HsaINT0000389 @ hg19
Intron Retention
Gene
ENSG00000165029 | ABCA1
Description
ATP-binding cassette, sub-family A (ABC1), member 1 [Source:HGNC Symbol;Acc:29]
Coordinates
chr9:107564335-107565597:-
Coord C1 exon
chr9:107565565-107565597
Coord A exon
chr9:107564441-107565564
Coord C2 exon
chr9:107564335-107564440
Length
1124 bp
Sequences
Splice sites
5' ss Seq
TAGGTAAGT
5' ss Score
9.66
3' ss Seq
ATGTCAGGCTGTTCTTTTAGGTA
3' ss Score
7.41
Exon sequences
Seq C1 exon
CTTAAAGAACAAGATCTGGGTGAATGAGTTTAG
Seq A exon
GTAAGTTGCTGTCTTTCTGGCACGTTTAGCTCAGGGGGAGGATGGTGTTGTAGGTGTCTTGGATTGAAGAAAGCCTTGGGGATTGTTTGTCACTCACACACTTGTGGGTGCCATCTCACTGTGAGGAGGACAGAAGCCCTGTGAACATGTGGAGCACACAGGGGCACAGACAGATTTAGATTAGGCCTGCTTTATAGAGTTTCTGCCTAGAGCATCATGGCTCAGTGCCCAGCAGCCCCTCCAGAGGCCTCTGAAATATTTGATATACTGATTTCCTTGAGGAGAATCAGAAATCTCCTGCAGGTGTCTAGGGATTTCAAGTAAGTAGTGTTGTGAGGGGAATACCTACTTGTACTTTCCCCCCAAACCAGATTCCCGAGGCTTCTTAAGGACTCAAGGACAATTTCTAGGCATTTAGCACGGGACTAAAAAGGTCTTAGAGGAAATAAGAAGCGCCAAAACCATCTCTTTGCACTGTATTTCAACCCATTTGTCCTTCTGGGTTTTGAAGGAACAGGTGGGACTGGGGACAGAAGAGTTCTTGAAGCCAGTTTGTCCATCATGGAAAATGAGATAGGTGATGTGGCTACGTCAGGGGGCCCGAAGGCTCCTTGTTACTGATTTCCGTCTTTTCTCTCTGCCTTTTCCCCAAGGGCCAGGACCCCTGGATCTCTGGGCAGAGCAGACGCAGGCCCCTATAATAGCCCTCATGCTAGAAAGGAGCCGGAGCCTGTGTATAAGGCCAGCGCAGCCTACTCTGGACAGTGCAGGGTTCCCACTCTCCCAACTCCCCATCTGCTTGCCTCCAGACCCACATTCACACACGAGCCACTGGGTTGGAGGAGCATCTGTGAGATGAAACACCATTCTTTCCTCAATGTCTCAGCTATCTAACTGTGTGTGTAATCAGGCCAGGTCCTCCCTGCTGGGCAGAAACCATGGGAGTTAAGAGATTGCCAACATTTATTAGAGGAAGCTGACGTGTAACTTCTCTGAGGCAAAATTTAGCCCTCCTTTGAACAGGAATTTGACTCAGTGAACCTTGTACACACTCGCACTGAGTCTGCTGCTGATGATACTGTGCACCCCACTGTCTGGGTTTTAATGTCAGGCTGTTCTTTTAG
Seq C2 exon
GTATGGCGGCTTTTCCCTGGGTGTCAGTAATACTCAAGCACTTCCTCCGAGTCAAGAAGTTAATGATGCCATCAAACAAATGAAGAAACACCTAAAGCTGGCCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000165029-ABCA1:NM_005502:33
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.172
Domain overlap (PFAM):
C1:
PF126982=ABC2_membrane_3=FE(1.9=100),PF126932=GspL_C=FE(18.2=100)
A:
NA
C2:
PF126982=ABC2_membrane_3=FE(11.2=100),PF126932=GspL_C=PU(49.1=75.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains
- Pre-implantation embryo development
Other AS DBs:
FasterDB (Includes CLIP-seq data)
AS-ALPS (AS-induced ALteration of Protein Structure, links to PINs)
APPRIS (Selection of principal isoform)
DEU primates (Only for human)