MmuINT0142977 @ mm9
Intron Retention
Gene
ENSMUSG00000059013 | Sh2d3c
Description
SH2 domain containing 3C [Source:MGI Symbol;Acc:MGI:1351631]
Coordinates
chr2:32604673-32606587:+
Coord C1 exon
chr2:32604673-32605205
Coord A exon
chr2:32605206-32606471
Coord C2 exon
chr2:32606472-32606587
Length
1266 bp
Sequences
Splice sites
5' ss Seq
CTGGTAAGT
5' ss Score
10.65
3' ss Seq
CCCTTTGGGCGTCTTTGCAGGTT
3' ss Score
9.67
Exon sequences
Seq C1 exon
TAACCCGAGTCCATGCTCCTTCTGCCACCCCCTCTACTTCAGCACAGCCTGCCTCCCCAGTTGCCCGCCGCTCCAGCGAACCTCAGCTATGTCCTGGAAATACTCCAAAGCCTCCTGGGGAGTCAGACAGGGCCCCTCACGCAAGCCCATCCCACACCCTCTGCAAGGCCTCGCCATCACCATCACTCAGCAGCTACAGTGACCCGGACTCTGGTCACTACTGTCAGCTCCAGCCTCCGGTCCGTGGCAGCCGAGAGCAGGCCGCAGGAGAGACTCCCCGGAAGGCTAGGGGCTCCGGAGAGAGGCAAAAGGAACTGTTAGAAAATGGAGTCTCTGACGGGGAGTGGGGCAAGACCTTCACAGTCCCTGTAGTAGAAGCCACCTCCTCTTTCAACCTGGCTACCTTCCAGTCCCAGCTGATCCCCAAGGAGAACCGGCCTCTGGAGGTGGCCCTTCTGCGCAAGGTCAAGGAGCTGCTGTCTGAGGTGGATGCCCGGACACTGGCCCGGCATGTCACCAAGGTTGACTGCCTG
Seq A exon
GTAAGTATTAGGAATGCTCACAGAGGGGACAATACCTTTATCATCTGGCTTTGGGGTCAGGAGTCAAGCAAGATGGTGAGGGACTGATTCCCAAATCCCCTAAGTACAGTGAAGCCAGTAGCTTGGGTTTTGACATCCCGGGTGTCTTTCTTGGTTCTGGGACTATGGATTGTCATCTGGCATGTCAGTCTCCATTTTCTTAGTTTAGATTGTTTTGCTTTGTTTTATTAGGGTCTCACTATGTAGCCTTGGCAGGGCTGGAACTATGTAGACAAGGCTGGCCTTGAACTCACAGAGATCTGCCTGCCTCTGCCTCCCAGTTGCTGGGATTAAAGGATTATGCCCCCCCCCACTTGCAGTCACCGCCTTCTCCTCCGCCCCCCTTCTCCTTTTCATTTCAGTTTTTAATGTGCATTGGTGTTTTGCCAGTATGTGTGTCAGTACTGGAGTTATAGGCATTGTGAGCCATCATATAAGTGCTGAGAATCGAACCCCAGTCTTTTTGGAAGAGCAGCCAGTGCTCTTAACCACTGAGCCATCTCACCAGCCCGATTTTCTTCTTTGGAAAAGTAAAAACCAAGACATTTCTACAGCTGCAGATGTGGAAGGAGGGCTGATGTTTTGGGAGTAACTTAAAGAACTTCTTGGTTCTAGTCTGCAGAAAGTGAACATCTGGTTGGGGGGGGGCGGGGAATCTGCCTGCCCCCTTGCCCCCTAACCCCCTAGTGGACAACAAGCAAAATGTTCCTTGACCCAAAAACTGTCCAGATGCCAGTGTGAGGCTTTGACTCCGTACGAACCACAGCTCTTTCCATACCCCAGTTTCTCGCTATGTAGTTTGGTATATACGCTGGTCTGAGAAATCAGGAAGTGAAAAGAATCATGTGGGGATGCAGCTGCGGGAGAAGAGGGAGAAACTGAGGTGCAGGCTCAAGTGTACAAACTTGGACAAGAAAGTTCATTCCCTTCCTGGGCCTTGGGTTGGCAATCGGGGATAATGGGATCTTGGCTCTTGATTTTAAGTATTTAACATGGCACACACCTATGGGCTTCTTTCTACTCCCCATTTTACAGATGGGGAAACTGAGGCTCACTCAGAAAGGGGGAAATCACTTGCTCCGTGTTTGCAGAGGAGCTGGGATTCAACCACCCACCCCACCCTCTGGACCCCTCTGCCAGGCGACCCTCTTAGATGAAGCTCTGACTCCCAGATGGGTTGGACTAACCCTGACAGGAAATTAATCAGCCCTTTGGGCGTCTTTGCAG
Seq C2 exon
GTTGCTAGGATACTGGGCGTTACCAAGGAGATGCAGACCCTAATGGGAGTCCGCTGGGGCATGGAGCTGCTCACCCTCCCCCATGGCCGGCAGCTACGACTAGACCTGCTGGAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000059013-Sh2d3c:NM_013781:7
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.635 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0061714=RasGEF=PU(10.1=9.6)
A:
NA
C2:
PF0061714=RasGEF=FE(22.5=100)
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:
CCGGAGAGAGGCAAAAGGAAC
R:
TCCAGCAGGTCTAGTCGTAGC
Band lengths:
352-1618
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: