MmuINT0053347 @ mm9
Intron Retention
Gene
ENSMUSG00000050272 | Dscam
Description
Down syndrome cell adhesion molecule [Source:MGI Symbol;Acc:MGI:1196281]
Coordinates
chr16:96937665-96939786:-
Coord C1 exon
chr16:96939590-96939786
Coord A exon
chr16:96937762-96939589
Coord C2 exon
chr16:96937665-96937761
Length
1828 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAAA
5' ss Score
8.59
3' ss Seq
CTTTTCTGCTTTGGTTGCAGATT
3' ss Score
10.39
Exon sequences
Seq C1 exon
TTCCTGCCATGATAACCTCTTACCCCAACACCACCCTGGCCACTCAGGGTCAAAGGAAGGAAATGAGCTGCACAGCCCATGGGGAGAAGCCCATCATTGTCCGCTGGGAGAAAGAGGACAGGATCATTAACCCTGAAATGGCCCGCTACCTGGTATCCACCAAGGAGGTGGGAGAGGAAGTGATATCTACGCTGCAG
Seq A exon
GTAAAAAATGCCAGCTGTGGTAGAATGGGGCAGGGTGTCCTGCGACAGTTAGTCCGCCCTCTCCCATGGCTGAGCACATGGTGGTGATGATTTGTGAATATCCTCCTGGGATTTCCTGGTGACACTCCGTCCCTCTGCCCATCTACACAGGACAAGGTCACTGAATGACCTTCAGAAGTAGTTCTTTACAGCCACAGTCCACAAACAAATAATTAAGCACTGAGAAAGAAGTCTCCCATGATAGTTGTCCTCAGAGGGGGTGACAGTATGTTTAACATTCTACAATATATATCAAGATCTTTGAGACAAAATGAATACCACAATAAAAAAATTTTTTTTCCCAGAACTAGGGAGATAGCTCAGCAGTTAAGAGTAAAATTGCTTCTTCAGAAGATCTAGATTCAGTTCCTAGCACCCGTATTAGGTGGCTCACAACCATCTATAACTCCAGACCTAGGGGACCCAATACCTTCTTGTTGTCTCCATGGGCTCATGCATACATGTACACATGCCCCCACACATATACATGTAACTGCAAATAATATAAGGGTTTTTTTAAAAAATATTTTGCTTATTTGGAGAAATCCAACATAGAGAATATACTGTCATTAATCTAGACTCACAAGCGCCTAGAGGAAGCATGTCTGTTCTTTCTCCAGCACTGTAGGTGATTGTCTAAGCAATGCTTTTGTAATACAGAGGGCTGGTACAGACATGGCAGAAGCTTGGAGCTATGTGCTTAGAACAGACAGTGGCTCTGTCTCTGGCATGCAATTTCGAAGCCCTATGGTATAGAATACTAGTGCGGTCCCAAGGATGCTGGCTGGACAGCCATGCCTTAGTTCCCATAGACAGCAGATATGAAGATGATATAGTCATTTCTATGGACACCATAGATGTCGCACATAATATATTCCCCATACTCTTGAACCCAGTCTGTGATTTGCTCAAAATAGCAAACACAGTGTGCAGAATGGCTGTTTAGAAAATTCTGACAAGAAATGGTGGGAACAAAAAACATAACGCTGCATCTGTGGGAACAGAGAGGTAGGTTCAGAGGGCTGACGCAATCATAGATGTCCCTTATGCATGGTTCTTTAAAATAATACCACTTAGAAAAAGAGGGAAGTATATGGAGTATATGGACCCACCCACAAAAGCTCATGTGAGTCACACATTCAGTCCACACATGGGAGCAGTTTTCCCTCAGATTGTATAGACATGTGTGTGCATTTGTATGCCAGTGTGTATCAGCATCTGTTGGCCTGTGGGTGAGTATGTCTTTGTCAGTGTGTTTGTATGTGAGTGCATATGTGAGGCCAAGTCTGTGAGCTTGTGTGTACATGTAGGAATGGATATGTGCAAGTGCTATGGTTTGTGTCTAAGTACACATCTCTGAGTGATTCTGTGAATGTGTGTGTATCTCTGTATGTCTCTCTGTATACCCATGGGTGTGAATGGGAAACAATATGTAAGAGTGTTTCCATGTAGGGTATGTGTGTATGAGTGTGCCTGTGCCCATGAATGTGTTGTTTGTGCGTCTGTATGTATTTGTGTGTATTAGTGTGTGTGACTATGGATATGTCTGTGTATCTGTGTGTCCATATATGTGAGTGTGTATCTGTGTGTGTCCATGTAGAAGTGGGAATCTTTATGTGTGTCTCTGTTTGTATTGTGTATGTGTCCATGTTTGTAAGCAATGACTGAGTGCTGGAGTTGGGAGGAAGGAGGGAAAGGGTAAAAGCCTATTTTCCCACCAGAAGCCATGATGGCTGATCTCCAGCTCAAGTTAGTAACTAAAGTGAGCACTTTTCTGCTTTGGTTGCAG
Seq C2 exon
ATTTTGCCAACAGTGAGAGAAGATTCCGGTTTCTTCTCCTGCCATGCTATCAATTCATACGGGGAGGACCGTGGAATAATTCAACTCACAGTGCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000050272-Dscam:NM_031174:12
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.106 A=NA C2=0.212
Domain overlap (PFAM):
C1:
PF0767911=I-set=PU(66.3=95.5)
A:
NA
C2:
PF0767911=I-set=PD(31.6=90.9)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TTCCTGCCATGATAACCTCTTACC
R:
CTTGCACTGTGAGTTGAATTATTCCA
Band lengths:
294-2122
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: