HsaINT0039673 @ hg38
Intron Retention
Gene
ENSG00000114270 | COL7A1
Description
collagen type VII alpha 1 chain [Source:HGNC Symbol;Acc:HGNC:2214]
Coordinates
chr3:48582609-48583048:-
Coord C1 exon
chr3:48583013-48583048
Coord A exon
chr3:48582654-48583012
Coord C2 exon
chr3:48582609-48582653
Length
359 bp
Sequences
Splice sites
5' ss Seq
CGGGTAAAC
5' ss Score
4.58
3' ss Seq
CTTCCCTTCCTCTCCTCCAGGGG
3' ss Score
12.92
Exon sequences
Seq C1 exon
GGCGAACGTGGACCCCCAGGCCCAGCGGGATCCCGG
Seq A exon
GTAAACCCACTGGCTGCAATGCTCATACCAGCTGACCTGGCTGTGCCCTTTCTGGTTCTGACTTCTTGCCCTTGACCCCTGCTACCCCTGCTCCTCACCCCTCCTCAATGACCACTTATCCCTGCTGATACAGGCTCTAACCCTCAGCCCCAGGGACCTGGCTTTGAACCTCTGACCCTGCTGAACTGACCTTGATTTTCACTGACCTGGTCTCTGTTCTCCTGCCAAGTCTTACCCCTGCCAACCTAAATCCCAATCTTCCCTGACCCCTCTCCAGCCCCCACCCCAGCCTCTAGCCCTGTCTGTCCATATCCCCCGTCCCCACCCACCTGCACAGCTCTTCCCTTCCTCTCCTCCAG
Seq C2 exon
GGGCTGCCAGGGGTTGCTGGACGTCCTGGAGCCAAGGGTCCTGAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000114270:ENST00000328333:43
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(16.1=75.0),PF0139113=Collagen=FE(18.3=100)
A:
NA
C2:
PF0139113=Collagen=FE(23.3=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:
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