RnoINT0040396 @ rn6
Intron Retention
Gene
ENSRNOG00000020579 | Col7a1
Description
collagen type VII alpha 1 chain [Source:RGD Symbol;Acc:1311417]
Coordinates
chr8:117716593-117716762:+
Coord C1 exon
chr8:117716593-117716625
Coord A exon
chr8:117716626-117716699
Coord C2 exon
chr8:117716700-117716762
Length
74 bp
Sequences
Splice sites
5' ss Seq
CGGGTGAGT
5' ss Score
9.89
3' ss Seq
TCCCGAACTTCTTCTTCCAGGGT
3' ss Score
8.49
Exon sequences
Seq C1 exon
GGGGAGCCCGGAGAGACAGGACCCCCAGGACGG
Seq A exon
GTGAGTGGTGTAGCGGTTGGAGAGGTTACAAGGACACTTGTGGATATACCACTGTCCCGAACTTCTTCTTCCAG
Seq C2 exon
GGTCTGCCTGGACCTACTGGAGCTGTGGGACTTCCTGGCCCTCCTGGCCCTTCAGGCCTCGTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000020579:ENSRNOT00000027994:83
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(14.5=100),PF0139113=Collagen=FE(13.9=100)
A:
NA
C2:
PF0139113=Collagen=PD(0.1=0.0),PF0139113=Collagen=FE(27.8=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:
GGGAGCCCGGAGAGACAG
R:
CCAGGAGGGCCAGGAAGTC
Band lengths:
79-153
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]