MmuINT0032450 @ mm9
Intron Retention
Gene
ENSMUSG00000024670 | Cd6
Description
CD6 antigen [Source:MGI Symbol;Acc:MGI:103566]
Coordinates
chr19:10868632-10869194:-
Coord C1 exon
chr19:10869054-10869194
Coord A exon
chr19:10868728-10869053
Coord C2 exon
chr19:10868632-10868727
Length
326 bp
Sequences
Splice sites
5' ss Seq
ACGGTAGGT
5' ss Score
10.15
3' ss Seq
CTCTGCCTCCCTCCCCCCAGCCC
3' ss Score
10.66
Exon sequences
Seq C1 exon
AATCTTCTGTGCCGGTGAGCGTGAAGGATAAGGACTCACAAGGGCTGACACTTCTCATTCTCTGTATTGTCCTGGGAATTCTCCTCCTCGTCTCCACCATCTTCATAGTTATTCTTCTCTTGAGAGCCAAAGGACAATACG
Seq A exon
GTAGGTGTGACGTTTCCAGAGCTACTGCACAGGAAACTGCAGTTATGAGGCACAGGCATGCCCCAGTAGGTGAAGTGTAGAAGAGACGTGGTCCTGCAAGACTACCCAGCTCAGGCCTAGGGAAAACCAAACCTCTTGATGGTGGGAAAGATTTTCCCAGCATGCCCAGTAGTGGAGCCTGCTTGCAGAGGCCTCTTAGGAGAAGCAGACTCTGTGTTTGTGTTGGGTATGGGTGAAGCAGATGCGTCCTTGAACCTGGAACTTGAAAGACTGGGAGACAGACACAATGAAAGTGATGCATAGACTCTCTGCCTCCCTCCCCCCAG
Seq C2 exon
CCCTCCCTGCTTCAGTGAACCACCAGCAACTGTCTACTGCCAACCAAGCAGGGATCAATAACTACCATCCTGTCCCTATCACCATTGCCAAAGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000024670-Cd6:NM_009852:7
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=0.114
Domain overlap (PFAM):
C1:
PF054546=DAG1=PD(59.2=93.8)
A:
NA
C2:
PF054546=DAG1=PD(16.4=57.6)
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:
AATCTTCTGTGCCGGTGAGC
R:
GGCAATGGTGATAGGGACAGG
Band lengths:
230-556
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: