Special

MmuINT0142976 @ mm9

Intron Retention

Gene
ENSMUSG00000059013 | Sh2d3c
Description
SH2 domain containing 3C [Source:MGI Symbol;Acc:MGI:1351631]
Coordinates
chr2:32602542-32605205:+
Coord C1 exon
chr2:32602542-32602666
Coord A exon
chr2:32602667-32604672
Coord C2 exon
chr2:32604673-32605205
Length
2006 bp
Sequences
Splice sites
5' ss Seq
CTGGTAAGC
5' ss Score
8.69
3' ss Seq
TCTCTTTCTCCTCTCTGTAGTAA
3' ss Score
9.09
Exon sequences
Seq C1 exon
CACCTCATTACCCCATCCTCGAGACTCCATCCGAAACTGTGCCCTCAGCATGGACCAGATCCCAGATCTCCACTCACCCCTGTCTCCTATCTCCGAGAGCCCCAGCTCTCCTGCCTATAGCACTG
Seq A exon
GTAAGCTAGCAGGGGGTAGTCTGTAATGCTGTTGTCGTTGGTGGGGGACATCGGTTACCTGACTGTTTCTGCCTCTGGGCTGGGAGCAGTGTCCCCACGAATGTTCTAGAAAAGCCTGTGGCAGAATCGCTGGTGTTGACACACAAGCAACATCCGGTGAATAGTGTTCCCATGGGTGCCAGGCAATGGGCACAGAATGGGTTCTCAGTGAGAGTGGCAGGGTAAAGTCTGCTGGGGGTGCAGCTTGTCACGGGGCCAGGCCTTGGGGCTGTGATGTGCACAGTGTTTGACTCCAGCAGACAAAGTTCCCACTACAGCTGCCTTACCAAGGGCGTTGGTAACAAGAGCATCATTCCTACCTAGGTCCTGCTTTGAGCTTAGACCAGGCTAGCTCAGGCTAGCTCAGGCTAGTGTGCTTTGCTGCTCTTTTTTTTTTTTTTTAAACTAACTTTTAGAGCAGTTTAAGATTTCTGAAAAACTTGAAATCATGGGATCCTGTGCTTATAAATACAAATAAAGTAAAAATATGTCCCCAGTTTATTTCTCAAAACAAAGCAAAACAAACCTCAGACTGTTAAGCAAAATGTCTTGCCCCGCAAGGCAGTCAGAGCATTGAGAGGGGTGGCTTCCTGGAAGTCTCGGCCTGGAGGGAGCACTCCATGCCTCTGGAGTGTTACTATGTGCCCCCAGAAGTCTTTCCTGTCGTCACATACACTTGCTTTCAAAACAGCATGGTCATGTGAAAACATTTATTTACTTATTTGTTTTATTATTTTAGACGGAGACTCAGTATGTAGCCTTGGCTGGCCTGGAGCTCACTATGTAGACCAGACTCAGAGCTCTGCCTGCCTCTATCTCCTAAGGACTGGAATTAAACATGCCTACCACCACACCCAGCTTATGGGTTTGTTTTTGTTTTTTTTTTTTTTGTTGTTGTTGGTTTTTTTTTTTGGTTTTTAATGGGACAATTTCCAGTAATCACCTAGGAGATAACGGCTTCTATCCTAGCCCTACCAGGTTGAGTGACCTCGGCAAGTCTCTAAGCCCTGAGCCTCCACTTTCTCAGCTCAAGACTGAGGACCATAAAAGTCCTTACTGCCATAGAATGGGACACTTGGGGTATTGTTTGTTTGTTTTTGAGACAAGGTCTCACTAAGTAGCTCTGGCTGCCTGGAACTTGTTATATAGATCAGGCTAGCTCAAATCTACAGAGACCTGGTCATCCCTGAGCGCTAGGGCTGCAGGTGTGCACCACCCCACTGGCTTTGCTGTTTTGCTTCTGAGTTCTTTTACATCCCTTTACTTATTTGTGTGTGGGGTATGGGGGGACACAAAGGCCAAGTGACAACTTCCCTGAGTTCACTTGGTGACAGCTTCACCAGGCATCATACTTCAGCAGAGCTTAGCTTCCCTGGACCGCCTATGTGGCTTCTGATGTTCTAGTCTCTTGGGGCAGCGGCTCCACTGATACAGGGAAGTGCTGAGGACCATAGAGTACCTCCCTCTACATTTTGGGATGTGGGACATTACTCTATACACAGGATGCAGACTATTCTTTGAGAGAACAGGGAAGGGAGGCCCCATTAAAAAAAAAAAAGATTTGTTTATTATGTATACAGTATCCTGTCTGCATGTCTGCCTTCAGGAGAGAAGAGGGCACCAGATCTCATTAGAGATGGTTGTGAGCCACGATGTGCTCGCTGGGAATCGAACTCAGGACCTCAGGAAGAACAGCCAGTGTTCTTCACTACTGATGTATCCCTCCAGCCTCGGAGGCCCCTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGAGACAGGGTTTCTCTGTGTAGCCTTGGCTGTCCTGGAACTCACTCTGTAGATCAGGCTGGCCTCGAACTCAGAGATCCGCCTGCCTCTGCCTCCCAAGTTCTGGGATTAAAGGCGTGGGACCACCACGCCCGGCGGGAGGTCCCATTTTTAAGGGTAGAGGAGATAACTAGTTTTCTCTTTCTCCTCTCTGTAG
Seq C2 exon
TAACCCGAGTCCATGCTCCTTCTGCCACCCCCTCTACTTCAGCACAGCCTGCCTCCCCAGTTGCCCGCCGCTCCAGCGAACCTCAGCTATGTCCTGGAAATACTCCAAAGCCTCCTGGGGAGTCAGACAGGGCCCCTCACGCAAGCCCATCCCACACCCTCTGCAAGGCCTCGCCATCACCATCACTCAGCAGCTACAGTGACCCGGACTCTGGTCACTACTGTCAGCTCCAGCCTCCGGTCCGTGGCAGCCGAGAGCAGGCCGCAGGAGAGACTCCCCGGAAGGCTAGGGGCTCCGGAGAGAGGCAAAAGGAACTGTTAGAAAATGGAGTCTCTGACGGGGAGTGGGGCAAGACCTTCACAGTCCCTGTAGTAGAAGCCACCTCCTCTTTCAACCTGGCTACCTTCCAGTCCCAGCTGATCCCCAAGGAGAACCGGCCTCTGGAGGTGGCCCTTCTGCGCAAGGTCAAGGAGCTGCTGTCTGAGGTGGATGCCCGGACACTGGCCCGGCATGTCACCAAGGTTGACTGCCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000059013-Sh2d3c:NM_013781:6
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=1.000 A=NA C2=0.635
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF0500012=RNA_pol_Rpb1_4=PD(23.5=80.0)

							
A:
NA

							
C2:
PF0061714=RasGEF=PU(10.1=9.6)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000073866





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000108868, ENSMUSP00000122613
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr9:127745100-127751171 
ALTERNATIVE
HsaINT0149197
(SH2D3C)
Human
(hg19)
chr9:130507379-130509425 
ALTERNATIVE
HsaINT0149199
(SH2D3C)
Rat
(rn6)
chr3:11785252-11787552 
LOW PSI
RnoINT0134567
(Sh2d3c)
Cow
(bosTau6)
chr11:98441820-98443330 
LOW PSI
BtaINT0132414
(SH2D3C)
Chicken
(galGal4)
chr17:4919761-4919954 
LOW PSI
GgaINT0123787
(SH2D3C)
Chicken
(galGal3)
chr17:5547951-5548144 
LOW PSI
GgaINT0123787
(SH2D3C)
Zebrafish
(danRer10)
chr10:10300892-10303614 
LOW PSI
DreINT0134220
(sh2d3ca)
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
No suggested primer sequences

				
R: 
No suggested primer sequences

				
Band lengths: 

			

		

	





	
Functional annotations
(Submit an annotation)

	


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






Retrieved from "https://vastdb.crg.eu/wiki/Special:VastDB"