Special

MmuINT0141104 @ mm9

Intron Retention

Gene
ENSMUSG00000028064 | Sema4a
Description
sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4A [Source:MGI Symbol;Acc:MGI:107560]
Coordinates
chr3:88255942-88257053:-
Coord C1 exon
chr3:88256893-88257053
Coord A exon
chr3:88256005-88256892
Coord C2 exon
chr3:88255942-88256004
Length
888 bp
Sequences
Splice sites
5' ss Seq
ATGGTGAGG
5' ss Score
7.61
3' ss Seq
CTTTCAACTCTCCACTTTAGATA
3' ss Score
8.88
Exon sequences
Seq C1 exon
GAGACGGGCACAGGGCCCTCAGCTTCTTCCAACAAAAAGGCCTCCGAGACTTTGACACGCTGCTCCTGAGTGACGATGGCAACACTCTCTATGTGGGGGCTCGAGAGGCCGTCCTGGCCTTGAATATCCAGAACCCAGGAATCCCAAGGCTAAAGAACATG
Seq A exon
GTGAGGAGGCCAGGGGCCAGAGTCCAAGACAGCAGCTTCCCTGGACCAGTTCTGCTTCCATATGAACAGCCGCCACCTGCCACTCTGAGTCAGCAGTGACAGCAGGGACTGCTGTGGTCTTACAGTAACCCCAGCCACTCAAATGGCTGATATGGAAATCACTGGCATAGGAGATTTAAAACATTGACTCAAATCAGTGACTCAAATAGTTTGATGTGCACCTATGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAATCCCTGATTCTTGTGCTATCCTCTCCCTAATGGCAGCAATATTGAAGGGAGGGGATGGGGAGGAAGAAGGCACTTCACATGGATCCTTCTCAGTGTGTGGTCTCTTGACCTCCTGCACATGCAGGGTATAGGTAAAATTCCAGAGTCGTGGACCAGGAGCGTCGTTCAGTGGCAGAATATTTCATCTAGAGTGCTGGAGAGCCTAAGTCTGATATCTGCACCCCTCCTTTGCAGCTTCTTTAAGGGGTTGACAGGCTCCCCCAGGAAATGTGTGGTTTATAACCACTGCTGCGAATGCCAGGCACTTACACATGCATTCTGGCTGTAACCACTAACAGGTTATGAAATGGAGCCAGCATGCAGTCAGTTGGTGGCCAAGCCTAATTTTGAACTCAGATCTGTCTTGTTCTACCCCAGAGCCACGTCCCTATGAATCCTAATACTATGCAAGTTATAGTCCTGATCAAATTGGCATATGACTGCCTACCAGAACGTCACTAAGAGCTTACTGGTGGCTTTACTTCAGAGCTGGGGTGTGCGGGGCACAGGAGGTGGTGGTGGCTTACAGAAAAACCAAAGAGCTCCTTTCCTTTCATCTACCCCTTTCAACTCTCCACTTTAG
Seq C2 exon
ATACCCTGGCCAGCCAGTGAGAGAAAAAAGACCGAATGTGCCTTTAAGAAGAAGAGCAATGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000028064-Sema4a:NM_001163489:3
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.002 A=NA C2=0.057
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF0140314=Sema=PU(72.0=66.7)

							
A:
NA

							
C2:
PF0140314=Sema=FE(11.7=100)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000029700





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000029700f2240A, ENSMUSP00000103155, ENSMUSP00000103156, ENSMUSP00000114330, ENSMUSP00000118706, ENSMUSP00000119028, ENSMUSP00000123061, ENSMUSP00000125909, ENSMUSP00000128510, ENSMUSP00000128887
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr1:156156575-156158069 
ALTERNATIVE
HsaINT0147327
(SEMA4A)
Human
(hg19)
chr1:156126366-156127860 
HsaINT0147327
(SEMA4A)
Rat
(rn6)
chr2:187813879-187814652 
ALTERNATIVE
RnoINT0132918
(Sema4a)
Cow
(bosTau6)
chr3:14675856-14677153 
LOW PSI
BtaINT0130797
(SEMA4A)
Chicken
(galGal4)
chr10:19531475-19531745 
ALTERNATIVE
GgaINT1024725
(SEMA4B)
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
chr7:29981132-29981209 
LOW PSI
DreINT0018768
(SEMA4B (2 of 2))
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
CACAGGGCCCTCAGCTTCTTC

				
R: 
CATTGCTCTTCTTCTTAAAGGCACA

				
Band lengths: 
214-1102

			

		

	





	
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






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