Special

MmuINT0073436 @ mm9

Intron Retention

Gene
ENSMUSG00000026930 | Gpsm1
Description
G-protein signalling modulator 1 (AGS3-like, C. elegans) [Source:MGI Symbol;Acc:MGI:1915089]
Coordinates
chr2:26200671-26203755:+
Coord C1 exon
chr2:26200671-26200879
Coord A exon
chr2:26200880-26202326
Coord C2 exon
chr2:26202327-26203755
Length
1447 bp
Sequences
Splice sites
5' ss Seq
CAGGTGGGT
5' ss Score
8.56
3' ss Seq
TCCATTGTGTGTCTGCCCAGTCC
3' ss Score
7.27
Exon sequences
Seq C1 exon
CTCAGTCCTCCGTGACAGCTTCACCACAGACAGAGGAGTTCTTTGACCTCATTGCCAGCTCCCAGAGCCGCCGGCTGGACGACCAGAGGGCTAGCGTAGGCAGCCTGCCTGGGCTACGCATCACCCTCAACAATGTGGGGCACCTCCGAGGCGACGGGGACGCCCAGGAGCCGGGGGATGAGTTTTTCAACATGCTTATCAAATACCAG
Seq A exon
GTGGGTCTGCCCTCAGAAGGCAATGGGTGGAGCTTCATGCAGGCCCGCCTAGTGGTGGTCCTCTGCCAGCTGCAGAAGACACCTAGCTGGACCACAGCAAGCCCTGTCTTTGCTGTCTCTGGCCTCATCTGAGGGATACCTGAGGAAGACGCATAGTAACAAGTACAGCCAGAGTGAGGGACCATCCTCAGATGCGCAGGCTTGAAGCCCTCCTTCTGCCAAGGGGCCAAGGACCTCCTGAAATAAGTCTCAGCATACTCTGGGGCCGGAGTTCAGCTTGGGGCTGCCAGGTCCCCAAATCCAGGATGTCTGTTACAGGCTTCCACATCTGGGCAGAGAAAACTGAGTGTCAAGTGGCACCTTGGAGTTGTGAGGGAGGGAGAGAGGGAGGGAAGGAGGGACAGAGGGAGGGACAGAGGGAGGGAGATCTGGGATGTTAGTGCTGGCTGTAGGAATGGGAGCAGAAACGGTCCTGAAGAAGACCACACAGCATGGGCTGACAGGTGAGATGGAGAGCCTAGGCCTGGGAACACAGAACCAGGGCAGAGCTACCCATGGATGGGTTCCACTGTATGGGATTGGGTGAGGCTGGGGTGCTGCGAGCTGAGCCACCTACCAAGGCCTGGCAGCAAAGGGGGTGGGTGGTACGTTTATCCTGCTGGCTAGCTGCCCTCCAGCAGGAGCAGGTACATGGTGGGGAGTAAGCAGGGTCAGCATTCTGCCTGTGTATCAGGCTAAGTTTCCAGATCAATGTTCATTCTCACAGAGGAGACAGAACCACAGAATCGTCCAGACAGCCTCCTCTAAGCCAGCCCCTCCTGAGAAGCCTTGCCCACTCAAATACCTGGGCCATCAGCTGCACCGGCTCCACTCCCATCTGCTCCAGGCCCTGAAGAGAAGCCAACACTTTTCAGGCCCCTCAACCTCCACATCAGAACAGGCAGAGCCTGTGGTGTCAGCTGTTGATCCAAAGGCAACCCTTGGTGGGGTTGGGGTTGTAAAGTAGTGATGCTAATTTCTAAGCAACAAGCTCTGAGCTGCAGCCCCCAGGCCCTCCAGGGCAGTCCAGGGCAGTGCCAGGGTTCAGGGTAGTTCTAGGGGTCTAGTATCTGGATCAACAAGTCCCAGAGTTGGGCCCAGTGGCTGCTGACTTGTTCTATGACCAGAATATACGACCTAGCCTTTTTTATTTGGTTGGCCAGCCACAGCTCCGAGTAAGTCATCAGGCGATGCTGCCAAGGCAAAGCTTTTAGCATTACCCCAGAGCCAGGGGCAGGAGGTGGCTGAAATAGGTCCCACTTGGATTACATCATTCTTCCCAAGCCAGTGTTTGCTGTCTTCAGATTTCCAATAAGCCCATCACCTTCCCAGTGCCAGGATAGGTCCATAGGCCCTCTAAAGACCCAAGAAATACAAGACCACCAACCTCCATTGTGTGTCTGCCCAG
Seq C2 exon
TCCTCCAGGATTGATGACCAGCGCTGCCCACCCCCTGATGTGCTGCCCCGTGGCCCTACCATGCCTGATGAGGATTTCTTCAGCCTTATCCAGAGGGTGCAGGCTAAGCGGATGGATGAGCAGCGTGTGGACCTTGCTGGGAGTCCAGAGCAAGAGGCCAGTGGGCTGCCTGATCCCCAGCAGCAGTGTCCACCGGGTGCCAGCTAAGGCCTCGCCCCTACAGCCAGCCATACCCTACTCTGGACTCTGTAGGCTCACGGTTGTCCACAGTGGCCATGATCCCCCAATAAGCCAAATCTTCCCAAGGCCATGATGGACAGCCAGCTCAGCCCCAGCCCCTTCCCACTGAGCCAGATGGTGGGTGCACAAGGCCCCCCCATCCCAGGTGGTGGGTGCAGGCTAGAGCTGCTATATGGGGGAGGGCATGCTTCTGTCCCCATGGATCTCCACAGCTTCCTGCAGGCCTGCCCTGCCCTGCCCTAGGCCGGGCCTTCAGCATGTTGGCCCCGAGCCCCGGTGCTGTCCAGAGTCTTTTCCCTCAAGCCCTGCCCTGCCAAATGTGAAACTCTGCCAACTCTCCCAAGGCCCCCAGAGGGGCTTCAAGGACTTCTTCTGGTGGGGGCTACAGTGCTAAGGCATCTTCTGTCCCCCAGCTGGTCCTGGGATGGCTATGAAGGAGGTACACTCTGATCTGCCTCACGACCCCAGGGCAGGCACTATCCTGGCCTGGCTGTGCCCAACCCTGCTGAGGGAGATTGGCAGCTACAAAGTCCAGACACCCTGACCTGGTAGTCCCCAGCCTTGCACTTGGCCTTTGAGGAAAGATGGAGCTTGCCCCTGGCAGAGGGGAGAGGCAGGTCTCCAAGCATAGGGTCTTGTACTAGGAGTGCTGAGCTCTGGCTGGTAGTGGACGTTCATGAGGGATCCTCTCAACTAGATCCTTCAGTCCTCTTAGTGAGCATCTACCTTCTATTACTAGGGAGATGATATCTTGGCTTTCTCCCCAAGGAGGGGTCCATATCTTAATTGGACACAGGGCACTGTAGTTGGGGTGGAGACTCAGCCAGAACTGCCGGGGCATCCATGAGACAGACCCTTCGGGACCGTGGTCCTAGTTCTTGCCTACAAGTCCTATAGGTAGCCCTACTGGAGGGCTCTGTACAACTGTCTAACCCAGGGCCTCTTACCCAGAGGGCCAGGGCAAGGGAAACTGAGGACCCAACTTCTGAGAGGGAGAGGCAACATCACTCTGAGAGCAGAAACAGATACTAGAGCACAGGGTCTCGGGCGGGACATGGTGGCCGCCCCGCATACTTGAATGTACATGCGTATTTATTGCTTACATGTGTTTGCCATGTTGTTCATGGGTCCTTTCTGACCCGAGAGGTACATTTGTTTTGTTTTACCCAAAAATAAAAGTCTGCCAAGT
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026930-Gpsm1:NM_153410:13
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
Alternative protein isoforms





