RnoINT0039678 @ rn6
Intron Retention
Gene
ENSRNOG00000003357 | Col3a1
Description
collagen type III alpha 1 chain [Source:RGD Symbol;Acc:71029]
Coordinates
chr9:52048692-52048881:+
Coord C1 exon
chr9:52048692-52048745
Coord A exon
chr9:52048746-52048827
Coord C2 exon
chr9:52048828-52048881
Length
82 bp
Sequences
Splice sites
5' ss Seq
AAGGTAACA
5' ss Score
8.92
3' ss Seq
ATCATTTGGTCTTTTCTCAGGGT
3' ss Score
8.32
Exon sequences
Seq C1 exon
GGTCCTGCTGGTCCTATTGGTCCCCCTGGCCCAGCTGGTCAGCCTGGAGATAAG
Seq A exon
GTAACAACACTATTGGAAACAAAAAATAATTCTTGCTTTAATAGACCTAGAACAGTAGTAATATCATTTGGTCTTTTCTCAG
Seq C2 exon
GGTGAAGGTGGTGCCCCTGGACTTCCAGGTATAGCTGGACCTCGAGGTGGCCCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000003357:ENSRNOT00000004956:33
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:
NO
A:
NA
C2:
NO
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:
TCCTGCTGGTCCTATTGGTCC
R:
CCTCGAGGTCCAGCTATACCTG
Band lengths:
99-181
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]