RnoINT0040191 @ rn6
Intron Retention
Gene
ENSRNOG00000031782 | Col6a4
Description
collagen, type VI, alpha 4 [Source:RGD Symbol;Acc:1564060]
Coordinates
chr8:114739957-114740398:-
Coord C1 exon
chr8:114740253-114740398
Coord A exon
chr8:114740050-114740252
Coord C2 exon
chr8:114739957-114740049
Length
203 bp
Sequences
Splice sites
5' ss Seq
CTTGTGAGT
5' ss Score
7.15
3' ss Seq
ACACAGGTTCTGTGTTTCAGGAC
3' ss Score
8.1
Exon sequences
Seq C1 exon
GGCTCTCCGGACTCCTGGTCATCGGCCTGGGAGGCGCACACAAGTTAGAAGAGCTGCAGGAGCTGGAGTTTGGCAAAGGGTTTGCGTACAGGCAGCCTCTGAGCTCCAGCCTGCCATCCCTCCCAAGTGTCTTACTAAAGCAACTT
Seq A exon
GTGAGTCCCCTTCCAAAGCTTTGCTCTTCACTTGGTCCTGATGACGACGACGACGATGATGATGATGACGATGACGACGACGATGACGACGACTTTGAAAACTTGTAGAGGATGGGATGGGGGTCGGGGGAGAATGTTGCCTGTCTAGTGTGTAATGTGACCCAGAAGGAAACACCATATGTGACACAGGTTCTGTGTTTCAG
Seq C2 exon
GACACAATTGTGGAGAAGGCATGCTGTTACGTGTGTGCCAAATGTTATGGAGATGATGGGGTCAGAGGTGACCCTGGGAGTCTCGGGAAGGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000031782:ENSRNOT00000047563:10
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.290
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0139113=Collagen=PU(18.8=51.6)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Mouse
(mm9)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTCTCCGGACTCCTGGTCATC
R:
CTCCTTCCCGAGACTCCCAG
Band lengths:
237-440
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]