RnoINT0039277 @ rn6
Intron Retention
Gene
ENSRNOG00000003897 | Col1a1
Description
collagen type I alpha 1 chain [Source:RGD Symbol;Acc:61817]
Coordinates
chr10:82754656-82754871:+
Coord C1 exon
chr10:82754656-82754709
Coord A exon
chr10:82754710-82754817
Coord C2 exon
chr10:82754818-82754871
Length
108 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGG
5' ss Score
11.08
3' ss Seq
CTCCACCTCCCACTTTACAGGGT
3' ss Score
7.98
Exon sequences
Seq C1 exon
GGTCCTGCTGGTGAGAGAGGTGAACAAGGTCCCGCTGGCTCCCCTGGATTCCAG
Seq A exon
GTAAGGCCTCGTGACTTAGGTCTGTAGGGAAGCGTGAAGAGCGGTCCTTTGTTAACAGTTAAAGATTCTAAACTCTTCACCTTCTTCCCTCCACCTCCCACTTTACAG
Seq C2 exon
GGTCTTCCTGGTCCCGCTGGTCCTCCTGGTGAAGCAGGCAAGCCTGGTGAACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000003897:ENSRNOT00000005311:28
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:
GTCCTGCTGGTGAGAGAGGT
R:
CTGTTCACCAGGCTTGCCTG
Band lengths:
107-215
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]