RnoINT0039263 @ rn6
Intron Retention
Gene
ENSRNOG00000003897 | Col1a1
Description
collagen type I alpha 1 chain [Source:RGD Symbol;Acc:61817]
Coordinates
chr10:82751434-82751665:+
Coord C1 exon
chr10:82751434-82751478
Coord A exon
chr10:82751479-82751611
Coord C2 exon
chr10:82751612-82751665
Length
133 bp
Sequences
Splice sites
5' ss Seq
CCCGTAAGT
5' ss Score
9.09
3' ss Seq
AACCTCCATTTTATTCACAGGGT
3' ss Score
7.43
Exon sequences
Seq C1 exon
GGTGCTCGTGGTAACGATGGTGCTGTCGGTGCAGCTGGGCCCCCC
Seq A exon
GTAAGTATGGCCTTGACTTTGAGTTTGGGAGTGGGGTGAGACTTCAGGGTCAGCTCTTGGGACTGACATCAGCCATTGAAACTTAAAAGCTCTCAGTCTCCGCCTTGTAGCTAAACCTCCATTTTATTCACAG
Seq C2 exon
GGTCCCACCGGCCCTACTGGCCCTCCTGGCTTCCCTGGTGCAGCTGGTGCTAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000003897:ENSRNOT00000005311:15
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(23.3=100)
A:
NA
C2:
PF0139113=Collagen=FE(28.3=100),PF0139113=Collagen=PU(8.6=33.3)
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:
GTGGTAACGATGGTGCTGTCG
R:
CAGCTGCACCAGGGAAGC
Band lengths:
84-217
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]