGGGCCCTGGCCGCTGAGCATCTGAGTGGCCACACATGCAGCGGATGGGCCAGTGTTGGGGACAGTCCCACTGAAGGGCTCCCCCATCTGTGTTTCTCACAG
Seq C2 exon
GGTCAACCTGGTGCAGCAGGGATCCCTGGTGACCCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000114270:ENST00000328333:103
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(35.6=87.5),PF0139113=Collagen=PU(29.9=95.8)
A:
NA
C2:
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
- Autistic and control brains
- Pre-implantation embryo development