HsaINT0000403 @ hg19
Intron Retention
Gene
ENSG00000165029 | ABCA1
Description
ATP-binding cassette, sub-family A (ABC1), member 1 [Source:HGNC Symbol;Acc:29]
Coordinates
chr9:107549154-107550335:-
Coord C1 exon
chr9:107550201-107550335
Coord A exon
chr9:107549258-107550200
Coord C2 exon
chr9:107549154-107549257
Length
943 bp
Sequences
Splice sites
5' ss Seq
CTGGTGAGT
5' ss Score
10.1
3' ss Seq
TTATTTTATTCTAATTACAGGAT
3' ss Score
7.86
Exon sequences
Seq C1 exon
GTTGGTGAGTGGGCGATTCGGAAACTGGGCCTCGTGAAGTATGGAGAAAAATATGCTGGTAACTATAGTGGAGGCAACAAACGCAAGCTCTCTACAGCCATGGCTTTGATCGGCGGGCCTCCTGTGGTGTTTCTG
Seq A exon
GTGAGTATAACTGTGGATGGAAAACTGTTGTTCTGGCCTGAGTGGAAAACATGACTGTTCAAAAGTCCTATATGTCCAGGGCTGTTGTATGATTGGCTTGTCTTCCCCCAGGGACAGCAGAGCAACCTTGGAAAAGCAGAGGGAAGCTTCTCCCTTGGCACACACTGGGGTGGCTGTACCATGCCTGCAGATGCTCCCAAATAGAGGCACTCCAAGCACTTTGTTTCTTAGCGTGATTGAGGCTGGATATGTGATTTGATCTTTCTCTGGAACATTCTTTCTAATCATCTTTGTGTTCATTCCCTGAAAATGAAGAGTGTGGACACAGCTTTAAAATCCCCAAGGTAGCAACTAGGTCATAGTTCCTTACACACGGATAGATGAAAAACAGATCAGACTGGGAAGTGGCCCTTGACCTTTTTTCTTCTGTAGATAAGAGCATTGATGTTATTACGGGAAGAAGCCTTTGAGGCTTTTATGTATTCCACCTCGGTCTGGAATTTGTTTCTGTAAGGCTAACAGTTGCAATATACTAGGGTAATCTGAGTGAGCTGGAATTAAAAAAAAAAAGGAATTTCACCCCAATCTTATACTGACTTCAATAGAGGTTTCAGACAAAAAGTTGTTTTGTATATACTTATCAGTCATGAAAAGATAATTACAACTAAATGGCCTTTTTCCTTCCCTATTTATTTGGAGAAATTTAATTACATAAAAAAGTACTCAGAATATTTGAGTTTCCTGCATCAATAAGACATTTATAATAATGACCTTGTTTACAAATGAATTTGAAAGTTACTCTAATTCTTTGATTCATCAAGAAATAACTAGAATGGCAAGTTAAAATTTAAGCTGTTTCAAAGATGCTTCTGCATTTAAAAACAAATTTATCTTTGATTTTTTTTCCCCCCAGCAAATAAGACTTATTTTATTCTAATTACAG
Seq C2 exon
GATGAACCCACCACAGGCATGGATCCCAAAGCCCGGCGGTTCTTGTGGAATTGTGCCCTAAGTGTTGTCAAGGAGGGGAGATCAGTAGTGCTTACATCTCATAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000165029-ABCA1:NM_005502:46
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.029
Domain overlap (PFAM):
C1:
PF0000522=ABC_tran=PD(17.2=54.3)
A:
NA
C2:
PF0000522=ABC_tran=PD(2.8=11.4)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTTGGTGAGTGGGCGATTCG
R:
TATGAGATGTAAGCACTACTGATCTC
Band lengths:
238-1181
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Genotype-Tissue Expression Project (GTEx)
- 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)