MmuINT0053358 @ mm9
Intron Retention
Gene
ENSMUSG00000050272 | Dscam
Description
Down syndrome cell adhesion molecule [Source:MGI Symbol;Acc:MGI:1196281]
Coordinates
chr16:96871600-96873804:-
Coord C1 exon
chr16:96873687-96873804
Coord A exon
chr16:96871764-96873686
Coord C2 exon
chr16:96871600-96871763
Length
1923 bp
Sequences
Splice sites
5' ss Seq
TAGGTAACC
5' ss Score
6.66
3' ss Seq
TTTTTCTTCCTGTGAGGCAGTAA
3' ss Score
0.5
Exon sequences
Seq C1 exon
CTCCTGCACGGATCCTCACGTTCAGCGGGACAGTGACTACTCCATGGATGAAGGACATTGTCTTGCCTTGTAAAGCTGTTGGAGACCCGTCACCTGCCGTAAAATGGATGAAGGATAG
Seq A exon
GTAACCAGCAACCCAATGTATGCCTCTTAGTGAGCCCTTAGCCAATACCTCAAGCAGCCTTGTGGACATCGGTGTGTAAAGAGTGTTTCTTGTAGTTCATGCTAGCTCCAAATTCATGGTGTATTATTAAGGGTGATATTAAGTTTCTGTCCCCCCACCTCCATTCTCATGGTGTTAGGATAACAGGCATATACCATCATGCCCAGTACATTTGGTGCAAAGCGTCAAACCCAACACTTCACGTATGCTAGGCAAGCACTCTACCAACTGAGCTACATCCCAACACCTACTTTATGATAGTAATAGAAGCTGAAGAAACCCAGCGCTCCACTGAAACGAGGCAGAAAAATCAGTCCACACCTACTTTTGAGCATGCCAACTGTATCAGGGGAAATTGCTTTAAAACATGTGGTTTTGATCATCTGTATGTGTATCAGTCTTCTATTAATCCAGACCCTAAAATTCAGGAAAACACTTGTGAGGAAAGGAGCCAGACCAACTAAGCATCACTGTGGGAGTTTGCTCTATATTACTGGGGAATGGAGACTAGGTGCTCAAGTTATCAGGAACTTTACTAGCTCTCTCCCTCTCCCTCTCCCTCTCCCTCTCCCTCTCCCTCTCCCTCTCCCTCTCCCTCTCTTTTGAGATAATGGACAATCTAACCTAAGGCATAAGCCCCGGGAAGGAACTTACTTAAGTAATGGAATTCAGGGGTTGGAGAGATGGCTCAGTACTGACCTTGCAAGGGACCTGAGTTTTATTCCTAGCCCATATGAGTTGTGAGATACTGGATAGTGCCTCATAACTGCCTGTAACTCCAGTTCTGAGGGGATCCAAAAGCCTATTGACACCATGTGCACCCCTCTGCCCACCAACACAGAACTAAAGTAAAGTAAGAGAACACAGTTTTATGTAGATCCAGCACTTGAGAGACTAGAGCAGGAACATTGCCAGTTGCAAGGCCAACATTCTGGGCTACATAGCAAGACCCTGACTTGAGAAAAAGAAATGAAACCCATTAGGACTTGCCTAGCGGAAAAAGCTGGTTCTCCATGCTCAATATTGATTACTATAATAATAAACCAAAAAGAGAAGGGAAAGAGGATATGATGAGTCCTGTTCACGTGTCTCTTAAACATGCTTTATCGCTTTGCAGGGGAAGAAATTAAGATATAAATAGAGGCTGAACATCCACTAATAGTCATGGAGATTTAAAATAGCGGATTCAGAAGGGTGCCTATTTTCAAACAAAAGCACTTACAAGCATAAATGATCGAAATAATGGGTTGGACCCAGCAAGCAATTTTCTCATTGCATTTTAAGTTGGTTAATCCAAAGCAAATTCATAAGCTCCCTGGGTCAAGCTGGCCCTCTGCCTTACCTAGGAGTGACTCCAGAGGTCATGATGACAGACACCTCTTCACAGGAGGGTCAGCTCCATGCTCCCTCGAGATGCCATCTTACCCTGTGCATGTCAAGTTCATTAAGAACTGTGATTTTAAATTGATTTTAAGTCTGTAAGAGATCACAAAATTTGGTTTGCCATGCATGATTTTGTCAAGCTGGCCCCTCTACCAGAAAGAGAGTGTCACACAGTTGCCACTGGGAGAAAATCTCCAAAGCCAGAGCTGGGGGAGGAAGGAGAGACATGTTAGATTTGACAATAGTCATGGCTTTTGGCCAATAATTAACAAGATTCCTGGCCATTGACACAGATCTAGCCTTCTGCATGATAATTTTTCTTTTAATCTCTGCTAGTCAATGGTTTGGTCACATAATCAGAGCACAGTTATTTCATAATGCAAAAATAATTGAGGTTGCAATTTCCTGTTTGCTCCAGAGAAAGGCTTGATGCTTCTTGGTGACCTCAGCTAATGTGGTTATAATTTCTCTAATCTGTGCATTTTTCTTCCTGTGAGGCAG
Seq C2 exon
TAACGGGACACCCAGCCTGGTGACGATTGATGGCCGCAGGAGCATCTTCAGCAATGGGAGTTTCATCATTCGGACGGTGAAAGCAGAGGACTCTGGCTATTACAGCTGTGTTGCCAATAACAACTGGGGATCAGATGAGATCATATTAAATTTGCAAGTACAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000050272-Dscam:NM_031174:22
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.050 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0767911=I-set=PU(40.0=90.0)
A:
NA
C2:
PF0767911=I-set=PD(58.9=94.6)
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:
CTCCTGCACGGATCCTCACG
R:
ATGATCTCATCTGATCCCCAGT
Band lengths:
262-2185
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: