Special

MmuINT0141077 @ mm9

Intron Retention

Gene
ENSMUSG00000034684 | Sema3f
Description
sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3F [Source:MGI Symbol;Acc:MGI:1096347]
Coordinates
chr9:107592017-107594618:-
Coord C1 exon
chr9:107594499-107594618
Coord A exon
chr9:107592111-107594498
Coord C2 exon
chr9:107592017-107592110
Length
2388 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGC
5' ss Score
9.88
3' ss Seq
AGCCCCTTTCTGCCCTGCAGGAT
3' ss Score
10.04
Exon sequences
Seq C1 exon
GGAGAGTGTGGTAACTTCGTCCGGCTCATCCAGCCTTGGAACCGAACACACCTGTATGTGTGTGGGACCGGTGCCTACAACCCCATGTGCACCTATGTGAACCGTGGCCGTCGCGCACAG
Seq A exon
GTAAGCTCCTGCCAACCCTAGCTCTGTGCTGTCCCCCTCTGGTGGCTGTGTTCCAAGGTCCTGATGGGAGGATGGGCTTAAGCCCCATCCTTAACCCTTCCAGGCCCCATGGCCTTGGGTGAGTAAGTTGTTCAGCTCTCTGAGCCTCGATTTTTCTCACCTGGAAATTGGGTTCACAGTTCCTTTCGAACAGGTCGATGTGAGGAAGAGGCAGTGAGTTAGTGCTCTCCAGCTAACGCTGTGCCTGGCGCATTAGTAAGCATTTGCCCTGCACGGGGCAACCGTTCTCTTGGCCATGTCTATGGAGCTGCCGAGTCGGAGGGCCTTGGTGGCGTCTTCGGTATTCCAGGAGGCTGGAAGCCTGAGCCAGCTTCCACCCTCTGGCCCCAGGGGAGAGCTGCCTTCTCCCCCAGCTCCGCTCCACCCTGCCTGCTTCTGCCCTTTTCCATTTCCATGTGGGCATGGATGTGAGTTGATGTGACCTCGTAGGGCATGCGTGAGAGCGACTGAACATACGGGGCACATGGTGTGCAGGCGTGAGCCAATCCTGTGTGTATGTGTGTGTACACATGCATATCTGTTCTCTGGGGGCCCATGTGTTCACGTGTGTTCCTGGCCTGTGTGGTATGAGAGGCTGGCAGCCCAGGCCCGCTCCCCCAGCCCCTGCCACCCCCAGCTCTAACATCTATCGCCCCCAGCTCTAACATCTATCTTCCCAGGCCCTACCGTGGACCCAGATGCAGGTGGTCAGAGGCCGAGGCAGCAGGGCCACCGATGGTGCCGACCGCCCGACGCCCACAGCCCCACGCCAGGTGGGCCTCCTCCTTCTAGTCTCTCGCCAAGCTAAACGACCTCTGAGCTCAGTTTACCCTGGGCCTGGCCCCAGGGCCAGCCCCCCAATGTCTCCCTATACCCTCATGCCCCCACCCCACTCCCACCCCTTCCCCTGCAGTGCCCTCAGGTTCTGAAAGCAGCTCCAGCTGGACTCTTGTCAGCCTCAGTGGGACCCCTGCAGGCAAGGAATCCTGAAGCCACCAGGTGGGGAAGACAGGAGTCCTGGGGTCAGTCATGCCTCAGCCCTGAGAAATGTGTGGAGACGCACATGACCACATAGCAACCTGTGCCTGAGCATATTCACAGTGGGTCTGGCACAGGACTCCTCCGTGTCTGTTCCCATGCCTTCCATGGGGCATGTATGTAGATACAGGTGTCCTGCCCATTCTCATATGTGGGATCTCCTTCAAGGTAGTGTGTCTGACAGTTAGTCTAGCCTGGGGGTCTGGGCTGGGGAAGGCAACCTGGGGCTGGGCAGGGGCGGGCAGGGGGGCAGAGGCTGCCGGTGAGTGACAGCATGTGAGTATGTGTGAGAATATATATTTGTGCATGACTCTGTGTGTGTGTGTGTATGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTTTATCTGTCTGATGGGGAGTGTTGAACATCTCAGGCTATCTAGATTCTGTGTGTGTGAGTTTGGGATGAACAGTGGCTTAGGTGTGCCAGTTTGTTGTGTGCCGATCTGTGTGCAGCTCGTGTGTGTACAGGAAGTAACGTGAGCAGAGTGTAGCTGAAAGCAGACCTGTGCGTGCCTTCCCGTCACCATCCTGCCGCCTGCTGCCACTTCCTCTGTGCGTCTCTCCTCTTCCCTCTCCCTCCCTCTTCCCTGCCTTTCCCACCAGGCCTGTGAGCTCATCCTGGTCCCAGGGACTTCGCAGGCCTTCCTCCTAGCATCTTCCAGGGTGAAATGGGCAGTGTGGGGTTGGATGATGGTTAACTTTGTGAATTCCACGTGGTCTCAGCTGGATTCCCCCAACTTGGCTCTCTGGGGAGATGTGGAGGGATAGAAAATCCATGACCTCTTGGTCCATCCTGAGGTCCACAGGTAGAGCAAAAACCTGGAGACAGCCTTGGAGCTCCCTGGTTGGACCTGAAAGTAGGACAGGACCCCAGGTCCTTGAACTGTGGCTCCTGCCCTACCCAGGTCTGCAGCCCCTCCCTGGCCTAAGATAAACAGCTGTAGCTCAAACTATCCAGCCTCTGTAGTCCCAGGGGTTTGTTGGCATCTTCTGGGCTAGTTGGCACAAAAGTACTTTAGCCCTATAAGCCCACCACCAGTGGTCCTGAAGACCTGGACCTCTGAGAGTTGATTCTTAGGTCTTACCTGAGGCATAGAATCAGAGAGTAACCCCCTTGGAAATACCATGGGCTTGCCCTAGGAGACCTGGCAAGGACCCTGGGAGTGGGGTATGGTGGGTGGACTTTGGGTGGCCCTTGGGGCTCATTCTTGCCCTAGGAACCTTATGAAACTTATCCTTGTCTGTGGGACTGGCCTGGGTGTGCTGAGCCCCTTTCTGCCCTGCAG
Seq C2 exon
GATTACATCTTCTACCTGGAGCCTGAGAAACTGGAGTCAGGAAAAGGCAAATGTCCCTATGACCCCAAGCTGGACACAGCCTCAGCCCTCATCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000034684-Sema3f:NM_011349:5
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=0.229
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF0140314=Sema=FE(31.7=100)

							
A:
NA

							
C2:
PF0140314=Sema=FE(6.6=100)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000079400





     
      









    
Other Inclusion Isoforms:
ENSMUSP00000040904, ENSMUSP00000040904f3315A
          









    
Other Skipping Isoforms:
NA
  



Associated events







Other assemblies


mm10




Conservation


Human
(hg38)
chr3:50175189-50176767 
ALTERNATIVE
HsaINT0147298
(SEMA3F)
Human
(hg19)
chr3:50212622-50214200 
ALTERNATIVE
HsaINT0147298
(SEMA3F)
Rat
(rn6)
chr8:116448585-116450159 
ALTERNATIVE
RnoINT0132892
(Sema3f)
Cow
(bosTau6)
chr22:50739901-50741533 
ALTERNATIVE
BtaINT0130771
(SEMA3F)
Chicken
(galGal4)
chr12:3178544-3181614 
ALTERNATIVE
GgaINT1027092
(Sema3F)
Chicken
(galGal3)
chrUn_random:37252900-37256379 
ALTERNATIVE
GgaINT0002848
(Q8AXA8_CHICK)
Zebrafish
(danRer10)
chr6:42888599-42892974 
LOW PSI
DreINT0132619
(sema3fa)
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"