MmuINT0032448 @ mm9
Intron Retention
Gene
ENSMUSG00000024670 | Cd6
Description
CD6 antigen [Source:MGI Symbol;Acc:MGI:103566]
Coordinates
chr19:10870816-10872468:-
Coord C1 exon
chr19:10872166-10872468
Coord A exon
chr19:10870879-10872165
Coord C2 exon
chr19:10870816-10870878
Length
1287 bp
Sequences
Splice sites
5' ss Seq
CAGGTATTC
5' ss Score
6.49
3' ss Seq
TGTGTGGTACTTTCCAACAGGCT
3' ss Score
9.18
Exon sequences
Seq C1 exon
AGCACCAGTCCTGGCGCCTGACTGGAGGCATTGACTCCTGCGAAGGGCAAGTGGAAGTGTACTTCCGGGGTGTCTGGAGCACGGTGTGTGACAGCGAGTGGTACCCATCTGAGGCCAAAGTGCTCTGTCGGTCCTTGGGTTGCGGATCAGCAGTGGCTCGGCCCAGGGGGCTGCCACACTCCCTGGACGGTAGAATGTACTACTCCTGCAAAGGACAGGAGCCCGCCCTCAGCACCTGTTCCTGGCGGTTCAACAACTCCAACCTGTGCAGCCAGTCGCGGGCAGCCAGGGTTGTCTGCTCAG
Seq A exon
GTATTCCTTCCCCAGCCCCTCCACCACTAGATTTAGTCCACAAATTTTGTCTCTGCCGACAGCTGGCATATACTGGCCCAAGAAAGACCATTGCACTTACCATGCACAGGCAGACATTAATTAGGATGGTTTTGTTTTTTTCTGCAGTATGGTCAGCTCAGACCCAAATTCATGGGTTAAGTATTTATCAAGGAAGTCATTATTATGTTTATTGGAAATGGTTCAGTAGGTGGTGATTTCGGGAAAAATCAGGTTGGGAAACACAGATGGTAATAACAATCAAGACAACATCTGGAGCTATAAAATCACATGTCAAGCACTGCCAAGCTCTCTGTAGCTTGTCTCAGTTTAGCCTTATGCCCACTGGGCTTCTACTGTCCTTCACCAACTCTAAGACTACAGTGGCAAGTCACAGCATTAGTGTCTTATAGACCATAAAGACAAATGAATGCAGTCTGGAATTGTAGCTCAGTGGTAAACCACTTGCCTAATTTGCATGAAGCCCTGGGTTCAAACCTCAACACCTCAAGGAAGAAAAGAAAGGAGGACGGGAGGGAAGGAGGAAAGAAACACCTAGAATTCTGATATGTTTGGTGTGGTGAAAGAAACTAAAAATAAATATTGTCCAGACTCTTGACATGCTGTCATATCTAGTAAGGCCATGGTTCCAACTGCAGAGGCGTTATAGTATGAAGCTAAGGTTCCCACCCGTGGGAACACAGTGTTGGCCTCTCTGTGGAGTGCAGACCCCTGACTCTGAGCTCCAGCTCCCGTTTACCAGCCAGGACTGGGACAGTTCCTCAACTCCTGTGGCTTCAGAATAAAGGATGCTTTACCAGGTAGCTGGAGATGCTACAGCTAATGGACCCGTGTAGGCTCCAAACCCTAAGAAGCAATTAGAAGGGGGTGTGGATTATGCTAATGAGGACAAAGCTCCCTGGCTCCTGAGGTCCCAAACAGCAAACTGAAAGTTGAGTGGAGGGCTGGCAAGATGGCTCAGCAATTAATATTAAAAAAAAAAAGAAAGTTGAGTGGAGAAAGGACAGAGGGTCTGTAGCAGCTTACAAAGGAAGAAGGAATCCCACCCCCATTCTAACTGAAGCATTGCCTGGCCAGCTTGCCACAGGGGATCCCCTCATGGCAGGTGGCCTGGGCAGCTTCTGTACCCTTTTCCCCACAACAGGAATACTCCAGGGTTCTAAGGCACGCGTCTGTCTTATTCAGTTTCTAGGTACGCAGTAGGAACTCAGTAAGCTCACTAAGTGAATGTGTGGTACTTTCCAACAG
Seq C2 exon
GCTCCCAGAGACATCTCAATCTGTCTACTTCTGAAGTGCCTTCCAGAGTTCCAGTCACGATAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000024670-Cd6:NM_009852:5
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:
PF0053013=SRCR=WD(100=92.2),PF054546=DAG1=PU(24.1=27.5)
A:
NA
C2:
PF054546=DAG1=FE(18.1=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal4)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCTGACTGGAGGCATTGACTC
R:
TGACTGGAACTCTGGAAGGCA
Band lengths:
344-1631
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: