Special

MmuINT0141148 @ 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
chr13:51796617-51800365:-
Coord C1 exon
chr13:51800322-51800365
Coord A exon
chr13:51798901-51800321
Coord C2 exon
chr13:51796617-51798900
Length
1421 bp
Sequences
Splice sites
5' ss Seq
TGGGTGAGT
5' ss Score
8.73
3' ss Seq
CGTTTATTTTGATGTTCCAGATA
3' ss Score
8.5
Exon sequences
Seq C1 exon
GGGCTGGATTCAGGACATGAGCGGTGACACATCCTCATGCCTGG
Seq A exon
GTGAGTGGATCTCCTTTGCTTCCCACCCCTGGGCTGGCAAAGCTCCCGGGGCGTCAGTTCCATGGTTTTCCTGTGCGGTCTGTCTTCCTTTCTCCTCTCTGAACAGAAGTCAAGTGTCACGCAGCAGACCTGTGACCTCTCCTTGTGGTGAACCTGTGATCTTTCTCTGTCCCTTTGGTTACAGAAAGAGGGCTCAAAGGCACACAGGGTGTATCGGTTCACTGGAAAGCACACCCTGGCCCACACCATGCTCCTCTGTTCTGCTTAGCTGGGCCCCGTAAACAAAACTGGAGCCTGCTAGGAATGAGAGCGAAGGAGCCCTTGGGTATGACCAGATAGCCCTAGCCTAAAAACAATACTCAGGAACAGTGTGGGACAGTGTCATGCTTCAAGATGAAAATCCTACCCTAGAAAGAAGTGCCTTAAACGCTAAGGAGATGGCTCAGTTGGTAGGATCTGAGTTCGATCCCCAGAACCCATGTAACAGCTGGGCATTGGTGGTTCATGCTTGTGATCCTAGCCCCAAGGAGGGTGAGGCAGGTGGATCCCTGGAGCTTGCTAGCCTCACACAGCCTAGCCGACTTGGCAAGTACCAGACAAATGAGAGACTCCATCACAGAAAAAGACAAAGAGGGTAACTGCTATCTGAGGATGATACTCAGATTTCTGGCCTCTTTCTATATAAACACACATGTACGTACACACACACACACACACACACACACACACACACACAGAGCAAATGGCATCAGATTGCCTTCAGGCATGTGTAAATGTCACACAAATTTCATGTGTAGCTTTCAGTCCCCTTCCAAAGATAGTTGTCTCGTTTTATATATGCAAATATTTCCAAGCCCAAAGCATTTTTCATCTTCCGTATTTCAGACAAAAGACACAGTTGTGGTTAGTTCTGGTGTCCTCTTGGGGCACCCCCTCCTGATGGCTGGCCATCAGGAAACGGCTGTGACCAGAGGTAGGCATAGAATCTTGCCAGAATTCTAGTCTGCCTTCCCAGCCCCGTACCCCCTTCTCTGACTAGCCACATCAGAGTAAGAAGAGGGTCCCTGGTTGCTAGCTGGCCTGCTTTAGCCATTAGCAGAAGTATTTGTCAGCTGACTGGGTGCCACTGTGAGGGAGCTGAGCCGTGCCCAGCCCCTTCCTCAGCCTGCTGACCTTTCTCCAGGGCCAGGGTGAGAACAGAAATTCTCAGAGCTGTCGCCAGTTCCTTCAGTGTATGGAAGGGGGACGGGGTGGGGGCTGCTCTAGGGTCATGGATGTCTTTACCTTGGTCCTGAAGATTGCACCTGGCTCCAGTGGGTGGAAGTCTCATGCCGTCCTGTGGGTATTAACCTGTTTTTTGAAAGCAGTCGAGCGGTCAGACGGAGTTGTTGACGGTGAGCACGTTTATTTTGATGTTCCAG
Seq C2 exon
ATAAGAGTAAAGAAAGTTTCAACCAGCATTTTTTCAAGCACGGCGGCACAGCGGAACTCAAATGTTTCCAAAAGTCCAACCTAGCCCGGGTGGTATGGAAGTTCCAGAATGGCGAGTTGAAGGCCGCAAGTCCCAAGTACGGCTTTGTGGGCAGGAAGCACCTGCTCATCTTCAACCTGTCGGACGGAGACAGCGGCGTGTACCAGTGCCTGTCAGAGGAAAGGGTGAGGAATAAAACGGTCTCCCAGCTGCTGGCCAAGCACGTTCTGGAAGTGAAGATGGTACCTCGGACCCCCCCCTCACCTACCTCAGAGGATGCTCAGACAGAAGGTAGTAAGATCACATCCAAAATGCCGGTTGCATCTACCCAGGGGTCCTCTCCCCCTACCCCGGCTCTGTGGGCAACCTCCCCCAGAGCCGCCACCCTACCTCCCAAGTCCTCCTCCGGCACATCCTGTGAACCAAAGATGGTCATCAACACGGTCCCCCAGCTCCACTCAGAGAAGACGGTGTATCTCAAGTCCAGTGACAACCGCCTGCTCATGTCTCTCCTCCTCTTCATCTTTGTCCTCTTCCTCTGCCTCTTTTCCTACAACTGCTACAAGGGCTACCTGCCCGGACAGTGCTTAAAATTCCGCTCAGCCCTGCTGCTTGGAAAGAAAACACCCAAGTCAGACTTCTCTGACCTGGAGCAGAGTGTGAAGGAGACACTGGTCGAGCCTGGGAGCTTCTCCCAGCAGAACGGCGACCACCCCAAGCCAGCCCTGGATACGGGCTATGAAACGGAGCAGGACACCATCACCAGCAAAGTCCCCACGGATCGTGAGGACTCGCAACGGATCGATGAACTCTCTGCCCGGGACAAACCGTTTGATGTCAAGTGTGAACTGAAGTTTGCAGATTCGGATGCTGACGGGGACTGAGGCCAGCGTGTCCCAGCCCATGCCCCTCTGTCTTCGTGGAGAGTGTTGTGTTGAGCCCATTCAGTAGCCGAGTCTTGTCACTCTGTGCCAGCCTCAGTCCTGTGTCCCTTTTTCTCTTGGGTTGAGCCTGTGGCTCATCCCCTTTGTCCTTTTGGGAAGCAAGTATCTATTCCAGTCTCAAGTCCTGCAGTTGCTGGAGCGCTTACGCACCTGAGCCCTTTGTGTCCTGGGGGAGAGATGGCCACCTCCGTGGGCTGCGAAGAGCCACCCCTTCCTCTTCCGATTCTCCTAGCAGCCACTCAGAGATAATTTAATTCCAGATTGGAAACGCCCTTTTAGTTTATCAGATTGGTAACTTACATCCTGCTGCCCAGATGGCACGGACAGTTTTCTTTCACTTAATTATTATTTTTTTTTTAAGGATTTTCGCTCCTATTGTGTTGATGTCTTAGGTCATTTTCTTTTTTTCTTTCTCTTTTTTTATTACCAGAGGAGATGTTTTAATATTCATGAGAAGAGGAACATTTTCTAGATTTTTTTGTTGTTATATATTGAGATATAAAATATGGCTATGTTGCTTAAGATTCTCAGGGATAGACTTATTTTTGTTAACTTCATTCTTTCCTGCTGTTAGGAACATAGGCCTAAAATTGTCTCTTGAGTTTGCTCACCCTTTTGTTTTGGTAGGGTTTTTTTGTTGTTGCTGTTATTGTTTCTAGTTTTTAATCTTATTCATTTTGAAGGATTTTTCTTTCTGAACTTTTTAAATTTTTATATTTTCCTGCCATACATCTACAAAGTGGGTTTTGAGTGAGGGCAGGTGGCCCAGTGGCTTTGGGTGGCGACTGAGCTGGTCCCACGAGGGGAGGAGGGTTTATATACCCCATGACCCTGCGGCTTCTTGGCGCCTCCTGCCCATGAGGATCACATCCTGTCTCTCCTTGCTTCCATCTCTCATCACTGCCCTTGGACTTCCGCCTTGACTGTCCATGAAAGACAGAAATGGGTTGGGTAGTTGGGCTCCCAACCTCGGATGGTGACCGCAACATCCCGTGTGGGCGGCCGGCCGCTCCTGCAGCCCGACTCTCCTGCCAGTGTCTTTCAGGATGTCAACGGGTGGTACGATTCTGGCATTTGTTTCTCGCTCACCGTGTGTGGAACACTCATTCCATGTAGAGGGTGACGAACTCTGGATTCCCCCCCACCCCCACCCCGTGCCGTGTAGACACTCATCTTCTGCATGACATGATCTACCATTCGGTGTAAACATTTGTGTTTATAAGATTTACTTTGTTTTTATTTTTCTACTTGGAACTGTACACATTTGAAAAGTACCCAAATAAACCAGAAGCTTTATCGTT
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000021451-Sema4d:NM_013660:15
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
Alternative protein isoforms





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.000 A=NA C2=0.326
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF0143720=PSI=PD(26.4=87.5)

							
A:
NA

							
C2:
PF0004720=ig=WD(100=18.8)

						

					

				








    
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)
chr9:89377052-89381054 
ALTERNATIVE
HsaINT0147369
(SEMA4D)
Human
(hg19)
chr9:91994545-91995969 
HsaINT0147381
(SEMA4D)
Rat
(rn6)
chr17:13534929-13536188 
LOW PSI
RnoINT0132965
(Sema4d)
Cow
(bosTau6)
chr8:90246260-90247242 
BtaINT0130838
(SEMA4D)
Chicken
(galGal4)
chrZ:43460693-43461792 
ALTERNATIVE
GgaINT1024733
(SEMA4D)
Chicken
(galGal3)
chrZ:42878204-42879303 
GgaINT0067172
(SEMA4D)
Zebrafish
(danRer10)
chr21:2755332-2756873 
LOW PSI
DreINT0018779
(SEMA4D)
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
GTGACACATCCTCATGCCTGG

				
R: 
TGTCTGAGCATCCTCTGAGGT

				
Band lengths: 
347-1768

			

		

	





	
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"