HsaINT0039643 @ hg38
Intron Retention
Gene
ENSG00000114270 | COL7A1
Description
collagen type VII alpha 1 chain [Source:HGNC Symbol;Acc:HGNC:2214]
Coordinates
chr3:48589327-48589718:-
Coord C1 exon
chr3:48589599-48589718
Coord A exon
chr3:48589471-48589598
Coord C2 exon
chr3:48589327-48589470
Length
128 bp
Sequences
Splice sites
5' ss Seq
ACGGTGGGG
5' ss Score
4.97
3' ss Seq
GCCTCCATCCCTGTTCCCAGGCC
3' ss Score
8.47
Exon sequences
Seq C1 exon
ACCCACTGGGCCCAGTGAGGACGGTCCATGTGACTCAGGCCAGCAGCTCATCTGTCACCATTACCTGGACCAGGGTTCCTGGCGCCACAGGATACAGGGTTTCCTGGCACTCAGCCCACG
Seq A exon
GTGGGGACTGGGGTTTGGGAGGGGGCAGGTCAGGGTGGAATGGGGGCTGGGGGTTTATTGGGGGTCCAGGTGGGGCTCTGGGGCACAGAGTTTGCTAGCCCTGGAGCTGCCTCCATCCCTGTTCCCAG
Seq C2 exon
GCCCAGAGAAATCCCAGTTGGTTTCTGGGGAGGCCACGGTGGCTGAGCTGGATGGACTGGAGCCAGATACTGAGTATACGGTGCATGTGAGGGCCCATGTGGCTGGCGTGGATGGGCCCCCTGCCTCTGTGGTTGTGAGGACTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000114270:ENST00000328333:16
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.341 A=NA C2=0.694
Domain overlap (PFAM):
C1:
PF0004116=fn3=PU(46.8=90.2)
A:
NA
C2:
PF0004116=fn3=PD(51.9=83.7)
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:
GAGGACGGTCCATGTGACTCA
R:
TCCTCACAACCACAGAGGCAG
Band lengths:
245-373
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