RnoINT0040121 @ rn6
Intron Retention
Gene
ENSRNOG00000020525 | Col5a3
Description
collagen type V alpha 3 chain [Source:RGD Symbol;Acc:70922]
Coordinates
chr8:21790244-21790418:-
Coord C1 exon
chr8:21790365-21790418
Coord A exon
chr8:21790280-21790364
Coord C2 exon
chr8:21790244-21790279
Length
85 bp
Sequences
Splice sites
5' ss Seq
GTGGTGAGT
5' ss Score
8.95
3' ss Seq
TTCCCTACCTCTTCCCACAGGGC
3' ss Score
11.8
Exon sequences
Seq C1 exon
GGTCTTCCTGGTCCTGTTGGCTCCTTAGGTCACCCTGGGCCCCCAGGTGTGGTG
Seq A exon
GTGAGTGTGGGAATATTGGAGGGATGGGGAGGTCACCATGACGGGTGGGGTTGAAGACCCTAACCTTCCCTACCTCTTCCCACAG
Seq C2 exon
GGCCCTCTGGGACAGAAGGGTTCCAAGGGGTCCCCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000020525:ENSRNOT00000027897:60
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(19.3=88.9),PF0139113=Collagen=FE(27.0=100)
A:
NA
C2:
PF0139113=Collagen=FE(17.5=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:
GGTCTTCCTGGTCCTGTTGGC
R:
GGACCCCTTGGAACCCTTCT
Band lengths:
87-172
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]