HsaINT0039624 @ hg38
Intron Retention
Gene
ENSG00000114270 | COL7A1
Description
collagen type VII alpha 1 chain [Source:HGNC Symbol;Acc:HGNC:2214]
Coordinates
chr3:48568090-48568534:-
Coord C1 exon
chr3:48568499-48568534
Coord A exon
chr3:48568171-48568498
Coord C2 exon
chr3:48568090-48568170
Length
328 bp
Sequences
Splice sites
5' ss Seq
CCGGTAAGA
5' ss Score
10.1
3' ss Seq
ATGGACCCTCTCCCTGCTAGGGA
3' ss Score
7.09
Exon sequences
Seq C1 exon
GGTCAACCTGGTGCAGCAGGGATCCCTGGTGACCCG
Seq A exon
GTAAGATGCCCCTGCTCCCACAGGGGCCCCCTGTCCCCAGAGGGCCCCCGTCACCATGGTGGTCCCACCAGTGTGGTAGCTTTTGACCTTATAGTGACCCAGTGCTCTCATGGTGTCCTCATGTCACCCAGGGTCCCCCACCTCCACAGTAGCCGCCTATGATGGTGTCCCCTGCCTATGGTGACCCTTGTCCCCATGGCAAGCCCCAGTGGCTCTGGCCTCCAGAGGTGACTCCCACCCCATGGTGTTCCCTACCCACTATCCAGGGCGATTCTCTTTGGTCCCTCACTGACCTCCTCTGACCTCACATGGACCCTCTCCCTGCTAG
Seq C2 exon
GGATCCCCAGGAAAGGATGGAGTGCCTGGTATCCGAGGAGAAAAAGGAGATGTTGGCTTCATGGGTCCCCGGGGCCTCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000114270:ENST00000328333:104
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(14.3=100)
A:
NA
C2:
PF0139113=Collagen=FE(33.8=100),PF0139113=Collagen=PU(10.3=29.6)
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