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.817 A=NA C2=0.895
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF0218812=GoLoco=WD(100=32.9),PF0218812=GoLoco=PU(47.8=15.7)

							
A:
NA

							
C2:
PF0218812=GoLoco=PD(43.5=14.5),PF0218812=GoLoco=WD(100=33.3)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000067964





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000065000, ENSMUSP00000077686, ENSMUSP00000109769, ENSMUSP00000109770, ENSMUSP00000115680
  



Associated events







Other assemblies


mm10




Conservation


Human
(hg38)
chr9:136356551-136358013 
ALTERNATIVE
HsaINT1014794
(GPSM1)
Human
(hg19)
chr9:139251003-139252465 
HsaINT0071928
(GPSM1)
Rat
(rn6)
chr3:3791487-3792885 
ALTERNATIVE
RnoINT0067119
(Gpsm1)
Cow
(bosTau6)
chr11:103867924-103868910 
Chicken
(galGal4)
chr17:7923605-7923763 
ALTERNATIVE
GgaINT0124005
(GPSM1)
Chicken
(galGal3)
chr17:8612704-8612862 
LOW PSI
GgaINT0124005
(GPSM1)
Zebrafish
(danRer10)
chr5:70956863-70957063 
LOW PSI
DreINT0074554
(gpsm1b)
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
GCTACGCATCACCCTCAACAA

				
R: 
CGTGAGCCTACAGAGTCCAGA

				
Band lengths: 
356-1803

			

		

	





	
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"