DreINT0024347 @ danRer10
Intron Retention
Gene
ENSDARG00000016818 | abcg2d
Description
ATP-binding cassette, sub-family G (WHITE), member 2d [Source:ZFIN;Acc:ZDB-GENE-050517-38]
Coordinates
chr1:49940886-49941334:-
Coord C1 exon
chr1:49941182-49941334
Coord A exon
chr1:49941044-49941181
Coord C2 exon
chr1:49940886-49941043
Length
138 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAAC
5' ss Score
5.54
3' ss Seq
TTTGACTTGTATGTCTGCAGGTG
3' ss Score
9.82
Exon sequences
Seq C1 exon
GATGACATTGTAATGGGCACTCTAACGGTGAGAGAGAACCTGAGTTTCTCAGCTGCTCTGCGTTTGTCTTCTCATGTCAGTCCCAGAGAAAAGGAGGCAAGAGTCAACCATCTCATCTCCGAGCTGGGCCTCAACAAAGTCGCAGATTCCAAG
Seq A exon
GTGAACATTTTATTTCATAGATCTCAAACTGGATTTCTGGATAAATAACGCAATAGCCAATAGATGGCAGCAAGCCCCTGATGAGTCATTCAGGGAAATGATTCGTTCATTCAGTGTCTTTGACTTGTATGTCTGCAG
Seq C2 exon
GTGGGCACTCAAATAATCAGGGGGATCTCGGGTGGAGAGAGGAAGAGGACCAGCATCGGGATGGAGCTGATCATTGACCCCTCTGTGCTCTTTTTGGATGAACCCACCACCGGTTTGGACGCTAGTACAGCTCATTCTGTGCTGCTGCTGCTCAAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000016818:ENSDART00000022733:4
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=0.000
Domain overlap (PFAM):
C1:
PF0000522=ABC_tran=FE(34.2=100),PF030589=Sar8_2=PU(56.7=74.5)
A:
NA
C2:
PF0000522=ABC_tran=PD(24.7=67.9),PF030589=Sar8_2=PD(40.3=50.9)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ATGGGCACTCTAACGGTGAGA
R:
CGGTGGTGGGTTCATCCAAAA
Band lengths:
253-391
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]