MmuINT0007880 @ mm9
Intron Retention
Gene
ENSMUSG00000028125 | Abca4
Description
ATP-binding cassette, sub-family A (ABC1), member 4 [Source:MGI Symbol;Acc:MGI:109424]
Coordinates
chr3:121829039-121829877:+
Coord C1 exon
chr3:121829039-121829178
Coord A exon
chr3:121829179-121829739
Coord C2 exon
chr3:121829740-121829877
Length
561 bp
Sequences
Splice sites
5' ss Seq
CAGGTGCTT
5' ss Score
4.83
3' ss Seq
CACCTTCCTTCTGCCTCCAGGTG
3' ss Score
12.61
Exon sequences
Seq C1 exon
CCTCACGGTGGCTGAGCACATCTTGTTCTATGCCCAGCTGAAAGGGAGATCCTGGGAGGAGGCCCAGCTTGAGATGGAAGCCATGCTAGAAGACACGGGCCTCCACCATAAGAGGAATGAAGAAGCTCAGGACCTTTCAG
Seq A exon
GTGCTTGGTATTGGGAGGAGACGGGGTCACTTACGGAGCATCCGTTGCCTGGCAACGCGCCTCAGCAGAAGGTTGGGGTAGCAGAACAGCAGCTCTTCAACCTGTAGGCCCCGCCCCCCCCACGTCAGATGTCAGATGTTTACATCATGATTCATAACAGTAGCAAAGTTACAGTTATGAAGTAGCAACGAAAATAATTTTATTGTGTGTGTGTGGGGGGGGGGGTCACCACAACATGAAGAACTATATTAAAAGGGTCACAGCATTAGGACGTTGAGAACCACTGGGGTAGGGCCTTATAACGGGAGCTCTCCTTACATTTCTGTGAAGCTCAAGGCACAGTTTTCAGATGATCAGGTGCTAGGAAGCAGGGTGGTCTTTCAGCATTGGTGAAGCATGGACGATACTGTGACGTCTGACAGTGTAGGCATATCTGTGGTGGCAGTACCAAACTGTAGCCAGATTTAAAGATCCTCCACATGTGACCAGCTTTGGGCCTTCCTCTTCCCCGTACCGAGATGTCTGTGATATCCCGTGTCATCACCTTCCTTCTGCCTCCAG
Seq C2 exon
GTGGCATGCAGAGGAAGCTGTCTGTTGCCATTGCTTTTGTGGGAGATTCTAAGGTGGTGGTCCTGGATGAGCCCACCTCTGGGGTGGACCCCTACTCCAGACGCTCCATCTGGGACCTGCTCCTGAAGTATCGCTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000028125-Abca4:NM_007378:21
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.167 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0000522=ABC_tran=FE(32.4=100)
A:
NA
C2:
PF0000522=ABC_tran=PD(17.9=55.3)
Main Inclusion Isoform:
NA
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:
CCTCACGGTGGCTGAGCA
R:
CTGAGCGATACTTCAGGAGCA
Band lengths:
278-839
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types
Other AS DBs: