MmuINT0142974 @ mm9
Intron Retention
Gene
ENSMUSG00000059013 | Sh2d3c
Description
SH2 domain containing 3C [Source:MGI Symbol;Acc:MGI:1351631]
Coordinates
chr2:32600271-32601809:+
Coord C1 exon
chr2:32600271-32600399
Coord A exon
chr2:32600400-32601354
Coord C2 exon
chr2:32601355-32601809
Length
955 bp
Sequences
Splice sites
5' ss Seq
GAGGTGAGC
5' ss Score
8.7
3' ss Seq
TTTCTCCGTTCCTTCTGTAGGTC
3' ss Score
13.56
Exon sequences
Seq C1 exon
TTCTCCAAGGAGAAGTACATTCTTGACTCCTCGCCAGAGAAACTGCACAAGGAGCTGGAAGAGGAACTGAAGCTCAGCAGCACGGACCTCCGTAGCCATGCCTGGTACCACGGACGCATCCCTCGTGAG
Seq A exon
GTGAGCAAGCCCCAGGCCTATTCATTGGCAAGGCTGAGGTTTTAGTCTTACCATTTACTGTGTGACCTTGAGGGAATCACCTTGCCTCTCCAGGCTCCAGCATCCTCATCTGAGGAATGGAGAGATAGTTCCTCAAAAGGCAGTCATGTTCTGCATAGAGAGACCCAAAGGGAGGGACTGTTGTGAAGGTGAGATGAGCTAAGGCAGATAGGGTAGGATGCCTGGTGCCGGTAAATGCAAGCATGAGGGGTGTTGTTCGAACTGTGTTTCGTTATTCCTGGTTTATAGATCAGCCTCCTGTGGATTTGGCTAGAGAATATCCATTTTTGGGCTACTCAGTTTTGGCCAAGTTTGAGTATCTGGCCTGAGATAACTTTATAAGTCACAGACCTGAACCGGTGGGTCACCTGGCCCTTTGCCCCAGCACAGGGGCTCCAGGATGTAGAGAAGAGATGAGGTGGCAGCTTCCTTAGAGGATGCTAACCCAGAAGGGCACAGAGTATCAAGCCTTTCACAAAGGTGTAAGTATAGAGGAGTGCTGCACAGATGTGCTGTAGGCAGAGAAAGCATCTCGAGGGAGCAGACACCCAGAGCTGTGGCTGGGGCCTGAATGGCTACAGGAGAGTGCCTGGAACTTACTTTGCCTTGTAGGAACCCTGAGAGGGGCTGGGTCTGAGACCTAGATCTCTGATCACAGTGATTTCAGCATTTCCTGCATCCCTGCATCCAATCCCAAGTGCCACCTTTGGCCATTCCTGGGCCTCTGTGTCCCTGACCCATGGCCTCAGCTGAGGTGCCACCTTAGGCTCCGGTCCTAAGCATTAGATGTCTGATGTCTATTAACCAGATCCTCTACGCTCTAGATGCTGTCTTGGTGTCCCAAATTCAAAGTCACCATGTCCCCTAACCCTTTCTTCTTTAGCCACCACGCCTAATTTCTCCGTTCCTTCTGTAG
Seq C2 exon
GTCTCTGAGACTCTGGTGCAGCGGAACGGCGACTTCCTCATCCGAGACTCACTCACCAGCCTAGGGGACTATGTGCTCACGTGCCGCTGGCACAATCAGGCCTTGCACTTCAAGATCAACAAGGTGGTGGTGAAGGCCGGAGAGAGCTACACCCACATCCGGTACCTCTTCGAGCAGGAGAGCTTCGACCACGTGCCTGCCCTCGTGCGCTACCACGTGGGCAGCCGTAAGGCCGTGTCCGAACAGAGCGGGGCTATCATCTACTGCCCTGTCAACCGCACCTTCCCACTGCGCTACCTCGAGGCCAGCTATGGCCTGAGCCAGGGCAGCAGCAAGACTGCCAGCCCAGCCAGCCCCTCAGGCTCCAAGGGCAGCCACATGAAGAGGCGAAGCATTACCATGACTGATGGACTCACCACTGACAAGGTCACCCGCAGCGATGGCTGCCCCAACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000059013-Sh2d3c:NM_013781:4
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.054 A=NA C2=0.283
Domain overlap (PFAM):
C1:
PF0001719=SH2=PU(9.9=18.6)
A:
NA
C2:
PF0001719=SH2=PD(87.7=46.7),PF0500012=RNA_pol_Rpb1_4=PU(74.5=25.0)
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:
CTGCACAAGGAGCTGGAAGAG
R:
AGATGATAGCCCCGCTCTGTT
Band lengths:
349-1304
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: