MmuINT0007877 @ mm9
Intron Retention
Gene
ENSMUSG00000028125 | Abca4
Description
ATP-binding cassette, sub-family A (ABC1), member 4 [Source:MGI Symbol;Acc:MGI:109424]
Coordinates
chr3:121824549-121826608:+
Coord C1 exon
chr3:121824549-121824723
Coord A exon
chr3:121824724-121826476
Coord C2 exon
chr3:121826477-121826608
Length
1753 bp
Sequences
Splice sites
5' ss Seq
CTTGTGAGT
5' ss Score
7.15
3' ss Seq
CTTAACCCTGTGTTCGGCAGGTC
3' ss Score
8.15
Exon sequences
Seq C1 exon
ACTCCTTTTTTGAACGCGAGCTTCCAGGGCTGGTGCCTGGTGTGTGTGTGAAGAACCTGGTGAAGGTTTTTGAGCCCAGTGGCCGGCCAGCTGTGGACCGTCTGAACATCACTTTCTATGAGAACCAAATCACGGCGTTCCTGGGTCACAACGGAGCGGGAAAGACCACCACCTT
Seq A exon
GTGAGTTCTCTGCCAGAGAGGCTGTCTCCCATCCTATCATTCCCCGGCTTCATTCTCTCTCCCCAATAACTCCACTCTGTTCTTCCTTACTGAATTTCGGTGGAAACATATACACTCACACACACCTCCCACGGTGAGGATAAAAAGCCGTGGCTGCCCATGTCCCCGGGCTATTTTTATGTAGCACTCCGTTTCCTACCAATTAATAATTAGGATGCTTTAGTGCTGGTGTGGGACCTCTGATGGGATGGCTACCTTTCTGAGAAAGTGTAGGGAGAACAGTGAAGTAGACTCGCTGCCTGGCAGAAGGCCAAGGGCAGGAAGCTTTGAGGCTCTGGGTGGACTCCTCCATCCATCCTTTAGTTCTGGAAGGGGTGCGAGCGCCACCTGCTGAGAACAGGCAGTCAGGGCTCCGGTGCAGACCTCCGATGGGCCGATGGGCCGGTGGAGGAGGGGTAGGGGTCAACAAGCCATGTGACAGCAGCCATCAAATCCTTGGCTTGCAGAGCCCCGGGAAGGAACAGCAGTGTACACCCTGCTCCGGAATGTGCTCCCGGGCCTTTCAATGGGAATGGAATGCGGGGCTGGTGCCATTGGGCTTGGTACTGTTTCCCTCTAGTGGTTGATCAACATTTCAGCTTCGAAGTACAGGTTCAGATAGCATGCGATTTTATCAGAACTTGGGACAGAACTGGGCGTGGCATCCTAAGGCTATCTCCTTGCTAACTCACGTGGTGGGAGGACAGGAAACTCCATTCGAGACCCCAGGACCTCTAGAAGACAAACACATTACTTCACTCAGTGCAGAAACTAAACTTCCACTGGGGTCGGAACACAAGCGCTGTCCTAATGCTGGGAATAGCATAACATTTTAAGTTTCACTTTGTGCTGGGGCCTGTTTTTGTTTTGTTTTGTTTTTCAAGCATGTTCGATTCACTTAACTTAGACAACTACCCAAGCAGGTGGGAGACATGTTTTGTATAATTGAAGAAAGAAAAGAGAAATCACAACATTGTTCACATTTTTACATTTGGAATTCCCAAACGAATTTGTTTGTGTTAGCCAGTCAGCAGACAGGCTGCCCAGCTTCTCACTGGCATCAACTGAGCTTTGGAGAGTCACCAACCCTGCTTCTCCACTGTCAAGGGCTGCACGCCCAGGCAAAGCAGTGGGGCTGGGTCCTAAATCCCTTTAACTGACCACAACTGTGACTACGACAGTGGCCACAATGGCTGGCCACATCAATAGCCACGGAGCAACCACTATGACAGACCTTCACGGTGGACACTACCGCTGACCACAGAGTAAAACAACAGTGAACACTGTAGCTGACCACATCCGTGAATATCACTCTGACAGACAGTCATAATGGGCACCACAACTGACCACCACAGTGGCCATCCAGTGGGCACTACAACTGACCGCTGCAATGATGGCTGGGTGATGATGGGGTGGGGTGTCTGAGTCTGGGAATCCCCGAGGCTCTTGATACTGGCCCAGGAACACTTGGAAATAAAAAGTAGAGAAAGAAGGCCCTTGTGGTCTAGGCACTAGGACTTGAAGCAAGGCACTGGTGCTAAGTAAACCCTGTGTGGAAATGTTCTGGGCCCCTCAGCTACATCAGGTTTGAGTTTGATAGAGAGATAGGGCAGGTGTCACTACAAGCATCCTTCTGACCCTGTATGGGGTTACCCTCATCCCCTGGTGAGTTCTAACAACCATCTCTTCTGCCACTTAACCCTGTGTTCGGCAG
Seq C2 exon
GTCCATCCTGACAGGACTGTTGCCACCGACGTCAGGAACTGTGCTCATTGGGGGAAAAGACATTGAAACCAACCTGGATGTAGTACGGCAGAGCCTGGGCATGTGTCCACAACACAACATCCTGTTTCATCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000028125-Abca4:NM_007378:19
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.017 A=NA C2=0.022
Domain overlap (PFAM):
C1:
PF0000522=ABC_tran=PU(18.6=45.8)
A:
NA
C2:
PF0000522=ABC_tran=FE(30.3=100)
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:
TTTTTGAACGCGAGCTTCCAG
R:
ACAGGATGTTGTGTTGTGGACA
Band lengths:
294-2047
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: