RnoINT0039265 @ rn6
Intron Retention
Gene
ENSRNOG00000003897 | Col1a1
Description
collagen type I alpha 1 chain [Source:RGD Symbol;Acc:61817]
Coordinates
chr10:82751901-82752133:+
Coord C1 exon
chr10:82751901-82751999
Coord A exon
chr10:82752000-82752088
Coord C2 exon
chr10:82752089-82752133
Length
89 bp
Sequences
Splice sites
5' ss Seq
GCTGTAAGT
5' ss Score
8.56
3' ss Seq
CTCCTTTCTCTCTGTGACAGGGA
3' ss Score
10.06
Exon sequences
Seq C1 exon
GGTGAAGCTGGTCCCCAGGGAGCCCGAGGCTCTGAAGGTCCCCAGGGTGTGCGTGGTGAGCCCGGACCCCCTGGCCCTGCTGGTGCTGCTGGTCCTGCT
Seq A exon
GTAAGTGTCCTCTCTGCTGCTGACCCCAGTGCCACTTGCCAGTTTCACCATTCTAGGCTGTCACTCACCCTCCTTTCTCTCTGTGACAG
Seq C2 exon
GGAAACCCTGGTGCTGATGGACAACCTGGTGCTAAAGGTGCCAAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000003897:ENSRNOT00000005311:17
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(3.3=6.1),PF0139113=Collagen=FE(45.7=100)
A:
NA
C2:
PF0139113=Collagen=FE(20.0=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:
GAGGCTCTGAAGGTCCCCAG
R:
ATTGGCACCTTTAGCACCAGG
Band lengths:
119-208
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]