RnoINT0039615 @ rn6
Intron Retention
Gene
ENSRNOG00000058560 | Col2a1
Description
collagen type II alpha 1 chain [Source:RGD Symbol;Acc:2375]
Coordinates
chr7:139466694-139466930:-
Coord C1 exon
chr7:139466877-139466930
Coord A exon
chr7:139466793-139466876
Coord C2 exon
chr7:139466694-139466792
Length
84 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGC
5' ss Score
9.6
3' ss Seq
TTCTGTCTCCTCTGGTGTAGGGT
3' ss Score
9.32
Exon sequences
Seq C1 exon
GGTGCTCCTGGCAACCGTGGTTTCCCAGGTCAAGATGGTCTGGCAGGTCCCAAG
Seq A exon
GTGAGCAGAGGAAGAGGGGCTTGGTCCCTCCCTGTTTCCCTGGTTACAGAGCATTCCACTGACTTTCTGTCTCCTCTGGTGTAG
Seq C2 exon
GGTGCCCCTGGAGAGCGAGGGCCTAGTGGCCTGGCTGGTCCTAAGGGTGCCAATGGTGACCCGGGTCGTCCTGGAGAACCTGGTCTTCCTGGAGCCAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000058560:ENSRNOT00000086062:23
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:
CTCCTGGCAACCGTGGTTTC
R:
TCCAGGAAGACCAGGTTCTCC
Band lengths:
143-227
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]