RnoINT0040409 @ rn6
Intron Retention
Gene
ENSRNOG00000020579 | Col7a1
Description
collagen type VII alpha 1 chain [Source:RGD Symbol;Acc:1311417]
Coordinates
chr8:117719582-117719813:+
Coord C1 exon
chr8:117719582-117719653
Coord A exon
chr8:117719654-117719777
Coord C2 exon
chr8:117719778-117719813
Length
124 bp
Sequences
Splice sites
5' ss Seq
GTGGTGAGT
5' ss Score
8.95
3' ss Seq
CACCTCACTCTGACCCACAGGGA
3' ss Score
7.36
Exon sequences
Seq C1 exon
GGTCTGGCAGGCCCTCCAGGGAGAGAAGGTGCCCCAGGTCCCTTGGGACCACCTGGACCACCGGGGTCAGTG
Seq A exon
GTGAGTAGAACTGCCTGTATGCCCCAAGTCTGCCCACAAGAGTTATTGGTGGGGACTAGGCCATGAGGTTGGTTTTGGGGCAGACTTCAAGCCCATAGGTTCCTCACCTCACTCTGACCCACAG
Seq C2 exon
GGAGCACCTGGCGCCTCTGGATTCAAAGGAGACAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000020579:ENSRNOT00000027994:95
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=PD(8.6=20.8),PF0139113=Collagen=FE(38.3=100)
A:
NA
C2:
PF0139113=Collagen=FE(18.3=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:
GTCTGGCAGGCCCTCCAG
R:
TTGTCTCCTTTGAATCCAGAGGC
Band lengths:
106-230
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]