RnoINT0040388 @ rn6
Intron Retention
Gene
ENSRNOG00000020579 | Col7a1
Description
collagen type VII alpha 1 chain [Source:RGD Symbol;Acc:1311417]
Coordinates
chr8:117715240-117715427:+
Coord C1 exon
chr8:117715240-117715308
Coord A exon
chr8:117715309-117715382
Coord C2 exon
chr8:117715383-117715427
Length
74 bp
Sequences
Splice sites
5' ss Seq
AAGGTCAGT
5' ss Score
8.68
3' ss Seq
CTGACATCTAATCTAAACAGGGG
3' ss Score
7.22
Exon sequences
Seq C1 exon
GTGGCCATTGAAGAGCTAGGTCCTGGACCCGCTAGAGAACAAGGACCTCCTGGACTCAAGGGTGCTAAG
Seq A exon
GTCAGTGTAGAGTCAACTTGGGATCCAAACCTTACCATGACACTAGGACCTGAACTGACATCTAATCTAAACAG
Seq C2 exon
GGGGAGCCAGGCAGTGATGGTGTCCCAGGACCCAAAGGAGACAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000020579:ENSRNOT00000027994:76
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(1.6=4.3),PF0139113=Collagen=PU(24.2=69.6)
A:
NA
C2:
PF0139113=Collagen=FE(21.2=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:
GGCCATTGAAGAGCTAGGTCC
R:
CTGTCTCCTTTGGGTCCTGGG
Band lengths:
111-185
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]