DreINT0049881 @ danRer10
Intron Retention
Gene
ENSDARG00000052061 | col4a6
Description
collagen, type IV, alpha 6 [Source:ZFIN;Acc:ZDB-GENE-101001-2]
Coordinates
chr7:50660802-50661256:-
Coord C1 exon
chr7:50661113-50661256
Coord A exon
chr7:50660925-50661112
Coord C2 exon
chr7:50660802-50660924
Length
188 bp
Sequences
Splice sites
5' ss Seq
GAGGTATTG
5' ss Score
7.44
3' ss Seq
AGTATGTGTGAATCTTAAAGGGG
3' ss Score
1.73
Exon sequences
Seq C1 exon
GGGAGAAAGGATCTCTTGGGTTGTTGGGGTTCCAAGGATTACCTGGTTCTCCTGGAATTCCAGGAGGTCCAGGTATTAAAGGTTTGCCTGGTTTCCGTGGACAGGATGGCTTAATTGGCAGAGATGGGCCAAGAGGACCCAGAG
Seq A exon
GTATTGTGATGACATTTGAAAGACACCTGGCTATCAATGATTTGTCATTTGTAATGATCTAAGTTTTCAGTATTTCGAGAAGAAACCAGATGGCACATATGTTTTGTAAATTTAATTCAGAGTTCACTGCAGAAATAGAATTCAGAATTCATGTACTGTTTTAATTAAAGTATGTGTGAATCTTAAAG
Seq C2 exon
GGGATCGTGGTGAACCTGGTCCTCCAGGACCATCAACTCCACCAATTCCAGTGGAACGGCTTGTAAAGGGTGAACCAGGTGAACCAGGAATTGTTGGAGGGCCTGGTTTCACAGGACAAAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000052061:ENSDART00000121574:31
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=PD(30.9=51.0),PF0139113=Collagen=PU(72.6=91.8)
A:
NA
C2:
PF0139113=Collagen=PD(25.8=38.1),PF0139113=Collagen=PU(33.3=47.6)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTCTTGGGTTGTTGGGGTTCC
R:
TTTGTCCTGTGAAACCAGGCC
Band lengths:
252-440
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]