HsaINT0000406 @ hg19
Intron Retention
Gene
ENSG00000165029 | ABCA1
Description
ATP-binding cassette, sub-family A (ABC1), member 1 [Source:HGNC Symbol;Acc:29]
Coordinates
chr9:107543284-107547920:-
Coord C1 exon
chr9:107547677-107547920
Coord A exon
chr9:107546737-107547676
Coord C2 exon
chr9:107543284-107546736
Length
940 bp
Sequences
Splice sites
5' ss Seq
CAAGTAAGC
5' ss Score
7.47
3' ss Seq
CCATCTTAATCTTTTAACAGGTA
3' ss Score
9.43
Exon sequences
Seq C1 exon
GTTTGGAGATGGTTATACAATAGTTGTACGAATAGCAGGGTCCAACCCGGACCTGAAGCCTGTCCAGGATTTCTTTGGACTTGCATTTCCTGGAAGTGTTCTAAAAGAGAAACACCGGAACATGCTACAATACCAGCTTCCATCTTCATTATCTTCTCTGGCCAGGATATTCAGCATCCTCTCCCAGAGCAAAAAGCGACTCCACATAGAAGACTACTCTGTTTCTCAGACAACACTTGACCAA
Seq A exon
GTAAGCTTTGAGTGTCAAAACAGATTTACTTCTCAGGGTGTGGATTCCTGCCCCGACACTCCCGCCCATAGGTCCAAGAGCAGTTTGTATCTTGAATTGGTGCTTGAATTCCTGATCTACTATTCCTAGCTATGCTTTTTACTAAACCTCTCTGAACCTGAAAAGGGAGATGATGCCTATGTACTCTATAGGATTATTGTGAGAATTTACTGTAATAATAACCATAAAAACTACCATTTAGTGAGCACCTACCATGGGCCAGGCATTTTACTTGGTGCCTAATCCTATTTAAATTAGATAAAAAAGTACCAAATAGGTCCTGACACTTAAGAAGTACTCAGTAAATATTTTCTTCCCTCTTCCCTTTAATCAAGACCGTATGTGCCAAAGTAAATGGATGACTGAGCAGTTGGTGATGTAGGGGTGGGGGGCGATATAGAAAGTCAGTTTTTGGCCGGGCGTGGTGGCTCATGCCTGTAATCCCAGCACTTTGGGAGGCTGAGGAGCAGGCAGATCATGAGGTCAGGAGATCCAGATAATCCTGGCCAACAGGGTGAAACCCCGTCTCTACTAAAAATACAAAAATTAGCTGGGCATGGTGGTGCGCACTTGTAGTCCCAGCTACTTGCGAGGCTGAGGCAGGAGAATTGCTCGAACCCAGGAGGTGGAGGTTACAGTGAGCCAAGGTCTCGCCACTGCACTCCAGCCTGGGGACAGAGCAAGACCCCATTTCAAGGGGGGAAAAAAAGTCTATTTTTAAGTTGTTATTGCTTTTTTCAAGTATTCTTCCCTCCTTCACACACAGTTTTCTAGTTAATCCATTTATGTAATTCTGTATGCTCCTACTTGACCTAATTTCAACATCTGGAAAAATAGAACTAGAATAAAGAATGAGCAAGTTGAGTGGTATTTATAAAGGTCCATCTTAATCTTTTAACAG
Seq C2 exon
GTATTTGTGAACTTTGCCAAGGACCAAAGTGATGATGACCACTTAAAAGACCTCTCATTACACAAAAACCAGACAGTAGTGGACGTTGCAGTTCTCACATCTTTTCTACAGGATGAGAAAGTGAAAGAAAGCTATGTATGAAGAATCCTGTTCATACGGGGTGGCTGAAAGTAAAGAGGAACTAGACTTTCCTTTGCACCATGTGAAGTGTTGTGGAGAAAAGAGCCAGAAGTTGATGTGGGAAGAAGTAAACTGGATACTGTACTGATACTATTCAATGCAATGCAATTCAATGCAATGAAAACAAAATTCCATTACAGGGGCAGTGCCTTTGTAGCCTATGTCTTGTATGGCTCTCAAGTGAAAGACTTGAATTTAGTTTTTTACCTATACCTATGTGAAACTCTATTATGGAACCCAATGGACATATGGGTTTGAACTCACACTTTTTTTTTTTTTTTTGTTCCTGTGTATTCTCATTGGGGTTGCAACAATAATTCATCAAGTAATCATGGCCAGCGATTATTGATCAAAATCAAAAGGTAATGCACATCCTCATTCACTAAGCCATGCCATGCCCAGGAGACTGGTTTCCCGGTGACACATCCATTGCTGGCAATGAGTGTGCCAGAGTTATTAGTGCCAAGTTTTTCAGAAAGTTTGAAGCACCATGGTGTGTCATGCTCACTTTTGTGAAAGCTGCTCTGCTCAGAGTCTATCAACATTGAATATCAGTTGACAGAATGGTGCCATGCGTGGCTAACATCCTGCTTTGATTCCCTCTGATAAGCTGTTCTGGTGGCAGTAACATGCAACAAAAATGTGGGTGTCTCCAGGCACGGGAAACTTGGTTCCATTGTTATATTGTCCTATGCTTCGAGCCATGGGTCTACAGGGTCATCCTTATGAGACTCTTAAATATACTTAGATCCTGGTAAGAGGCAAAGAATCAACAGCCAAACTGCTGGGGCTGCAAGCTGCTGAAGCCAGGGCATGGGATTAAAGAGATTGTGCGTTCAAACCTAGGGAAGCCTGTGCCCATTTGTCCTGACTGTCTGCTAACATGGTACACTGCATCTCAAGATGTTTATCTGACACAAGTGTATTATTTCTGGCTTTTTGAATTAATCTAGAAAATGAAAAGATGGAGTTGTATTTTGACAAAAATGTTTGTACTTTTTAATGTTATTTGGAATTTTAAGTTCTATCAGTGACTTCTGAATCCTTAGAATGGCCTCTTTGTAGAACCCTGTGGTATAGAGGAGTATGGCCACTGCCCCACTATTTTTATTTTCTTATGTAAGTTTGCATATCAGTCATGACTAGTGCCTAGAAAGCAATGTGATGGTCAGGATCTCATGACATTATATTTGAGTTTCTTTCAGATCATTTAGGATACTCTTAATCTCACTTCATCAATCAAATATTTTTTGAGTGTATGCTGTAGCTGAAAGAGTATGTACGTACGTATAAGACTAGAGAGATATTAAGTCTCAGTACACTTCCTGTGCCATGTTATTCAGCTCACTGGTTTACAAATATAGGTTGTCTTGTGGTTGTAGGAGCCCACTGTAACAATACTGGGCAGCCTTTTTTTTTTTTTTTTTAATTGCAACAATGCAAAAGCCAAGAAAGTATAAGGGTCACAAGTCTAAACAATGAATTCTTCAACAGGGAAAACAGCTAGCTTGAAAACTTGCTGAAAAACACAACTTGTGTTTATGGCATTTAGTACCTTCAAATAATTGGCTTTGCAGATATTGGATACCCCATTAAATCTGACAGTCTCAAATTTTTCATCTCTTCAATCACTAGTCAAGAAAAATATAAAAACAACAAATACTTCCATATGGAGCATTTTTCAGAGTTTTCTAACCCAGTCTTATTTTTCTAGTCAGTAAACATTTGTAAAAATACTGTTTCACTAATACTTACTGTTAACTGTCTTGAGAGAAAAGAAAAATATGAGAGAACTATTGTTTGGGGAAGTTCAAGTGATCTTTCAATATCATTACTAACTTCTTCCACTTTTTCCAGAATTTGAATATTAACGCTAAAGGTGTAAGACTTCAGATTTCAAATTAATCTTTCTATATTTTTTAAATTTACAGAATATTATATAACCCACTGCTGAAAAAGAAAAAAATGATTGTTTTAGAAGTTAAAGTCAATATTGATTTTAAATATAAGTAATGAAGGCATATTTCCAATAACTAGTGATATGGCATCGTTGCATTTTACAGTATCTTCAAAAATACAGAATTTATAGAATAATTTCTCCTCATTTAATATTTTTCAAAATCAAAGTTATGGTTTCCTCATTTTACTAAAATCGTATTCTAATTCTTCATTATAGTAAATCTATGAGCAACTCCTTACTTCGGTTCCTCTGATTTCAAGGCCATATTTTAAAAAATCAAAAGGCACTGTGAACTATTTTGAAGAAAACACAACATTTTAATACAGATTGAAAGGACCTCTTCTGAAGCTAGAAACAATCTATAGTTATACATCTTCATTAATACTGTGTTACCTTTTAAAATAGTAATTTTTTACATTTTCCTGTGTAAACCTAATTGTGGTAGAAATTTTTACCAACTCTATACTCAATCAAGCAAAATTTCTGTATATTCCCTGTGGAATGTACCTATGTGAGTTTCAGAAATTCTCAAAATACGTGTTCAAAAATTTCTGCTTTTGCATCTTTGGGACACCTCAGAAAACTTATTAACAACTGTGAATATGAGAAATACAGAAGAAAATAATAAGCCCTCTATACATAAATGCCCAGCACAATTCATTGTTAAAAAACAACCAAACCTCACACTACTGTATTTCATTATCTGTACTGAAAGCAAATGCTTTGTGACTATTAAATGTTGCACATCATTCATTCACTGTATAGTAATCATTGACTAAAGCCATTTGTCTGTGTTTTCTTCTTGTGGTTGTATATATCAGGTAAAATATTTTCCAAAGAGCCATGTGTCATGTAATACTGAACCACTTTGATATTGAGACATTAATTTGTACCCTTGTTATTATCTACTAGTAATAATGTAATACTGTAGAAATATTGCTCTAATTCTTTTCAAAATTGTTGCATCCCCCTTAGAATGTTTCTATTTCCATAAGGATTTAGGTATGCTATTATCCCTTCTTATACCCTAAGATGAAGCTGTTTTTGTGCTCTTTGTTCATCATTGGCCCTCATTCCAAGCACTTTACGCTGTCTGTAATGGGATCTATTTTTGCACTGGAATATCTGAGAATTGCAAAACTAGACAAAAGTTTCACAACAGATTTCTAAGTTAAATCATTTTCATTAAAAGGAAAAAAGAAAAAAAATTTTGTATGTCAATAACTTTATATGAAGTATTAAAATGCATATTTCTATGTTGTAATATAATGAGTCACAAAATAAAGCTGTGACAGTTCTGTTGGTCTACAGAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000165029-ABCA1:NM_005502:49
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGAGAAACACCGGAACATGCT
R:
CCACAACACTTCACATGGTGC
Band lengths:
355-1295
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)