HsaINT0000885 @ hg19
Intron Retention
Gene
ENSG00000154258 | ABCA9
Description
ATP-binding cassette, sub-family A (ABC1), member 9 [Source:HGNC Symbol;Acc:39]
Coordinates
chr17:66986978-66988407:-
Coord C1 exon
chr17:66988316-66988407
Coord A exon
chr17:66987099-66988315
Coord C2 exon
chr17:66986978-66987098
Length
1217 bp
Sequences
Splice sites
5' ss Seq
CAGGTTGAG
5' ss Score
1.68
3' ss Seq
TCACACTGTTTTGATTTCAGAAT
3' ss Score
8.46
Exon sequences
Seq C1 exon
CCTTACCTTCATTTTCTCATTTTTCTTTTCATTCTGCGATGCCTAGAAATGAACTGCAGGAAGAAACTAATGAGAAAGGATCCTGTGTTCAG
Seq A exon
GTTGAGAAAATCAAATCGAATTTCATGTTTCATTTTGATATTCATTCTTTAAGGACTTTTTAATGTGCTGAATTAATTAAGTAAAAGACACTTCACAGGATGGTTTTTAAAGACTGTGATATACAAAATTCTTATAACCCATAATATAGGAATATATACTGAGCTTACAATCTAGAGAGAGAAACCATATTAGCACACACGAGACACTGGAAAATTAAGGCAGACCATAATTTTACTATAGAGGAAAGTTATGTGTAAGAGGTGGAATCTCTAAAATAATGGGTAAATATAGATAAGCATTGGGAAAGTTAATCCAATCCGGGAAGGAAGAATAGTTTGTGCAATAAAACCAAGGATGAGATGAAGGCACCAGGAGCTCCTTTGTAGGCTTATGTTGGGGGATGATGAAAAATGAAAGTGAGGCTAGATATTGGAGGATCTTGAAACAGAAAAGTATAGGAAAGGTTTTGCAAATTACATAATGTGAAACCAAGACACCAATGTGTCTTGAACACTTAGCCTTCCATATAAAATATAAACCAAGCTTAAGTCTAATGTTTGTGGTAGCAGAGAAGAGTGACAAGATGACAGCCATGTTTTAGGAAACCAACAGGCAACCAGAATGTCAGAGCGTGGCATGAGGGAGAGATAAAAGAATGAGCAGGAATCAATGGTGGGATGATGAAGGCAAGAACGAGTCTGTAGCAGAGAGGAAAGAGTGATTCTGTCACACATTCCCAAGAAGTGACTGTGCTCAGTAACTAATTAGGCATTGGTATGGTGATTAGATATCCTGGATTCTCTGGGACACATCCTTGATTCCAAATCTTTGGACTCATGGCTCTCACAAAGACCTCAGAATTCCAAAATATCTGTTGTCAAAACTATAGTTCCTAGATTCCTTTCCTCATGCAACTCTGCTTCACAATCCTTTGCCAGAGGGTGTATACCACTTTCTTCTTTGAAAGAAAACTGTCACCATCAACAGGGAGGATTAAGCTTTGGTAAAAAGCGAAGATGATATAAGGATATCATTACTCTACTCACTGAAGGAAACTAGGGTGTTTGAAAGGCGGATGGTGCAAGTAGAAGAATAGAGAGGATGTTGTGCTCTGAATGAATCTACTCCAAAAATTGGAAGTATAGAGAAAATTCATTAATTTTGATACAAGATTTTTAACCCGAAGTTTATCATTATCACACTGTTTTGATTTCAG
Seq C2 exon
AATTTCTCCAAGAAGCAACGCTATTTTTCCAAACCCAGAAGAGCCTGAAGGAGAGGAGGAAGATATCCAGATGGAAAGAATGAGAACAGTGAATGCTATGGCTGTGCGAGACTTTGATGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000154258-ABCA9:NM_080283:28
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=0.366
Domain overlap (PFAM):
C1:
PF126982=ABC2_membrane_3=PD(3.6=35.5)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TCTCATTTTTCTTTTCATTCTGCGA
R:
TCATCAAAGTCTCGCACAGCC
Band lengths:
198-1415
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)