DreINT0049894 @ danRer10
Intron Retention
Gene
ENSDARG00000052061 | col4a6
Description
collagen, type IV, alpha 6 [Source:ZFIN;Acc:ZDB-GENE-101001-2]
Coordinates
chr7:50651674-50652038:-
Coord C1 exon
chr7:50651889-50652038
Coord A exon
chr7:50651791-50651888
Coord C2 exon
chr7:50651674-50651790
Length
98 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGA
5' ss Score
9.22
3' ss Seq
TTGCTTTGAAATTATTGTAGGCC
3' ss Score
6.77
Exon sequences
Seq C1 exon
GTACTTCTGGTCCTGTTGGAAATCCAGGTTTTGTGTTCGCAAGTAACATAACAGCCAGAATGCCATCTGGGGATCCAGGCCAACCAGGGCTTGATGGATTTGCTGGTCAGCCAGGAATACCAGGTCTGCCAGGCAGTCCAGGCAACCCAG
Seq A exon
GTGAGAACTATTGAAGAAAAATAGAAAGTAATATGATATGAAAGTCTGATCAATTAACCATTCCAACTCCACTTTTGATTGCTTTGAAATTATTGTAG
Seq C2 exon
GCCCCAAAGGATTCAGAGGCCAAGTGGGTAGACTTGGTCCAGTTGGATTAGCTGGATCTCCTGGATTTACTGGTGATCCTGGTCCTTCTGGAATCCAAGGACCCACAGGACTCCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000052061:ENSDART00000121574:43
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(17.9=23.5),PF0139113=Collagen=PU(51.7=60.8),PF0139113=Collagen=PU(0.1=0.0)
A:
NA
C2:
PF0139113=Collagen=PD(46.7=70.0),PF0139113=Collagen=PU(68.4=97.5)
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:
AGGGCTTGATGGATTTGCTGG
R:
GAGTCCTGTGGGTCCTTGGAT
Band lengths:
178-276
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]