MmuINT0008085 @ mm9
Intron Retention
Gene
ENSMUSG00000020620 | Abca8b
Description
ATP-binding cassette, sub-family A (ABC1), member 8b [Source:MGI Symbol;Acc:MGI:1351668]
Coordinates
chr11:109814812-109816515:-
Coord C1 exon
chr11:109816349-109816515
Coord A exon
chr11:109814946-109816348
Coord C2 exon
chr11:109814812-109814945
Length
1403 bp
Sequences
Splice sites
5' ss Seq
CAGGTAATA
5' ss Score
8.55
3' ss Seq
CATGTTGAATGACATCTCAGAGG
3' ss Score
1.51
Exon sequences
Seq C1 exon
GCTCTTGATACTGGTAGTCGGCATCTGTCCTTTTCTTTTTGAAAATATCTCAACGAAAATACGTCAAAGCTCTTACACTTGGGAACTTTCCCCACACGATTACTTCCTTGCTCCGGGACAACAGCCCCAGGGCATGCTCACTCAGTTATTGATCATTAATAAGACAG
Seq A exon
GTAATAACGGATTTCCAATTCACACATGTATCTATGTTTCATTCTGAAAGTGCTGGGCAAGGACTTATGGTGGGGAGGTTTTAAGGAAAGGTCAAAGGTAGCAGAATGCAGAGGCAAGGGAAAGGAGAGTCTACTAAAAACACATCTCATTCAAAAATACCATAGAGATAATTGAGACCTTATAGTCTCATTTTAATTGTTTAATTAAAGAGAGTATTAATGCTATTCTATTATGTACATATTCCACATTGTATTTATCATCCACCTGTAAATGGATACATCCCCTACAAATGATTATGAATAATATTTTGATCAATGATTATGTATTTTTGTAAAGGTTTTTTTTTCATTTCTTTGGAGTATCCTCTTAGAACTGGGATTGTTGGATCACATAATACATATGTTTAAACTGTTAAGGATCTACTAAATTGTTTTCAAAGTGAGTGCATGTGTATGCTCGCGACGTATGTGTTCAAATTCCTGTACCTCTTGGATGATTCCCACTCCTGATTTTTTTATAAGTACCACACTTGTCACATGATATCTTCCGTTTTGTGTGGATGCATTTTCTATGTGGGTGCATGTCTTTGTAAGCAAGGGTGTGCATGCATGAGTGTATATTTAGAGGCCAGAGTTCAACACTGGATGTTTTCCTCAGTCACCTTATTATTTAAAACTCTCTCCCACTGAAACTTGAACTCATTTCGCTGCCTCTTCAGTGATTCCCCAGAGATAAGATTTCTGTGTGGGTGCTGGGGACTGAACTTCGGCCATCATCTTGCTCAGCAAGCACACTATTGACTGAATGCTCTCCTCAGTCCTTTTTCTCTTCTGGTCTCTATTTCTGTTTTGCTAATGGCTTGTGGTGCTGGGGGGGTCTTCTTGTGTGCTCGCTGACATTCTCGGAGAAGTGTTCTTGCCAATTTTAGTAGATTTTCTTAAGTATATCTTTCTTTATTTTCTGCACTTGCTTAGGACAGTTTCAAGAGTTACACACTGGTTGATTATCTGGGTAGAAGCTCTACAAAGTTGTTCATGCCACCAGATTGCCTTCCTGCCTTACGAAACTATTTGAAAATCAAGTAATAATCTCATAATAGTGACTTCTGTTTTTCAGACATTTAGTGATTAGAAATTACCTACCATTAAAACTCCACAGCTCTTCATTGCAAGATTCTAGGGGGAAAAAAAGCTATTTCAAGAGTCATATGGTATAAAAGAGCTATAGATTATCAGTAAACACGTTTGTTGTAGCATAAATTCCTAGAGCAATTAGTCGACTTTTAATTCACGATGCAAACGGTATTGTTATGTGGGAAAGTACACACTGAAGCATTGAGATTCAGAACTTAACACGGGCTTTTTTATCTTTGAAATACCTAACATGTTGAATGACATCTCAG
Seq C2 exon
AGGCAAGCATTGACGACTTTATCCATTCTGTGGAACGCCAGAACATAGCTTTGGAAGTCGATGCTTCTGGAACCAGAGATGGTACAGATGACCCATCCTACAATGGAGCCCTTATAGTGTCTGGCAATGAGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000020620-Abca8b:NM_013851:20
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=0.044
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF126982=ABC2_membrane_3=PU(10.0=62.2)
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:
GCTCTTGATACTGGTAGTCGGC
R:
TTGCCAGACACTATAAGGGCTC
Band lengths:
294-1697
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: