DreINT0023563 @ danRer10
Intron Retention
Gene
ENSDARG00000079009 | abca1b
Description
ATP-binding cassette, sub-family A (ABC1), member 1B [Source:ZFIN;Acc:ZDB-GENE-030131-9826]
Coordinates
chr14:6181712-6182161:+
Coord C1 exon
chr14:6181712-6181849
Coord A exon
chr14:6181850-6181940
Coord C2 exon
chr14:6181941-6182161
Length
91 bp
Sequences
Splice sites
5' ss Seq
CAGGTAACC
5' ss Score
8.66
3' ss Seq
TGCTTTTTTTCTTTCTTCAGGTC
3' ss Score
12.61
Exon sequences
Seq C1 exon
GTGGTATGCAGAGGAAGCTCTCAGTAGCTCTTGCTTTCGTTGGAGGGTCAAAGGTTGTCATTCTGGACGAGCCTACTGCTGGTGTGGATCCATATGCTCGTAGAGGCATTTGGGACCTTTTATTGAAGTACCGTGCAG
Seq A exon
GTAACCCAATGCATTTACACATTTGTTGTTCATTTTGTATTTATAATTGAAGAAACTTACAAGCAGATTTCTGCTTTTTTTCTTTCTTCAG
Seq C2 exon
GTCGTACAATACTTCTTTCTACCCATCATATGGATGAAGCAGACATTCTGGGTGATCGAATTGCTATCATCTCCCATGGAAAGCTTTGCTGTGTGGGCTCCTCGCTGTTTCTTAAGACTCAACTGGGCACCGGATACTATCTTACATTAGTGAAGAAGAACACTGAGCCTTCTCTCAGTTCTTGCAGGAACTCAAGTAGCACTGTGTCATTTGTTAAGAAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000079009:ENSDART00000051556:21
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=0.027
Domain overlap (PFAM):
C1:
PF0000522=ABC_tran=PD(17.9=55.3)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TCGTAGAGGCATTTGGGACCT
R:
TAGTATCCGGTGCCCAGTTGA
Band lengths:
180-271
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]