DreINT0049642 @ danRer10
Intron Retention
Gene
ENSDARG00000055009 | col4a1
Description
collagen, type IV, alpha 1 [Source:ZFIN;Acc:ZDB-GENE-081105-114]
Coordinates
chr9:8677175-8677522:-
Coord C1 exon
chr9:8677355-8677522
Coord A exon
chr9:8677265-8677354
Coord C2 exon
chr9:8677175-8677264
Length
90 bp
Sequences
Splice sites
5' ss Seq
GTGGTGAGT
5' ss Score
8.95
3' ss Seq
TATTTGAATTTGTTTTTCAGGTC
3' ss Score
10.18
Exon sequences
Seq C1 exon
GCCAGTCTGGAATAAAGGGTGACAAGGGTTATCAAGGACTACCTGGTTTGGACATGCCTGGCCCTCCAGGAGACAGAGGTAGCCCTGGTGTCCCAGGTCTACCAGGATCAAAGGGTTTGCCTGGGCAACCAGGAGTTCCTGGAAAAGATGGCTTTCCTGGCGAACGTG
Seq A exon
GTGAGTGTTTACTCCTTGCCATCTAATAAAGCCTATTAGATGCTGATTTTTTGTTGCTCAAAAGAATTCATATTTGAATTTGTTTTTCAG
Seq C2 exon
GTCCAAAAGGAGAAATTGGAATCATGGGAATGGCAGGACCACCAGGATTTCAAGGTTTAGTTGGAAATCCTGGAGATCCTGGGCAAAAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000055009:ENSDART00000077296:30
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(28.6=31.6),PF0139113=Collagen=PU(65.6=70.2)
A:
NA
C2:
PF0139113=Collagen=PD(32.8=64.5),PF0139113=Collagen=PU(40.0=77.4)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTGTCCCAGGTCTACCAGGAT
R:
TTGCCCAGGATCTCCAGGATT
Band lengths:
167-257
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]