Special

MmuINT0075112 @ mm9

Intron Retention

Gene
ENSMUSG00000022487 | Gtsf1
Description
gametocyte specific factor 1 [Source:MGI Symbol;Acc:MGI:1921424]
Coordinates
chr15:103250904-103251747:-
Coord C1 exon
chr15:103251621-103251747
Coord A exon
chr15:103250988-103251620
Coord C2 exon
chr15:103250904-103250987
Length
633 bp
Sequences
Splice sites
5' ss Seq
TGGGTAAGC
5' ss Score
8.84
3' ss Seq
AAATCTCTATTGTCTTGCAGTCA
3' ss Score
7.08
Exon sequences
Seq C1 exon
AATCATCCTGATGTCGCAAACAAATTGGCTACTTGTCCCTTCAATGCTCGGCATCAGGTTCCCCGGGCTGAGATCAGTCATCACATCTCGAGCTGTGATGACAAGAGCTGTATTGAGCAGGATGTGG
Seq A exon
GTAAGCCAGACTAGCTGAAATGCCCTAGGATTCCAGGGTTAGCTGCTCAGTTTGGAGTTATGCTACATCATTGTCTTGCTTTCTGGCTTTCACCATTTCAAAAGAATATTTTTCTGCCTTTGAGATGATTATATCATTGTAGCAGTGGGTTGTTAGCTTCTATATAGGTCAGACTGCTTTCTCTTCTGAACAGCCTGATTCATTTTACTATTATAATAAATCGTCTAAAAATAAAGTCCTTGAGGCTGAAGATGGAGCTCAGTGGGTCGAGCACTTGCCTCCCATGGATAAAGCCCTGGGTTCCAGCTCCTGTACCACAAAATGGGCATGGTAGTGGTGACTACTCAAGAGGTAGAAGCAGGAGATTCTGGAGTTCAAGGTCACCTTGAGTCTGAGGCCAGCTAGGAACACAAGACCCTGTCTCGATAAATAAATACTGTTACTGCCATAAATATGGTAACAATCTTTGTTTCTGCTTCTTGTTTCTGTCAGTTCTCACCCTATCCGTATTTAGAAACAAAGATTCAATAGGCTACCTTGCTGCCTTTAAAGGCCTTAAATCCCTTAAGCAGAATAACCTAGCAGATACCACACCCCCTGCCCTTTATATATCAAATCTCTATTGTCTTGCAG
Seq C2 exon
TCAACCAAACCAGGAACCTTGGACAAGAGACTCTGGCTGAGAGCACATGGCAGTGCCCTCCTTGTGATGAAGACTGGGATAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000022487-Gtsf1:NM_028797:4
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.018 A=NA C2=0.126
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF052537=zf-U11-48K=PD(0.1=0.0),PF052537=zf-U11-48K=WD(100=62.8)

							
A:
NA

							
C2:
NO

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000115670





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000023129, ENSMUSP00000114244, ENSMUSP00000114733, ENSMUSP00000115123, ENSMUSP00000116366, ENSMUSP00000119234, ENSMUSP00000120797, ENSMUSP00000122193
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr12:54462726-54463170 
ALTERNATIVE
HsaINT0073580
(GTSF1)
Human
(hg19)
chr12:54856510-54856954 
ALTERNATIVE
HsaINT0073580
(GTSF1)
Rat
(rn6)
chr7:145037808-145038455 
LOW PSI
RnoINT0068575
(Gtsf1)
Cow
(bosTau6)
chr5:25738468-25738899 
LOW PSI
BtaINT0069998
(GTSF1)
Chicken
(galGal4)
chr27:1063827-1064757 
LOW PSI
GgaINT0143675
(GTSF1)
Chicken
(galGal3)
chr27:1018384-1019314 
LOW PSI
GgaINT0143675
(GTSF1)
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
AATCATCCTGATGTCGCAAACA

				
R: 
TCCCAGTCTTCATCACAAGGAG

				
Band lengths: 
206-839

			

		

	





	
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"