RnoINT0039273 @ rn6
Intron Retention
Gene
ENSRNOG00000003897 | Col1a1
Description
collagen type I alpha 1 chain [Source:RGD Symbol;Acc:61817]
Coordinates
chr10:82753522-82753764:+
Coord C1 exon
chr10:82753522-82753575
Coord A exon
chr10:82753576-82753665
Coord C2 exon
chr10:82753666-82753764
Length
90 bp
Sequences
Splice sites
5' ss Seq
CCTGTAAGT
5' ss Score
7.52
3' ss Seq
CTTGTGCCTCCCATCCTCAGGGT
3' ss Score
10.87
Exon sequences
Seq C1 exon
GGTCTCACTGGCAGTCCTGGCAGCCCTGGTCCTGATGGCAAAACCGGCCCCCCT
Seq A exon
GTAAGTATGCCTGTTCTCTTACGCCTCACCCCTACCATCTGATGTGCCTACCTTAGTCCTTACCACAACACTTGTGCCTCCCATCCTCAG
Seq C2 exon
GGTCCCGCTGGTCAAGATGGTCGCCCTGGACCCGCAGGTCCTCCTGGAGCCCGTGGACAGGCTGGTGTGATGGGATTCCCTGGACCTAAGGGTACTGCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000003897:ENSRNOT00000005311:24
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(19.5=100)
A:
NA
C2:
PF0139113=Collagen=FE(36.8=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:
GGTCTCACTGGCAGTCCTGG
R:
AGCAGTACCCTTAGGTCCAGG
Band lengths:
153-243
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]