RnoINT0039266 @ rn6
Intron Retention
Gene
ENSRNOG00000003897 | Col1a1
Description
collagen type I alpha 1 chain [Source:RGD Symbol;Acc:61817]
Coordinates
chr10:82752089-82752327:+
Coord C1 exon
chr10:82752089-82752133
Coord A exon
chr10:82752134-82752228
Coord C2 exon
chr10:82752229-82752327
Length
95 bp
Sequences
Splice sites
5' ss Seq
AATGTAAGT
5' ss Score
8.62
3' ss Seq
GTCTGTCCTGACTCCTGCAGGGT
3' ss Score
9.34
Exon sequences
Seq C1 exon
GGAAACCCTGGTGCTGATGGACAACCTGGTGCTAAAGGTGCCAAT
Seq A exon
GTAAGTCACTAGTGGCCCTCCTCCTCCCCTGCCCACCTGCCACCTGCCCCATGCCCTTCACCCTTGGGCTAAAATGTCTGTCCTGACTCCTGCAG
Seq C2 exon
GGTGCTCCTGGTATTGCTGGTGCTCCTGGCTTCCCTGGTGCCCGAGGCCCCTCTGGACCTCAGGGCCCCAGCGGCGCTCCTGGTCCCAAAGGCAACAGT
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000003897:ENSRNOT00000005311:18
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(20.0=100)
A:
NA
C2:
PF0139113=Collagen=PD(20.0=42.4)
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:
GAAACCCTGGTGCTGATGGAC
R:
ACTGTTGCCTTTGGGACCAG
Band lengths:
143-238
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]