MmuINT0008084 @ mm9
Intron Retention
Gene
ENSMUSG00000020620 | Abca8b
Description
ATP-binding cassette, sub-family A (ABC1), member 8b [Source:MGI Symbol;Acc:MGI:1351668]
Coordinates
chr11:109842164-109843093:-
Coord C1 exon
chr11:109842992-109843093
Coord A exon
chr11:109842369-109842991
Coord C2 exon
chr11:109842164-109842368
Length
623 bp
Sequences
Splice sites
5' ss Seq
ATGGTACAG
5' ss Score
3.5
3' ss Seq
TCCCTTCTTGGGCTGTGTAGGAG
3' ss Score
6.03
Exon sequences
Seq C1 exon
GGCAACATGATCAAGAGAGAGATAAGTGTGCGCCAACAAACTTGTGCTTTATTACAGAAGAACCTTCTTAAGAAATGGAGACTGAAAAGGGAGTCCTTGATG
Seq A exon
GTACAGTTCTATGTCATTGCCACTGTCTGCTGATGATATAAGTGTATTTGGCCTGAGAATTGCACTTAAAAAAGTGTCTAAACTTATGCACTGGGAAAACAAATTAATTTATTGGGAGTTTGGGAATAGCTAGGGTCTCTAAGTACCAAAGCAAGGTGGTACCCCTCAGATGACCACCATTCTGCCAAGTACCCTTTAAAACATCTTGGTGTGTAATCCTTAGGCTATATCTACATTATGCTGCCTCTTCAACAACCAGATTTTCAACAAATCAAAGATGTCTTGAACTGGTTGCCAAGGTGACACTAGGTGAGAGCAGCACTGTAGACAACAGCTGGTTGCATTTTGTACTTTCTCATGAGGATCTGTCTCAGCACAGGCAGTCAGAGGCCCAATACATTCATGTCCCTATCAGTAACTGACTGGAATTACTGATGATTGCGAGCCACACATATTTCTTGTGGCTTGTCTTTAAGACGCCCTGGGCATTTTACAAAGAGAGAGGCAAATTCGATAACCAAATGGTTGTGGGTGAATAATTTGGAGTCATGGTTTTTCTCTCTGTTGGTCATGGATGAGTAATCTGGAATGGTGATTTTTCTCTCCCTTCTTGGGCTGTGTAG
Seq C2 exon
GAGTGGGTGAGCTCCTTGCTCCTTCTGCTTTTCTTGTATTGGTATCCCCATGGTCATGGAGCTACTGACCTGTCTTCAGTGCCCACCAAGGATCTGGGACGAGTCGATTCTTTCAGACAATCTGGGTTCATGATAGGGTACACGCCTGTCACCAGCATGACACAACAGATAATGGAGAAGGTAGCTGCAACCCCTTTCATGGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000020620-Abca8b:NM_013851:2
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF126982=ABC2_membrane_3=PU(1.0=12.5)
A:
NA
C2:
PF126982=ABC2_membrane_3=FE(17.4=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:
GGCAACATGATCAAGAGAGAGA
R:
ATGAAAGGGGTTGCAGCTACC
Band lengths:
302-925
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: