RnoINT0039612 @ rn6
Intron Retention
Gene
ENSRNOG00000058560 | Col2a1
Description
collagen type II alpha 1 chain [Source:RGD Symbol;Acc:2375]
Coordinates
chr7:139467741-139468060:-
Coord C1 exon
chr7:139467962-139468060
Coord A exon
chr7:139467795-139467961
Coord C2 exon
chr7:139467741-139467794
Length
167 bp
Sequences
Splice sites
5' ss Seq
ACGGTAAGA
5' ss Score
10.65
3' ss Seq
CGTTTCTTTCTCTCATGTAGGGT
3' ss Score
10.81
Exon sequences
Seq C1 exon
GGCGCTCCTGGAATTGCTGGTGCCCCTGGCTTCCCTGGGCCCCGTGGCCCTCCCGGTCCTCAAGGTGCAACTGGTCCTCTGGGCCCCAAAGGTCAGACG
Seq A exon
GTAAGAGCCCGAAATGATTGACAGGGCCTACCAATGTGCCCCTCTTTTCTGTGCCCTCCCAATCACTGGAGGAGGTTTTGGGGTGGGGTGTGTGTGTGTTGGGGGGGGTGTGTGAGCAGACTCTTTGGAGAGAAGCCAGTGTGAGCACGTTTCTTTCTCTCATGTAG
Seq C2 exon
GGTGAGCCCGGCATCGCTGGCTTCAAAGGTGAACAAGGCCCCAAGGGAGAGACT
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000058560:ENSRNOT00000086062:20
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(15.6=42.4),PF0139113=Collagen=FE(37.2=100),PF0139113=Collagen=PU(40.3=87.9)
A:
NA
C2:
PF0139113=Collagen=PD(18.6=88.9),PF0139113=Collagen=FE(23.6=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:
CTCCTGGAATTGCTGGTGCC
R:
CTCTCCCTTGGGGCCTTGTTC
Band lengths:
146-313
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]