HsaINT0039648 @ hg38
Intron Retention
Gene
ENSG00000114270 | COL7A1
Description
collagen type VII alpha 1 chain [Source:HGNC Symbol;Acc:HGNC:2214]
Coordinates
chr3:48587793-48588404:-
Coord C1 exon
chr3:48588282-48588404
Coord A exon
chr3:48587940-48588281
Coord C2 exon
chr3:48587793-48587939
Length
342 bp
Sequences
Splice sites
5' ss Seq
AGGGTGAGA
5' ss Score
6.65
3' ss Seq
CACCCTCACGCCTGCCCCAGGTG
3' ss Score
8.31
Exon sequences
Seq C1 exon
CGCCTGAGGCTCCGCCAGCCCTGGGGACGCTTCACGTGGTGCAGCGCGGGGAGCACTCGCTGAGGCTGCGCTGGGAGCCGGTGCCCAGAGCGCAGGGCTTCCTTCTGCACTGGCAACCTGAGG
Seq A exon
GTGAGAGGTGTCCCCAGGAGGAAGTTAGGGACCATTGGGGGCAGGGCTGTGGCAGACTCCGCAAGGTAGGCGAGGACAGTGATGGTGGGCGGGGTCTGTCACTGGGGGTCTGCGGGATCCGTGACAGTAGGTAAGATCAATCAATGAAGTGGGTGGGATCAATGAGTTCATGGAGGGTCAGTCTGGCAGGGTCCGTAAAGTGGGCAGGGTCAGTGAGGATGAGGAAGATCAGTCAGGAGGGTGAACCCAGTTAACAGAGCCAGTGAAGTGGGCAGGCCCTTTAATGCCCCCAGGTGTCACTATCCCACATGCTCTTGGCCCCCACCCTCACGCCTGCCCCAG
Seq C2 exon
GTGGCCAGGAACAGTCCCGGGTCCTGGGGCCCGAGCTCAGCAGCTATCACCTGGACGGGCTGGAGCCAGCGACACAGTACCGCGTGAGGCTGAGTGTCCTAGGGCCAGCTGGAGAAGGGCCCTCTGCAGAGGTGACTGCGCGCACTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000114270:ENST00000328333:20
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.310 A=NA C2=0.580
Domain overlap (PFAM):
C1:
PF0004116=fn3=PU(45.6=85.7)
A:
NA
C2:
PF0004116=fn3=PD(53.2=84.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CAGCCCTGGGGACGCTTC
R:
CTCTGCAGAGGGCCCTTCTC
Band lengths:
239-581
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