DreINT0050200 @ danRer10
Intron Retention
Gene
ENSDARG00000077139 | col6a3
Description
collagen, type VI, alpha 3 [Source:ZFIN;Acc:ZDB-GENE-070501-8]
Coordinates
chr9:24120280-24120813:-
Coord C1 exon
chr9:24120668-24120813
Coord A exon
chr9:24120373-24120667
Coord C2 exon
chr9:24120280-24120372
Length
295 bp
Sequences
Splice sites
5' ss Seq
CTGGTAAGA
5' ss Score
9.45
3' ss Seq
TTTATTTTTTTTTTTTTTAGGAT
3' ss Score
12.5
Exon sequences
Seq C1 exon
GTGTCAGCAGTTTCATTCTTGTTGGTCTTGAGAGAGTGCCACGATTTGAGGATGCAGTTCTCTTGGAATATGGCCGTGGATTCAGGTATACACGACCACTGCGTGTCAATGTCATGGATTTGGATTATGAGCTTCTGGAAGAACTG
Seq A exon
GTAAGAATGGTCCTGTCAAATAAGAATGCTCAGTCAAATAGGCAAAATAACTAATGACTCAATCCACTGAAGAAAAAGGGTGTTAAAATAGGTTAGCCATAATTTTATTGTTCTTATTGAAACTATACATTTAAGTACTGATAAATAATAATTAACTCCATGTACTTACTTTATGGTAAGGATAAGGGTTAGGTTTAGTTGCGTGCCATCATGCAGTCGTAAAAACTTTAGCTTTTTAACAGTGACATTGTAAATCAAAGTGTTACTTTTAAAGTTTTATTTTTTTTTTTTTTAG
Seq C2 exon
GATAACATTGCAGAACGGGAATGCTGTTCTGTTCCATGCAAGTGTAATGGCCCGAGAGGGGACAGAGGAGCCGTTGGTGTCCCTGGACAAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000077139:ENSDART00000138754:15
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=0.381
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0139113=Collagen=PU(25.8=51.6)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Mouse
(mm9)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTGTCAGCAGTTTCATTCTTGTTGG
R:
GGACACCAACGGCTCCTCT
Band lengths:
228-523
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]