RnoINT0040404 @ rn6
Intron Retention
Gene
ENSRNOG00000020579 | Col7a1
Description
collagen type VII alpha 1 chain [Source:RGD Symbol;Acc:1311417]
Coordinates
chr8:117718006-117718184:+
Coord C1 exon
chr8:117718006-117718050
Coord A exon
chr8:117718051-117718139
Coord C2 exon
chr8:117718140-117718184
Length
89 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGT
5' ss Score
10.47
3' ss Seq
TAACCGTCCTCTATGTGCAGGGT
3' ss Score
8.44
Exon sequences
Seq C1 exon
GGAGCCAAGGGTGACCGAGGACTGCCTGGACCACGGGGTGAAAAG
Seq A exon
GTGAGTGGGTCTGGGCTTCCAGTATAAGTGTTAGGCAGAGTGGGGATGAGGCCAGGAGGCCAGGGGCTCTAACCGTCCTCTATGTGCAG
Seq C2 exon
GGTGAAGCTGGCCATGCAGGAGAGCCTGGCGACCCTGGGGAAGAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000020579:ENSRNOT00000027994:90
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(25.5=100)
A:
NA
C2:
PF0139113=Collagen=FE(25.5=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGGTGACCGAGGACTGCC
R:
ATCTTCCCCAGGGTCGCC
Band lengths:
82-171
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]