Special

MmuINT0141088 @ mm9

Intron Retention

Gene
ENSMUSG00000021904 | Sema3g
Description
sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3G [Source:MGI Symbol;Acc:MGI:3041242]
Coordinates
chr14:32039572-32042697:+
Coord C1 exon
chr14:32039572-32039705
Coord A exon
chr14:32039706-32040927
Coord C2 exon
chr14:32040928-32042697
Length
1222 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGT
5' ss Score
10.67
3' ss Seq
CCCTCCGACTCTCCCTGCAGGTG
3' ss Score
13.66
Exon sequences
Seq C1 exon
AAGCAGCTTCGGGGCTCATGACCAGAGTCTTTGGCACAGAGCACAACAGCACCTTCCTTGAGTGCCTGCCCAAGTCTCCTCAGGCTGCAGTGCGCTGGTTCTTACAAAGGCCAGGGGATAAGGGGACTGACCAG
Seq A exon
GTGAGTGAAGACCCCACCCAGAGATCCTCTTCTCTTCCTGAACCCCAAATCCTAAGCTCTAGAAAGGAACTCTGGAGTGAGCTAGCCAAGTTCTTCCTGAGAAAAATGTGTACTATACCCTGGGATACCTATGAGGAGCTGCCCCCATTTCTGTCTAGGCTGCACGTAGCTCCAGCCTCCCTACTCTGTGAGGGGGATGCTGGAGGTCGAGGAGAGGGAATGGGGGCTAAGTTGTTCTGGAAGGTTCCTATGCTAACGCACGTGGCTTGGCTTTGAAGGGAGCTCTTCCCTCGAGTTTCTTAATTCTTCTCTGCCTCAGACCTGGTCCCTGACCAGCACATTACCTCCCAAAGCAAGCTGTCTGCCCAAGGCCTCTTTTCCCCTTGACTGGGAAGGTTTGTCAACCCCTAAGATGGCTTCAGTCTAGGGCTTGAGGCCAAGCATGGGCAGAGCGGGAGTCTGGAGCTGCTTTCCCATGGGGGGGGAACGACAGAAGGAGGGGTTTGGTTACAGGAGGGGCTCTTCCTCCAGCTCAGGAGCCAGGGGAGGCAAGCCTGGGACCAGCTGTAGGGCTGAGCACCGAGGAGACTCCTTGGAGTAGGGAGAGCAATGAGATGGGGTTACACAATGCTATGCTAACCACCCAGGCGGTTCCCCCTCAGCGCTCAGATGCACAGACAGGGTTAGCAGCCTGGGATCAGAGCCAGCTCTTGCCTCCCACACTCAAGTGGGCACTTAGCCCACCCCAGGCTTGGGCTGTGGACCTCACATTTGTGGGGGAGTAAGCAGAACAGACCAAGACAGGGAAGGCCCAGCATGACTGTTTGTGTGTGTGTGTAGAGTTTTCTTTAGCTCAGAGTAAAACCTCATAGACATGAACCTAACTCCTCAGCTCCTTGGGTGCTGGTGTAGACTTCTCTGAAGGTCTTAGGGCTCTGACCTGGAGACACACAACCATTCAGTCTTAGGAAAGCCTTCTTCATAGGTCCTTGTCCTGCTCTGCGGAAAGGTGAGGCCTGCCTGTCTGCAATTAGCTCATGGTCTCTCTGAGATCCTGTCACGTGGTTAGGCCCACCATGGGAAAGAGGGACTAGGCAAGGGGGGTGGAGGCAGGGCTTGGACCCGAGAATGGCAAACGTGGAAAAAGGAGTAAAGATCACAAGGTTAATGCTCTCCCCAACTCCTTGCTTCTGTCGCCTGTACCCTCCGACTCTCCCTGCAG
Seq C2 exon
GTGAAGACAGATGAGAGAGTTGTGCAGACGGCCCAAGGGCTGCTGTTCCGAAGGCTCAGCCGCCATGACGCAGGAAACTACACTTGCACCACTCTGGAACATGGCTTCTCCCAGACCGTGGTCCGTTTTGCCCTGGAGGTGATTGCAGCTGTGCAACTGGACAGCCTGTTCCTTCGGGAGTCAAGGCTAGAGGAGCCCTCAGCCTGGGGAAGCCTGGCCTCTGCCTCCCCCAAGACTTGGTATAAGGACATCCTTCAGCTCACGGGCTTCGCCAACCTGCCCCGTGTGGATGAGTACTGTGAACGTGTATGGTGCAGGGGTGTCGGGGAGCGCTCAGGCTCCTTCCGCGGAAAGGGAAAGCAAGCGAAGGGCAAGAGCTGGGCAGGGCTGGAACTGGGCAAGAAGATGAAGAGCAGGGTGCTGGCTGAGCACAATCGGACACCCCGGGAGGTAGAAGCCACATAGAAGATGACTGAGGAGCAGGTGGTCGGGCTGGGCTGGGGGACTCAACGGTATCTCTCTCCCACCCAGCTAGGAAAGAGGAGTCCAGAACTCCTGATTGATTACCTCTTAGAGGAAATCTCCACCACCTACAGGAAAGACTAGGGGTTGGTGGGAGGAGCCTTGCACCTCAGCCTACCCCTGCCTTTCTCCGAGTTCTCAGTCCCGGGCTGGAACTGGCACCTCCAGACCACTTGTAGTCCCAAGGGGCCTGCTATTTGTTCTCAGAGATGGTGTGGCTTCCGGAGCACATTTCCGGTTGTGCCCAGAGGCAAGGCGGGTGGTTCTTTCCCAGCTTGCTGAACAATGGCCATTCTGAGTGACCCTCTGAGTGGGTGTATGGGTGGCTCTAAGGGAGTATATATTGTCAGTCCACCAGAGGAGGGGAAAGTAGATTCCTAAGGTAGAACCTGATAAGAAACACTTGCCCCACAGAGGTGTGAGAGAAGGTGGAGGCGCTGAGGAGGTGGGGTTGTGCTGTTTATCTGTCTCCATGCTTTGGAATCTAGATGATTCCCTGCCTCAGCTCCCTCCCATCTCCTACTCACAGAGGCAGGAACTGCTGGGACCTGGAGGTTGCCTGGGCCTGGCCCTTGCCCCCTTTTTAAACTTGGAAGAGTTGTCTCACAATATGATACCCTTTCCCAGGTCCCACATTGTCAGGCCAGGCTTGCTGGGGTGCTCACACCTCACCATCAGAGTGTCTTCCTGGGACCAGGGGAAGGTTCTGTGGACCAGAAAGAGGAAGTGGGGAGCTGGAGGGTAGGAGTGCCTCGAAGGATGGGCTACCTTTCCGAGGGTGAGGCGGGCATGCTCAGGCCGGTGAGGTTAGCAACGGACACTCTGAAAACCAGCAGCCAGTGGTGAGGATCGGCCTCCTGGGCTTTGTCTAGGGCCACGAGGAACTAGAGAGAGGTGAGACCATGGGTCCATGGGTCCATGAGCAGGTGTCCTCAAGAGCCAAGGTGACATTAGTTGGTTCAGGAGCCCCTGGGCAGGCCAGATACTTCCAATGCTAGAGTCTCTACTGAGGGTGGTCATGACAGTTCGTTTACAAGACTCCCATGGTTTTTTGTGGTACTTGGGATTGAATCTAGGGTCTCATGCATGCTGGATAAATGCTCTACCACTGAGTGAAAGCCCAGCTCTCTCTCTATGGGAGAACAGAAAGCTGGTATGGTAAATCCTGCTGTTCTGGGGGTGGGGGTGGGGCTGAGTGACAAGGGCTGGGGAGAAGCTTGGCCATCAGCAGTTTCTGCAGCTGGGGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000021904-Sema3g:NM_001025379:15
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
Alternative protein isoforms





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.067 A=NA C2=0.123
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF0143720=PSI=PD(1.6=2.2),PF0004720=ig=PU(48.4=66.7)

							
A:
NA

							
C2:
PF0004720=ig=PD(48.4=19.4)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000087643





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
NA
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr3:52436074-52437526 
ALTERNATIVE
HsaINT0147308
(SEMA3G)
Human
(hg19)
chr3:52470090-52471542 
ALTERNATIVE
HsaINT0147308
(SEMA3G)
Rat
(rn6)
chr16:7312238-7313503 
LOW PSI
RnoINT0132902
(Sema3g)
Cow
(bosTau6)
chr22:49006725-49008034 
LOW PSI
BtaINT0130782
(SEMA3G)
Chicken
(galGal4)
chr12:3119304-3119390 
LOW PSI
GgaINT0022444
(SEMA3G)
Chicken
(galGal3)
chr12:2946836-2946922 
LOW PSI
GgaINT0022444
(SEMA3G)
Zebrafish
(danRer10)
chr8:26552160-26553651 
LOW PSI
DreINT0132548
(sema3bl)
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
GGTTCTTACAAAGGCCAGGGG

				
R: 
CCTGCACCATACACGTTCACA

				
Band lengths: 
356-1578

			

		

	





	
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"