DreINT0023582 @ danRer10
Intron Retention
Gene
ENSDARG00000079009 | abca1b
Description
ATP-binding cassette, sub-family A (ABC1), member 1B [Source:ZFIN;Acc:ZDB-GENE-030131-9826]
Coordinates
chr14:6195608-6195872:+
Coord C1 exon
chr14:6195608-6195728
Coord A exon
chr14:6195729-6195809
Coord C2 exon
chr14:6195810-6195872
Length
81 bp
Sequences
Splice sites
5' ss Seq
AAGGTCAGC
5' ss Score
7.09
3' ss Seq
GTTGTCTACTATATTTACAGGTG
3' ss Score
8.01
Exon sequences
Seq C1 exon
GTCTTTATGTCCTAAATTGAGTCCGATTGGAGAGGAAGATGAAGATGTAGCCAGAGAGAGGCAGAGGATCATGAGTGGGGCCGGACAGGGAGACATTCTCGAACTCCGACAGCTCACTAAG
Seq A exon
GTCAGCTGATGATCACACACAACAACCATAACTACAATTCAGTGATGAGACCTTCAATAATGTTGTCTACTATATTTACAG
Seq C2 exon
GTGTACAAGCGGAAACAAAAGCCTGCAGTGGATCGTCTGTGTGTTGGCATTCCTCCAGGAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000079009:ENSDART00000051556:39
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.049 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0000522=ABC_tran=PU(7.6=52.4)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGTCCTAAATTGAGTCCGATTGGA
R:
CTCCTGGAGGAATGCCAACAC
Band lengths:
175-256
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]