RnoINT0039629 @ rn6
Intron Retention
Gene
ENSRNOG00000058560 | Col2a1
Description
collagen type II alpha 1 chain [Source:RGD Symbol;Acc:2375]
Coordinates
chr7:139462094-139462502:-
Coord C1 exon
chr7:139462449-139462502
Coord A exon
chr7:139462148-139462448
Coord C2 exon
chr7:139462094-139462147
Length
301 bp
Sequences
Splice sites
5' ss Seq
CCGGTGAGT
5' ss Score
10.9
3' ss Seq
ACCTCCTGGTCCTCTCACAGGGT
3' ss Score
9.51
Exon sequences
Seq C1 exon
GGAGAAGTCGGACCTCCTGGTCCTTCAGGAAGTACTGGAGCTCGAGGCGCCCCG
Seq A exon
GTGAGTGTGTCCCTCTAAATCAGGCTCTCCCTGGCCCCAGGAGTGAGGAGGCCAGATATGTCCTCCAGCCTGGCCCTGTGCCTTGGGGTTAGGGGTGGAAGGAGAGAAGACATGAAAGGCAGAGGTCACAGGCCCAGGCATGGCCAGTGCTCTGGCTCCCTGGGACTCAGCTCACTCAGATGCCTCTTCTCTGGGGGTGGGGTGGGGAGTTGAACTTAGAGCTGGCCTGGGCAGTGAGTTCTCACTCTGAGGAGAGCACAGAGCAGGCGACGGGACATGACACCTCCTGGTCCTCTCACAG
Seq C2 exon
GGTGAGCGCGGAGAGACTGGGCCACCTGGACCTGCTGGATTCGCTGGCCCTCCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000058560:ENSRNOT00000086062:36
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(8.9=38.9),PF0139113=Collagen=FE(18.3=100)
A:
NA
C2:
PF0139113=Collagen=FE(18.3=100),PF0139113=Collagen=PU(2.5=11.1)
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:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]