Special

MmuINT0141146 @ mm9

Intron Retention

Gene
ENSMUSG00000021451 | Sema4d
Description
sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4D [Source:MGI Symbol;Acc:MGI:109244]
Coordinates
chr13:51800442-51804359:-
Coord C1 exon
chr13:51804244-51804359
Coord A exon
chr13:51800615-51804243
Coord C2 exon
chr13:51800442-51800614
Length
3629 bp
Sequences
Splice sites
5' ss Seq
AAGGTAATG
5' ss Score
8.99
3' ss Seq
CATCCGTCTCTCATACACAGGGG
3' ss Score
8.87
Exon sequences
Seq C1 exon
ACCGGGGAGCTCTGCATAAAGCAGTCATCCTCACAAAAGAGGTGCATGTCATCGAGGAGACCCAACTCTTCCGGGACTCTGAACCGGTCCTAACTCTGCTGCTATCGTCAAAGAAG
Seq A exon
GTAATGTGGGTTTGGTTGGTTGGTTGGTTGGTTTTAGGGGTGGGGGTCAGGTCCAGGCGCTTGTCTCCCTTGTAGCTTCTCTGTGGCTAGGACTGGCTAGGATGGGTCTCTCAAGGCTTGGCAGCCTCTGGCCCAGGTGAACTTGGCGTACACAGCATGGGATCTGAGGCTTGGGAGGAGGCATGGGAGAGCCAGGGGCCTTGATTGTACTAAGCCACTGGAGCTTTTGGGAGGTCCCTAACCTGGGGAAATGTCTGTGCCTTGAACCTGAAAAAAAAATGCAGATTGTGCTGGTGGGACATGACATTTTGCTAATTTGTAAGGAGAAATAACAGGGGCTGGTGAGATGGCTCAATGGTTAAGAGCATTGACTGCTCCTCCAGAGGTCCTGAGTTCAAATCCCAGCAACCACATGGTGGCTCATAACCATCTGTAATGAGATCTGATGCCCTCTTCTGGTGTGTCTGAAAACAACTACAGTGTACTTACATGTAATAAATAAATAAATCTTTTTTAAAAAAAAAAAAAGAGAACTAACAGGTCACCCTCTAGAGCTCCTGCCATACCGCCCTGTGCATCGGGCAGCCTTTGCAGAGGCCTCAGTCACGGGGGCTCAGCTCTGCACTGTGGCTCCCACGAGCCACGGAAACACATAGATGACCAAACCTGCCCTCGAAGCCATGCTATGTATTGCCCGAAGTTTTCATAAAAAGCTCCAGCCAGATGGTAGTAGTGCAAACCTTTGATCCTGGCACTCGGGAGGTGGAGGCAGGTAGATCTTTGTGAGTTCAAGGCCAGCCTGGTATACATAGTGTGTTTCAGGGCAGCCAGAACTATGTAGGGAGACCCTGTCTCAAAAATGAATGAATGAATGAATGAATGAATGAATGAATGAATAGGTATTTTTTAAGCCCCTAAGTGGGGTGCAGTATGGTTCATACCTCTAGTTCCAGACCTTAGAACATTGGAAGCAGGAAGATCAGGAGTTCAAGGCTAGTCTTAGCCATATAGCAAAGTCAAGGCCAGCCTGAGCTAAGTGAGACCCCATTGCAAAAAATAAAACAAGGTATATAGGAGTGAATAGAAATGGCCTGGGTGGGGCTGGAGAGATGGCTCAGTGGTTAAGAGCAGTGACTGCTCTTCCAAAGGTCCTGAGTTCAATTCCCAGCAACCATTGTGGCTCACAACCATCTGGAATGGCATCTCTGATGGATGCCCTGTTCAGGTGTATCTGAAGACAGCGACAGTGTACTCTATAAATAAAATAAGTCTTAAAAAAAAAAAAAAGCCTGGCAGTGATGGTGGCACATGCCTTTAATCCCAGCACTTGGGAGGCAGAGGCAGACAGGTTTCTGAGTTCAAGGCCAACCTGGTCTACAGAGTGAGTTCCAGGGCAGCCAGGGCTACACAGAGAAACCCTGTCTCAAAAAACCAAAATGAAAAAAAGAAAAGAAATGGCCTGGGAGCTGGGCTTGGTCCACTGGCTGGAACTTGTTCCTTGTCCTCTGGCCTTGGGAAGATGTGGACACCACATTTTACATCTAGGATAAAACAAGGAAGTTCAGAACATGGGTTGTCTCCAAATCCTGACTACACTGCCTGCTGTCATGTTACCCTGGGCATCACTATATGGTCCTCTTAAGGTGGTCTCTGTGTGTGTATGCTTTTCATTAATGTGACTGTTAAGAGGACATGTGAGCCTCCTAAGTGCTGAGGGCTGGCTTTGAGCAGCACAGAACCCAGGGAAAGCTAGGAGCAGGATCAGCTGCCACCTGCCCTGCTTCATGCCTGCTGGCCAAAGGTGCTCCCCTCCCCTTGCTAGGGCTCTGCTGTACCCCCCTGAGAAGATGGGTCCAGGGCCACACTTTTGGCTTCAAGTGCCAGTGCTAGCCTCTTGCCTCTACCCTTGTCTCTGATGCCTGGCTCTGGGACACTGCTGAACTGTGGCCTGGTGTGACTGTCCCCGTGGACTGCACATCTGTGGGCCCTGTGTTTCCAATTCAGTTCTCTTTAAGTAGCTGGCCACAGCAGTTACCAAGGGTCCATCAGTCTCACTTACCCGTGTGCTGGGCTTCTGCTAGCACCAGGTACAATGCTGGTCCTGGCTTGCACCCAGGAACATGGCACGCTCCTGTCCTGGAAGTCAGAGCGATGTTGATAGGCGTGGTCACATTGGCAGGCTGGATTCAGAGATGACTGATAAGGATGTGTCCTTATCACAGGTACCTACTGTCTGGCTCAAGACAAGACTGGCATTTAAAGGTTGTGCCCTGTGGATTCCAGCTGTAGTGCTGTGTCACTTACAGAGTCCAGGAGAGCAGTGGGGGGGGGGGGGGTCACATTAGGAGTGGGAAGCAACTGGAGAGGGCTTTTATGTGGTTTTCTCAAGACACAAATGAAAGTCTCTTCACCCAAGATAGAGCACCAAGGATAGACCAGTCGAGCTCAGTGAGCCAGTGAGTTTTGGGGAGGTAGCTACAGGGAAGAAGGAACAGGGGATTATTTACAAGCCCGTGGGTGGTTCGGAGGCAGCTGCATCCATATATCTCCCTTCACAGCTGGTAGGCAGCTCGGCAGGGCAGAGTCTCCTCTCTACCGCAATTGTGTGCTGCTTATATAACCTTGGGGCAGCGGGCACTTGTGAATCTTAAACCTCGTCAGGCTTCCTAAATTTCCTTCACTTTGAGTCTTGTGAGGCTCCCTCGGCGCTCCGGGAGGACGTGTTTCGATTGGGCAGACATAGAAACAGAGCTGTCTCTTCTGGGAAGAGGAGCTGCTTTGGGCGTGCAGTGTGCTTAGCCCAGCTACGGAAGGGTGGCGTCAGATCCCAGGCCCTGCAGTTCCTCCACTGGCGTTTGAATCCTCCTGGGACAGGGGACACCCTGCTTTTCCAAACAAGATTTGTGTCTTAATGTGCTTTTCTGTCACTGCGATAAACCACTCTGACCAAAAGCAGCTTGCAGGAGGAGAAAATTTCCTTCGGTTCACACTTCCAGGTTGTAGTCGTTGAGGGAAGCCAGGGCAGAAGCTGAAGCTGAAGCAGAGACTGCGGCGGGGGGGGGGGGGGGGGGGGGGGCGGAATGGATTATTAAGCTTGCCCGCTGGCTTCTGCTTAGCTGCTATCTTATAAAGTCAGGGGTGGCATCACTCACACTGGGTTGCACCCACCCTAATTACTTAGCAAATAAGAAAATGGCCCACAGGCTGGGCGGTGGTGGCGCACGCTTTTAATCCCAGCACTTGGGAGGGAGAGGCAGGAGGCCAGCCTGGTCTACAGAGTAAGTTCCAGGACAACCAGGGCTACACAGAAACCTTGTCTCAGAAAAGAAAAAAGAAAAAAAAAGAAGAAGAAAATGTCCCACGGACATGTCCACAGGCTAATCTGATATAGGCAGTTCCTCAGCTGCAGTTGTCTGCCCCGCAAGTGTGGCAAGGTGACAATGAAAACCCATCAGGACACTGTCATTTAGGTCTTAGCGGTCGGGCCTTGTGGCCTATTCTGAGTCAGTGAGTCCTTCCCTCCATGCAGTGTTTGACTGTGCTGTCTTCCCAGGAGCTGGTGGAGAAGCTAGCAGCCCCTCCCAGTGCCTGAGTCCTCCTTACACTTGCCATCCGTCTCTCATACACAG
Seq C2 exon
GGGAGGAAGTTTGTCTATGCAGGCTCCAACTCTGGAGTGGTCCAAGCGCCCCTGGCATTCTGCGAAAAGCACGGTAGCTGTGAAGACTGTGTGTTAGCACGGGACCCCTACTGTGCCTGGAGCCCAGCCATCAAGGCCTGTGTTACCCTGCACCAGGAAGAGGCCTCCAGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000021451-Sema4d:NM_013660:13
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=0.000
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF0140314=Sema=FE(8.8=100)

							
A:
NA

							
C2:
PF0143720=PSI=PU(71.7=65.5)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000021900





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000105666, ENSMUSP00000105667, ENSMUSP00000129797
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr9:89381347-89386366 
ALTERNATIVE
HsaINT0147367
(SEMA4D)
Human
(hg19)
chr9:91996262-92001281 
ALTERNATIVE
HsaINT0147367
(SEMA4D)
Rat
(rn6)
chr17:13531633-13534639 
LOW PSI
RnoINT0132963
(Sema4d)
Cow
(bosTau6)
chr8:90240389-90245957 
LOW PSI
BtaINT0130836
(SEMA4D)
Chicken
(galGal4)
chrZ:43462243-43465494 
ALTERNATIVE
GgaINT0067170
(SEMA4D)
Chicken
(galGal3)
chr28:2786690-2787120 
LOW PSI
GgaINT0145346
([1])
Zebrafish
(danRer10)
chr21:2757273-2758278 
LOW PSI
DreINT0018777
(SEMA4D)
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"