MmuINT0007906 @ mm9
Intron Retention
Gene
ENSMUSG00000028125 | Abca4
Description
ATP-binding cassette, sub-family A (ABC1), member 4 [Source:MGI Symbol;Acc:MGI:109424]
Coordinates
chr3:121872811-121873763:+
Coord C1 exon
chr3:121872811-121872945
Coord A exon
chr3:121872946-121873659
Coord C2 exon
chr3:121873660-121873763
Length
714 bp
Sequences
Splice sites
5' ss Seq
CTGGTGAGG
5' ss Score
8.3
3' ss Seq
TTTTCTCTCCTACTCTGCAGGAT
3' ss Score
10.98
Exon sequences
Seq C1 exon
GTTGCCAACTGGGGTATCCAGAGCCTGGGCTTGTCTCTCTACGCTGACCGCCTGGCAGGCACCTACAGTGGAGGCAATAAGAGGAAACTCTCTACAGCCATAGCTCTCACTGGCTGCCCTCCCCTGCTGCTGCTG
Seq A exon
GTGAGGGCATCGTACTCTGCAGAGTGGAAATGTCACGGACGTCCTGAGTTGAGAAAATTAATTCAGGGCTTGCAGCTTTAGAACGGCAATAGATTGCCCCTTTAAGGCAAATTAGCCAAGTGTTTGGTCACAGCACAGTCTGACCTTCAATGCCTGGAAAGTCTCTAGAAGGTCCAGAAACTCAGACTGGAAAGCCCTGTCAGCTCCAGGGAATGTTGCGATCTGGTTAGAAATTAGGATGAGGAAATCTGTGTGGACCGGAGCATCTACTTCAATCAGAGGCTCCGGGGACCCTCTCGTGAATTGGACCACAGTAGAGTCCCTGAGACCATGCAGTCTGGGTTTTAAATGACATGGGACATAGAGAGGACTGTAAAGTTACTTGGGCTATCCCCCTCCCCTGACCCTTCCTAAGGATAATTCTACTATTGTCTTTATTAATTTATTGTTATTGTTCATATTATTATTATTATCCTATTTCTGTATTTCTATTATCCTAACCTTAATTCACTCACAGCTGGCATGGTCCTATAGGTATGTACCATGTGTCTGTAGTCTCCAATTCCCCTTCTACCTATGTGTCCTACAAGACATGGTTCTGTCTTGCTTGCTGGGAAGTGGCTGTGCACTTGTCTGTTAGCCCAGGAAGGATGTAGTGATGGAGAAAGACCAACTCCGCGTCCACATCTCCCTCTTTTCTCTCCTACTCTGCAG
Seq C2 exon
GATGAGCCCACGACAGGGATGGATCCCCAGGCACGCCGCATGCTGTGGAACACCATTGTGAGCATCATCAGAGAAGGGAGAGCTGTGGTTCTCACCTCCCACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000028125-Abca4:NM_007378:45
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:
PF0000522=ABC_tran=FE(30.3=100)
A:
NA
C2:
PF0000522=ABC_tran=PD(2.8=11.4)
Main Inclusion Isoform:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTTGCCAACTGGGGTATCCA
R:
CTGTGGGAGGTGAGAACCA
Band lengths:
239-953
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: