HsaINT0000740 @ hg19
Intron Retention
Gene
ENSG00000154265 | ABCA5
Description
ATP-binding cassette, sub-family A (ABC1), member 5 [Source:HGNC Symbol;Acc:35]
Coordinates
chr17:67298859-67300951:-
Coord C1 exon
chr17:67300810-67300951
Coord A exon
chr17:67299048-67300809
Coord C2 exon
chr17:67298859-67299047
Length
1762 bp
Sequences
Splice sites
5' ss Seq
TCTGTAAGT
5' ss Score
7.96
3' ss Seq
TTAATATTTGTATTTTATAGGTA
3' ss Score
10.4
Exon sequences
Seq C1 exon
GCTTTCCTGGGTTCTTCTATATACAAGTTTAATTTTTCTTATGTCCCTTCTTATGGCAGTCATTGCGACAGCTTCTTTGTTATTTCCTCAAAGTAGCAGCATTGTGATATTTCTGCTTTTTTTCCTTTATGGATTATCATCT
Seq A exon
GTAAGTATTTTAACTTGTGATAGGAATAAAGAACTGTCAAAATGTTTGATAACATAGCAAAGTCTTTTTCTTCAGTTTACTTATAGTCAATTTGCCATGAAAGACAGATTTTACTAATTGATAAGTGACTTAATAAATAAATGATGTGGCATCACTGTATTCCTGTATTTTTAGTAATGTTACAAAATAGTTTTAGATTTAGATTTAGCTTTTGTCATATGATGTATTTCACATACAACTCCTCTATCTGTTGTCTTTATATAATGATGTATATAATTAAGACTGTCAAGTATTGGACTATTTTTGTTTGTCTTCATGGAATCCTTACTCTTTCAAGTTAATTTATGCTCCAGGATGATGATTTTTAAAGATACATCTTTGCAAATGTAACTCTTTAGCAGTCTTGATATTCATTTGATATATTGGCTGAATGAGAGGTTTTAATGACCAGCCTTTGTTTTAAGTGGTTCCATCTTCCATTCTGATTGGTTTATGTGCCCACCCTGTATCAGTTGTTAAATGTTTTGGCTATCATTTCTGCTCTTTAAAATAATAAATTGCAAATAACTAACATACTTCCATATGTAATTGCCTGGTTTTTTTTTAAATGTTTAATTTTACTTTTTTGAGACAGGGTCTTGCTCTGTGGCCCAGGCTGGAGTGCAGTGGCACACTCATGGCTCACTGCAGCCTTGACCTCCCAGGCTCAATCCTTCAACCTCAGCCTCCTGAGTAGCTGGGACTACAGGTGTGTGCCATCACACCTTGCTAATTTTTGTGTGTGTGTATGTATATATGTATATATATATATACATATATATATGTATGTATATATATATATACATATATATATATGTATGTATATATATATATATATATATATTTTTTTTTTTTTTTTTTTTTTTTTTTAGAGTCGAGGTCTTCCTAAGTGTCCAAGTTTGGTCTTGAACTCCTGGGCTCAAGTGATCCACTTGCCTTGGCCTCCCAAAGTGCTGGGATTACATGAGCGAGCCACTGCAGCAGGCCTTCTGGTTTTTTTTTTCTTTTTAAACTGTTTTTTTTATCTTATGAATAAATTAAGTTTAAAATATGGGTCTTGTACTTAAAATTTTTGTTGATTTATTATTTTTTCACATATTTTATGCATCTTACTGCAGAAACACATGGCTATTTATGGTTTCTGTAATGTAGAGGTGGTCATGTTTACCTATGATACAGATAAAAATACAGTATTTAATATTTGTTAGTTTAAGACCAGATGTGGTGGCTCACACCCGTAATCCCAGCACTTTGGGAGGCAAGGCAAGAAGATTGCTTGAGGCAAGGAGTTTGAGACCAGCCTGGGCAACATGGTGAAACCCTGTCTCTACAAAAAAAATACTAAAATGCTGGACGTGGTGCCCCACGCCTGTAATCCCAGCTACACGGGAGGCTGAGGTGGGAGGATCACCTGAACCCAGGAGGTGGAGGTTGCAGTGAGCCAAGATGGCACCACTGCACTTCAGCTAGGGTGACAGAACAAGACCCTGTCTCAAAAACAAAATCAAAACAAAAACACAAAAATATTTGTTAGTTTAAATTTTTAAAAGGTATATCACTATTTGTTTGAAAATAAAATACCATAGCATTTAGAAATTATAGTTGTATTTTTATGAATGCATTTTTCATGAAAATAGCTTGTTCTTTCAGAAGCAAACTTTAATTTTGTTTTCATACTGGTATATATGAACATTGCACTAACCTTAATATTTGTATTTTATAG
Seq C2 exon
GTATTTTTTGCTTTAATGCTGACACCTCTTTTTAAAAAATCAAAACATGTGGGAATAGTTGAATTTTTTGTTACTGTGGCTTTTGGATTTATTGGCCTTATGATAATCCTCATAGAAAGTTTTCCCAAATCGTTAGTGTGGCTTTTCAGTCCTTTCTGTCACTGTACTTTTGTGATTGGTATTGCACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000154265-ABCA5:NM_018672:6
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=0.000
Domain overlap (PFAM):
C1:
PF126982=ABC2_membrane_3=FE(12.1=100)
A:
NA
C2:
PF126982=ABC2_membrane_3=PU(48.2=93.2)
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCTTTCCTGGGTTCTTCTATATACA
R:
TGTGCAATACCAATCACAAAAGT
Band lengths:
330-2092
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)