RnoINT0040398 @ rn6
Intron Retention
Gene
ENSRNOG00000020579 | Col7a1
Description
collagen type VII alpha 1 chain [Source:RGD Symbol;Acc:1311417]
Coordinates
chr8:117716878-117717073:+
Coord C1 exon
chr8:117716878-117716913
Coord A exon
chr8:117716914-117716992
Coord C2 exon
chr8:117716993-117717073
Length
79 bp
Sequences
Splice sites
5' ss Seq
GTGGTAAGT
5' ss Score
10.36
3' ss Seq
ACTGAGTCTCTTCTTTTCAGGGG
3' ss Score
8.23
Exon sequences
Seq C1 exon
GGCCCACAAGGCTCACCAGGTTTGCCCGGACAAGTG
Seq A exon
GTAAGTCCTGGTGGGCTTGGCCGGACTCCATGGGTTAAGGGTCATTATGCAGATCCTTGACTGAGTCTCTTCTTTTCAG
Seq C2 exon
GGGGAGACAGGGAAGCCAGGACCCCCAGGCCGGGATGGTAGCAGCGGAAAGGACGGAGAAAGAGGAGGCCCTGGCGTGCCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000020579:ENSRNOT00000027994:85
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(15.3=100)
A:
NA
C2:
PF0139113=Collagen=PD(33.3=88.9),PF0139113=Collagen=PU(30.8=74.1)
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:
CCACAAGGCTCACCAGGTTTG
R:
CCAGGGCCTCCTCTTTCTCC
Band lengths:
107-186
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]