DreINT0023505 @ danRer10
Intron Retention
Gene
ENSDARG00000074635 | abca1a
Description
ATP-binding cassette, sub-family A (ABC1), member 1A [Source:ZFIN;Acc:ZDB-GENE-031006-12]
Coordinates
chr1:51963695-51964474:+
Coord C1 exon
chr1:51963695-51963900
Coord A exon
chr1:51963901-51964297
Coord C2 exon
chr1:51964298-51964474
Length
397 bp
Sequences
Splice sites
5' ss Seq
CGGGTATGA
5' ss Score
7.63
3' ss Seq
TAACGTGTTTTCTGCTGTAGATA
3' ss Score
9.49
Exon sequences
Seq C1 exon
TGTGTGAACTTGGATAAGTTGGAGCCGGTGGCGAACGAGGAGCGTCTGGTCAATAAATCCATGCGTCTGCTGGATGACCGCAAGTTTTGGGCAGGAATCGTGTTTCCCGACATGCAATCCAACACGTCTGATCTGCCACTCAACGTTAACTATAAGATCCGCATGGACATCGATAACGTGGAGCGAACCAATAAGATCAAGGACGG
Seq A exon
GTATGAACCAATAAGTCATCCTTACAGCTTCCTGATAATGCTGTCATTAGCAGCTGCTACTGGCAGGCTTAATATTTATCATGTTTTCATGTCCGTCTGCATGCTTACATCATATTTGCAACATTTCAGACACTAATAGATCAGTGTATGATGCAGAAATATAGTGATTTGTGATGCTAATGGCTACTTATGCTAATGACTTTCATAAAAACTACACAATATTCTTCAGAGTTTTTTTAAATGATGACAGAATGATAATAATTAAATAATAATTTATAGTAATTTAAATAATAATAAATAATTTTTGGTAGAACTATCCCTTTTAAAAAGCCTTGATGGTGTGTTTATTTATTATATTGCAATTAAACAAGCTCACATAACGTGTTTTCTGCTGTAG
Seq C2 exon
ATATTGGGATCCGGGTCCTCGAGCTGACCCATTTGAGGACTTGCGTTACATCTGGGGCGGCTTCACATACCTGCAGGACGTGATTGAGCACGGGATCATCAGAGCTCTGACCGGCAGCAAGGAAAAAACCGGAGTCTACATCCAGCAGATGCCGTATCCCTGCTATGTGGATGACAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000074635:ENSDART00000142465:12
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:
PF126982=ABC2_membrane_3=FE(19.2=100)
A:
NA
C2:
PF126982=ABC2_membrane_3=FE(16.6=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TTGGATAAGTTGGAGCCGGTG
R:
TCTGCTGGATGTAGACTCCGG
Band lengths:
346-743
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]