MmuINT0142978 @ mm9
Intron Retention
Gene
ENSMUSG00000059013 | Sh2d3c
Description
SH2 domain containing 3C [Source:MGI Symbol;Acc:MGI:1351631]
Coordinates
chr2:32606472-32607205:+
Coord C1 exon
chr2:32606472-32606587
Coord A exon
chr2:32606588-32607033
Coord C2 exon
chr2:32607034-32607205
Length
446 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGG
5' ss Score
10.51
3' ss Seq
TGATCCAACCTCTCTCACAGGTT
3' ss Score
8.47
Exon sequences
Seq C1 exon
GTTGCTAGGATACTGGGCGTTACCAAGGAGATGCAGACCCTAATGGGAGTCCGCTGGGGCATGGAGCTGCTCACCCTCCCCCATGGCCGGCAGCTACGACTAGACCTGCTGGAAAG
Seq A exon
GTAAGGTGCACTGCACCAGCCCACGGCTACCTTACGGGCTGTCCCAGGGTTTCTGACCACTCTTCCTATCCCACTAGCCAATCGCAGCTTCGTGGTCCTCGGCTCAAAGCCAGTCTGATTTCCCAAAGACTGCTGTTTTATCGACCGCTTTAGCCTCTCGCTTCCCCACGTCCATCAACCTTGGCCCCGCCCACCATTCCTGTCCACAGTGTTCTTTCTAAAACTCTGCCCTTTGGATTTTGCTGATCAATTACAAGTTTCTCCTCCTGCCATCCAGATTTTGCTCCTAACTTATATTGTCCAACCAGGCTCCCTTCTCTCTGCCTGTTACTTTGGCTGCGCCCCTTAGTCGCTGTGACCTACTCTGTTTTCTGTCATACTTAACAGCGTCCCTGTTGGCCCCGCCGCCGTATGTCACGCCCCCTATGATCCAACCTCTCTCACAG
Seq C2 exon
GTTCCACACCATGTCCATCATGCTGGCAGTGGATATCCTGGGCTGCACAGGCTCGGCGGAGGAGCGGGCAGCTCTGCTGCACAAGACCATACAGCTGGCGGCCGAGCTGCGGGGGACGATGGGCAACATGTTCAGCTTCGCCGCTGTCATGGGCGCCCTGGAGATGGCCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000059013-Sh2d3c:NM_013781:8
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:
PF0061714=RasGEF=FE(22.5=100)
A:
NA
C2:
PF0061714=RasGEF=FE(33.7=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Human
(hg38)
No conservation detected
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ACTGGGCGTTACCAAGGAGAT
R:
ATCTCCAGGGCGCCCATG
Band lengths:
270-716
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: