RnoINT0039660 @ rn6
Intron Retention
Gene
ENSRNOG00000003357 | Col3a1
Description
collagen type III alpha 1 chain [Source:RGD Symbol;Acc:71029]
Coordinates
chr9:52042222-52042477:+
Coord C1 exon
chr9:52042222-52042266
Coord A exon
chr9:52042267-52042378
Coord C2 exon
chr9:52042379-52042477
Length
112 bp
Sequences
Splice sites
5' ss Seq
ATGGTAAGC
5' ss Score
9.26
3' ss Seq
AGTGCTTGTGTTGCTTTTAGGGT
3' ss Score
9.42
Exon sequences
Seq C1 exon
GGCCCTCCTGGCAATAATGGCAGTCCTGGTGGGAAAGGTGAAATG
Seq A exon
GTAAGCAGCCCCACCCTCAGCTCATCCACACACAGGAAAACTAATTATTTAAACCAGATAGCAGAGACGAAGGTCTGAGCTTAGCTAATGATAGTGCTTGTGTTGCTTTTAG
Seq C2 exon
GGTCCAGCTGGCATTCCTGGAGCTCCTGGACTCCTAGGAGCTAGGGGTCCCCCTGGACCAGCAGGAGCTAATGGTGCACCGGGACAACGAGGTCCTTCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000003357:ENSRNOT00000004956:17
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=FE(20.3=100)
A:
NA
C2:
PF0139113=Collagen=PD(20.3=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:
CAATAATGGCAGTCCTGGTGGG
R:
GTTGTCCCGGTGCACCATTAG
Band lengths:
122-234
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]