RnoINT0040299 @ rn6
Intron Retention
Gene
ENSRNOG00000020579 | Col7a1
Description
collagen type VII alpha 1 chain [Source:RGD Symbol;Acc:1311417]
Coordinates
chr8:117720456-117720626:+
Coord C1 exon
chr8:117720456-117720491
Coord A exon
chr8:117720492-117720569
Coord C2 exon
chr8:117720570-117720626
Length
78 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGT
5' ss Score
10.47
3' ss Seq
CATTCCTCCCTGCCCCTCAGGGT
3' ss Score
9.65
Exon sequences
Seq C1 exon
GGCGACCCTGGTGCTGCAGGACTCAAGGGTGACAAG
Seq A exon
GTGAGTGTGGTTATCAGGGGGGGCTAGAGCAGGAAACTGGGGTTCTCCTGACACTTCTCATTCCTCCCTGCCCCTCAG
Seq C2 exon
GGTGACTCAGCTGTGATTGAGGGACCTGCAGGGCCACGAGGTGCCAAGGGGGATATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000020579:ENSRNOT00000027994:100
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(18.3=100)
A:
NA
C2:
PF0139113=Collagen=PD(6.7=21.1),PF0139113=Collagen=PU(18.8=63.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCTGGTGCTGCAGGACTCAA
R:
CATATCCCCCTTGGCACCTCG
Band lengths:
87-165
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]