HsaINT0039618 @ hg19
Intron Retention
Gene
ENSG00000114270 | COL7A1
Description
collagen, type VII, alpha 1 [Source:HGNC Symbol;Acc:2214]
Coordinates
chr3:48631801-48632593:-
Coord C1 exon
chr3:48632508-48632593
Coord A exon
chr3:48631982-48632507
Coord C2 exon
chr3:48631801-48631981
Length
526 bp
Sequences
Splice sites
5' ss Seq
GAGGTGGGC
5' ss Score
6.32
3' ss Seq
ATCTCTCCTGCCCGCCCCAGTGA
3' ss Score
6.3
Exon sequences
Seq C1 exon
GATGACGCTGCGGCTTCTGGTGGCCGCGCTCTGCGCCGGGATCCTGGCAGAGGCGCCCCGAGTGCGAGCCCAGCACAGGGAGAGAG
Seq A exon
GTGGGCACCGCAAGGGAGGACCCGGCCCGGGGCACTGCACCGTGCCACCCTCCGCTCCACTCGGCCTTCATCCCCAACACCCCCCGCCCACAACCCAGCCAACTCCACGACGCCCCGCGGATTCCTCCTAATTCTGGGACTCCCCGAACCCTCCGCGATCGGTGCTGGGTTCCCTAAACCGCCTCCTATCCTGTTCCTACCCAAATTCTGGCTCCCTGGATGCGTGCGGGGTCCCCTGCCTTATGCCAATCCACGCCGGCCCCTAGAGGCTGACCTCAGTCCCAAGTCCACACCCGTGCTGGCGACTCTCCCTCCCCCGCACACCCCCAACCCTCCGCGGGAGTCTGCTCTGGGACCCACCGAGCTCAACTCCCTCCAAGGCCCTCAGGCTCAGGCCGATTCGGCCCTGGTTTGCATAAGATGAGGCCTACTCTCCCCACCATCCCAAGTCCCAGTGAGGCCACCGTGCGGGTAGGCGGGTGGTTGGCCTCCCAGAAGAGGCCCTGATCTCTCCTGCCCGCCCCAG
Seq C2 exon
TGACCTGCACGCGCCTTTACGCCGCTGACATTGTGTTCTTACTGGATGGCTCCTCATCCATTGGCCGCAGCAATTTCCGCGAGGTCCGCAGCTTTCTCGAAGGGCTGGTGCTGCCTTTCTCTGGAGCAGCCAGTGCACAGGGTGTGCGCTTTGCCACAGTGCAGTACAGCGATGACCCACG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000114270-COL7A1:NM_000094:1
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0009223=VWA=PU(29.5=83.6)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GATGACGCTGCGGCTTCTG
R:
GGTCATCGCTGTACTGCACTG
Band lengths:
263-789
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
Other AS DBs:
FasterDB (Includes CLIP-seq data)
AS-ALPS (AS-induced ALteration of Protein Structure, links to PINs)
APPRIS (Selection of principal isoform)
DEU primates (Only for human)