MmuINT0106191 @ mm9
Intron Retention
Gene
ENSMUSG00000002341 | Ncan
Description
neurocan [Source:MGI Symbol;Acc:MGI:104694]
Coordinates
chr8:72636400-72636799:-
Coord C1 exon
chr8:72636625-72636799
Coord A exon
chr8:72636528-72636624
Coord C2 exon
chr8:72636400-72636527
Length
97 bp
Sequences
Splice sites
5' ss Seq
TCGGTGAGG
5' ss Score
8.99
3' ss Seq
CACTCCCCTCGTACTGTTAGGTA
3' ss Score
7.01
Exon sequences
Seq C1 exon
GCGTCGTGTTCCATTATCGGGCGGCCCGGGACCGCTATGCGCTGACCTTCGCTGAGGCCCAGGAGGCTTGTCGCCTAAGCTCTGCTACCATCGCTGCCCCACGGCACCTGCAGGCTGCCTTTGAAGATGGCTTTGACAACTGCGACGCGGGCTGGCTCTCAGACCGCACGGTTCG
Seq A exon
GTGAGGGGGTGCGCGGGAGGCATGGAACTGGGGGGTCGCTCCTGGAGAAAGAGGCTCCAAGAACACACGGCAATAGCCACTCCCCTCGTACTGTTAG
Seq C2 exon
GTACCCGATCACTCAGTCGCGTCCTGGTTGCTATGGTGACCGCAGCAGTCTCCCGGGTGTTCGGAGCTACGGGAGACGCGACCCGCAGGAACTCTACGATGTCTACTGCTTTGCCCGCGAGCTAGGGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000002341-Ncan:NM_007789:4
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:
PF0019312=Xlink=PU(60.4=98.3)
A:
NA
C2:
PF0019312=Xlink=PD(38.5=84.1),PF0019312=Xlink=PU(0.1=0.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGATGGCTTTGACAACTGCGA
R:
GGGCAAAGCAGTAGACATCGT
Band lengths:
167-264
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: