RnoINT0040042 @ rn6
Intron Retention
Gene
ENSRNOG00000003736 | Col5a2
Description
collagen type V alpha 2 chain [Source:RGD Symbol;Acc:70921]
Coordinates
chr9:52108995-52109265:-
Coord C1 exon
chr9:52109212-52109265
Coord A exon
chr9:52109049-52109211
Coord C2 exon
chr9:52108995-52109048
Length
163 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGT
5' ss Score
11
3' ss Seq
ATGTAAAATCTACTTTATAGGGT
3' ss Score
5.67
Exon sequences
Seq C1 exon
GGTCTTCCTGGTTCCTTGGGACCTCCAGGTCCTGCAGGCCCTACTGGAGAAAAG
Seq A exon
GTAAGTTGGAAGATGTTAGACCCAAATTGTTACTGTTTCTCAAGACTCTGTTTGAGGTAGACTATCTCAGAGTTTTCCCTACACTATCTACTTTCACATGTGCCTAGTAGTCTCCAATTGTATTGTAGATCAGATACTTAGCTATGTAAAATCTACTTTATAG
Seq C2 exon
GGTGAACCTGGTCCTAGAGGATTAGTTGGCCCTCCTGGCTCCCGTGGCAATCCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000003736:ENSRNOT00000005073:37
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(24.3=100),PF0139113=Collagen=PU(3.1=11.1)
A:
NA
C2:
PF0139113=Collagen=PD(8.6=33.3),PF0139113=Collagen=FE(26.6=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:
GGTCTTCCTGGTTCCTTGGGA
R:
GATTGCCACGGGAGCCAG
Band lengths:
106-269
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]