HsaINT0000689 @ hg19
Intron Retention
Gene
ENSG00000198691 | ABCA4
Description
ATP-binding cassette, sub-family A (ABC1), member 4 [Source:HGNC Symbol;Acc:34]
Coordinates
chr1:94480099-94481410:-
Coord C1 exon
chr1:94481295-94481410
Coord A exon
chr1:94480247-94481294
Coord C2 exon
chr1:94480099-94480246
Length
1048 bp
Sequences
Splice sites
5' ss Seq
TGGGTAAGC
5' ss Score
8.84
3' ss Seq
AGTTGTCTCATTTCACACAGATG
3' ss Score
6.94
Exon sequences
Seq C1 exon
ATGAATTATTCCGTGAGTGCTGGGCTGGTGGTGGGCATCTTCATCGGGTTTCAGAAGAAAGCCTACACTTCTCCAGAAAACCTTCCTGCCCTTGTGGCACTGCTCCTGCTGTATGG
Seq A exon
GTAAGCCGTTTGGGCCATTAGCTAATGCCTCTGAAGAGAAGCCTGGTGGTGGGGGTGGGGGATCATCTCCTGACAGAAAACCTGGGCTGTCCTGTGGTGGTAGCACCCACAAGTTTAGCTTCCGGCCCCAGGTAGGGTCTGAAGCTGATAACCAGGGATCTGTCTGGCTTCTGATTCTGACTCCACTGACAGAGGTATCTCTGAGGCCTGGTCCTGTCAGTGACAATGAGAGAAGTCCCACATGATCTGAATCTCCTACTCAAACTGAGGCCTTGACCAAAGCCTGGGGGCAGCCATTCCCCAACCCCTCACCCAGCTCTGACTCTCACTCATCTGTGGCCAATCTGTCCACCTCAGTGTCCCCATGTGAACTGGCCAAGAGTTACCGCCCACAGTAGAAGACTCCGGCCAAAAAGCTCCTCCTGAGTCAGGGACAGAGGATGACACAGGGGTTACATCAGCAGAGTTACAGGGCCCAGCATGCAACTTTCTTTCCCACGTGTGTAAATTTGAATGAGTAATTCATCCATCTCGGCCTCAGTTTCCTCATCTGTAAAAGAAAATAGTGATCCTGGTCCTTCCTCTGTGGGCCAGTAGAGCCTTGCCAAAGCATTGTTCTCCACATCTTTCTCTTGGAAATAGAGAATTTGGGAACCAACCTGACTATAAGCTGTGAAGATGAGCTCACTGGGCTCATCTGAGATGACCTCAGCTGGGCTTTGCTGACCCAGGCTAGAGTGGGAGGTGTTGCAGGCTGGAGAACCCTCCTATGAATTGTACAGGGCTTTGTAGTTTACAGAGTATATACACAGCTAGCAGCCCATTTGCTCCTCACAAAACCCCATGAAGTGGTCAAGGCAGGCATCATTATCTCCATTTAAAGTTGAGGCACAGAGACCAACAAATGGAGTATCTCTCTGGTCCCCTGGGACTCTGGCCAGTTCACACACATCACCTCAGGTGTAAGGGGAGTGCATTATATCCAGACGTATTGTAGGTGGAATGGAATGTGGAACTCCATCACTCTGAGTTGTCTCATTTCACACAG
Seq C2 exon
ATGGGCGGTCATTCCCATGATGTACCCAGCATCCTTCCTGTTTGATGTCCCCAGCACAGCCTATGTGGCTTTATCTTGTGCTAATCTGTTCATCGGCATCAACAGCAGTGCTATTACCTTCATCTTGGAATTATTTGAGAATAACCGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000198691-ABCA4:NM_000350:37
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(12.7=100)
A:
NA
C2:
PF126982=ABC2_membrane_3=FE(16.4=100)
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:
TGAATTATTCCGTGAGTGCTGGG
R:
CCGGTTATTCTCAAATAATTCCAAGA
Band lengths:
263-1311
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)