RnoINT0039668 @ rn6
Intron Retention
Gene
ENSRNOG00000003357 | Col3a1
Description
collagen type III alpha 1 chain [Source:RGD Symbol;Acc:71029]
Coordinates
chr9:52045034-52045476:+
Coord C1 exon
chr9:52045034-52045132
Coord A exon
chr9:52045133-52045422
Coord C2 exon
chr9:52045423-52045476
Length
290 bp
Sequences
Splice sites
5' ss Seq
GATGTAAGT
5' ss Score
9.11
3' ss Seq
ATCCTTTATCTTTTTTTTAGGGT
3' ss Score
10.86
Exon sequences
Seq C1 exon
GGAAGTCAAGGAGAAAGTGGTCGCCCTGGTCCTCCTGGCCCATCTGGCCCCAGAGGTCAGCCTGGTGTCATGGGTTTCCCTGGTCCTAAAGGAAATGAT
Seq A exon
GTAAGTTCTATAATTATTTTCTTCAGTAAATATTTGACAGAAGGCCTTTGACCACTCTATGAAAGTGCAAAAGCACTCAATGCTTAGTCTCTCCTTTAAACATGAAAGAATATGTGACAATTGACTAGTATGCATGAATAGGCACAAATATGTAGTTGGCAATGGGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGACTTTGTATGTGTAGCAGGATCAAAAATGGGATTTGTACTATGATTAGTGAATTTTTTGAGTATGTAAATCCTTTATCTTTTTTTTAG
Seq C2 exon
GGTGCACCTGGCAAAAACGGAGAACGGGGTGGCCCTGGGGGTCCTGGCCTTCCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000003357:ENSRNOT00000004956:24
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=PU(10.7=24.2)
A:
NA
C2:
PF0139113=Collagen=FE(22.7=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:
AGTCAAGGAGAAAGTGGTCGC
R:
GAAGGCCAGGACCCCCAG
Band lengths:
148-438
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]