HsaINT0039625 @ hg38
Intron Retention
Gene
ENSG00000114270 | COL7A1
Description
collagen type VII alpha 1 chain [Source:HGNC Symbol;Acc:HGNC:2214]
Coordinates
chr3:48567838-48568170:-
Coord C1 exon
chr3:48568090-48568170
Coord A exon
chr3:48567892-48568089
Coord C2 exon
chr3:48567838-48567891
Length
198 bp
Sequences
Splice sites
5' ss Seq
AAGGTAGGA
5' ss Score
9.45
3' ss Seq
CATCTGCTTTTCTCCCTCAGGGT
3' ss Score
11.68
Exon sequences
Seq C1 exon
GGATCCCCAGGAAAGGATGGAGTGCCTGGTATCCGAGGAGAAAAAGGAGATGTTGGCTTCATGGGTCCCCGGGGCCTCAAG
Seq A exon
GTAGGAAAGAAACAAGATTGGTTTTTTTCTGGTCAGGAAGGCCTAATGTTGAAGGGCGAGGGACCTGGGGTCAGATATTAGGGCACTGGGTCAGAGGTTGGAGTAGCTGAGGCCTGTTTGGAGAGTTAGTTTCAGGGTGAAGGGGGTCACAGAGTGAGGTGTCTGGGAATCACTTCTTCATCTGCTTTTCTCCCTCAG
Seq C2 exon
GGTGAACGGGGAGTGAAGGGAGCCTGTGGCCTTGATGGAGAGAAGGGAGACAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000114270:ENST00000328333:105
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=FE(33.8=100),PF0139113=Collagen=PU(10.3=29.6)
A:
NA
C2:
PF0139113=Collagen=PD(16.9=72.2),PF0139113=Collagen=FE(21.8=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:
GGATCCCCAGGAAAGGATGGA
R:
CTCCCTTCTCTCCATCAAGGC
Band lengths:
130-328
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