RnoINT0039983 @ rn6
Intron Retention
Gene
ENSRNOG00000008749 | Col5a1
Description
collagen type V alpha 1 chain [Source:RGD Symbol;Acc:70920]
Coordinates
chr3:6547781-6548015:+
Coord C1 exon
chr3:6547781-6547870
Coord A exon
chr3:6547871-6547961
Coord C2 exon
chr3:6547962-6548015
Length
91 bp
Sequences
Splice sites
5' ss Seq
GTGGTGAGT
5' ss Score
8.95
3' ss Seq
ATATTCTTACTACTTCTCAGGGA
3' ss Score
6.69
Exon sequences
Seq C1 exon
GGTGACCCAGGTCCTGCTGGCCTCCCTGGGAAGGATGGACCTCCAGGATTGCGTGGATTCCCTGGGGACCGAGGGCTCCCCGGCCCCGTG
Seq A exon
GTGAGTGAGGGGCCGGGTGGGTGTAGTGGTATGGCACACAGCCCTGGGGTTCTGTCTGAGGCCCTCAATCTATATTCTTACTACTTCTCAG
Seq C2 exon
GGAGCACTCGGACTGAAAGGCAGCGAAGGCCCCCCTGGCCCCCCAGGTCCTGCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000008749:ENSRNOT00000012334:40
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(29.5=93.3),PF0139113=Collagen=FE(40.3=100)
A:
NA
C2:
PF0139113=Collagen=FE(23.6=100),PF0139113=Collagen=PU(18.5=94.4)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGTGACCCAGGTCCTGCT
R:
CCTTCGCTGCCTTTCAGTCC
Band lengths:
119-210
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]