HsaINT0000640 @ hg38
Intron Retention
Gene
ENSG00000167972 | ABCA3
Description
ATP binding cassette subfamily A member 3 [Source:HGNC Symbol;Acc:HGNC:33]
Coordinates
chr16:2286694-2288329:-
Coord C1 exon
chr16:2288026-2288329
Coord A exon
chr16:2286968-2288025
Coord C2 exon
chr16:2286694-2286967
Length
1058 bp
Sequences
Splice sites
5' ss Seq
TCGGTAAGG
5' ss Score
10.48
3' ss Seq
ACTCTGCCATTGCTCCCCAGGTG
3' ss Score
9.92
Exon sequences
Seq C1 exon
CTCGCCCTGCACTGCCAGCAATTCTGGGCCATGTTCCTGAAGAAGGCCGCATACAGCTGGCGCGAGTGGAAAATGGTGGCGGCACAGGTCCTGGTGCCTCTGACCTGCGTCACCCTGGCCCTCCTGGCCATCAACTACTCCTCGGAGCTCTTCGACGACCCCATGCTGAGGCTGACCTTGGGCGAGTACGGCAGAACCGTCGTGCCCTTCTCAGTTCCCGGGACCTCCCAGCTGGGTCAGCAGCTGTCAGAGCATCTGAAAGACGCACTGCAGGCTGAGGGACAGGAGCCCCGCGAGGTGCTCG
Seq A exon
GTAAGGGGCATCCCGGGGGCGGGACGGGGGCATCGGGGGCCAGTCCTGCAGCCAGAGTTCGCCTTCCTGACTGCAGCAGGGTCGACATCTGGGGAGGATGGTTCTTGGCTGTTCCGAATGTACTGAGGGAGGTTCAGCAGCATCCCTGACCTTGCCCCACCCCATCATGACCATCAAACATGCCTGGAAACATTGCGGATGTCCCCTGGGTGGCAGATCACGGCACTGAGTCAGGGGAAGTGCCCTGGAGGTGCCAGAGACACTGGCATCCTGGGGCCAGGCTTTGTCAGGCGTCTTTTTACTGAAGCTGTGTCTTTCAGGATCATTCATGGGCAAAATGCAGAAGCATAGTGACTTCAAGTTACCTTTGCTTTGTGATGATGCTGGCCACAGTGTGCCTTCGTGTGACAGGGTGTTTTCTTTCAACATCTTAAAACTCACAGTTCTTGGCCAGGCACAGTAGCTCACACCTGTCATCCCACTACTTTGGGAGGCCGAGGCAGGTGGATCACTTGAGGTCAGGAGTTCGAGACCAGCCTGGTCAACATGGCAAAACTCTGTCTCTACTAAACACAAAAATTAGCTAGGTGTGGTGATGGGTACCTGTAATCCCAGCTACTCTGGAGGCTGAGGCAGGAGAATGGCTTGAACCTGGGCGGTGGAGGCTGCAGTGAGCCAAGATCGCACCATTGCACTCCAGCCTGGGTGACAGAGCAAGACTGTCTCAAAAAAAAAAAGAAAGAGTCTTGGTAGTCATAGTTGGATACTGCCCCAGGCTCAGAACAGGGACCGTGCTCTGGTTAATGGAACCTACTGGAAGGTTTTCTTATTTTGCAGCTCCTTTCCCGGTTCCTGACTGGCATTCAAAGTTCCACATACTGAATGATGACAAAACCTTGCCAGAAATTATACTCTCCTTAGGAGAAGGGTGATGGGGCGGGCAGCTCAGAGGATGCTGGCACCACTCTATTGGGTCCCTGATTAGCCATGCTCAGGTGGCAGGGGGTGCCCAGGTGTCACCTCTTCCTGTGTCCCCTGACTCTGCCATTGCTCCCCAG
Seq C2 exon
GTGACCTGGAGGAGTTCTTGATCTTCAGGGCTTCTGTGGAGGGGGGCGGCTTTAATGAGCGGTGCCTTGTGGCAGCGTCCTTCAGAGATGTGGGAGAGCGCACGGTCGTCAACGCCTTGTTCAACAACCAGGCGTACCACTCTCCAGCCACTGCCCTGGCCGTCGTGGACAACCTTCTGTTCAAGCTGCTGTGCGGGCCTCACGCCTCCATTGTGGTCTCCAACTTCCCCCAGCCCCGGAGCGCCCTGCAGGCTGCCAAGGACCAGTTTAACGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000167972:ENST00000301732:21
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.010 A=NA C2=0.011
Domain overlap (PFAM):
C1:
PF126982=ABC2_membrane_3=PU(19.7=77.5)
A:
NA
C2:
PF126982=ABC2_membrane_3=FE(22.6=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TCTGGGCCATGTTCCTGAAGA
R:
CCACAAGGCACCGCTCATTAA
Band lengths:
354-1412
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