Special

MmuINT0006346 @ mm9

Intron Retention

Gene
ENSMUSG00000079451 | 9930032O22Rik
Description
transmembrane protease, serine 11g [Source:MGI Symbol;Acc:MGI:2444058]
Coordinates
chr5:86914902-86918350:-
Coord C1 exon
chr5:86918208-86918350
Coord A exon
chr5:86916586-86918207
Coord C2 exon
chr5:86914902-86916585
Length
1622 bp
Sequences
Splice sites
5' ss Seq
GAAGTAAGT
5' ss Score
9.82
3' ss Seq
ATGTTTGTACTCTTTTCTAGGGT
3' ss Score
11.11
Exon sequences
Seq C1 exon
GTCCCTTTCCCAATTCTCTGCAAGAGGTTGAAATAGAGATCATAAGTAATGATGTATGTAATCAAGTTAATGTATACGGTGGTGCTATATCCTCAGGAATGATATGTGCTGGATTCTTGACAGGAAAACTAGATGCCTGTGAA
Seq A exon
GTAAGTATATTATAATTCACAAAAATAACTCTCTTGTTAAGGATGCAACCATTAATCACAGTGTAATGTCATTTAACACAGTTCCTTGAAATTAACGTGGGTAGGAAAGAGGAGCTATGAGAAGGGATTGAAGAACAAGCCATATAACGAACACCTCATGAAACACCATATTGAACAGAACTGTCTCAGCAAGGTTGTCATTGAAAAACAGGACTCTTAGTGGAGACCAGAATTTCATATAACTAGTAAAAGACAAGTATGAAGTCACAGAATAAAGGCTCAGCCATAACTGAACTTTGAATATCTCATTCATACTAGTTTCAAGCCACAATGGGGCAAGATATACTGATATTTGACCTTAACTAGCTTTTTCCAATTATTATTTAGAAATCTACATTATTGAGAAAAATAATAATCTTCACTCATTCCTATGAATGTAGTACATTACAGATCAGTTTTCAAATTACACCAATAGCATTTTGTTCATACTTATTAATTTTAAGCATTAACCGTTTGAGCACAGTATCAGTTCTAACATACAGTTATTTGAAGGACTGAAAATAAATAAGAATTTAAAGATGTGACCTATTGCATTTGTGGGTGGGCACAAGAACAAAACAATTCCCTGAGAAATTAATATCGGCATTTGTTGTAAACAATGCAGTCACCATTGATCTGACATTGGCTATCGTGTGATGGTAATAAACACTCATTCTCTTACTTATTCAGCTTTTCATTAACCAAAGTTTACCATACACATTACTGAGGGAAACTAACATTAAAAAAAATTGCAGTGACTTGACAATTTCATTAGGTCACAAGTTACTGAAACAAAAGAAAAAATTCAGGATTTAGCTAGACACTCAAGAATACAAGGTATTCTTCCATTCTCTCTCTCTGAGAAGGAGAAGCTAGGCATGTATCCAGCATATGGAATCACAAGACTTAGAGAATAAGCATGATCTACACAGGAGCTGACCTTCGTGACCCATTGACTCAGACTCCCTTACTGCCTTTCACCATTTGTACAGTAGGAGTGTGAGGATCTCAGTTATAATGGAGGCCTGAGGGAAGGGGGCTAAGGAGGACCATCTTCAGTGTATGGCGATGTTCACCAGATGCTGGAAGAGACTAAGAAGAAGAGGAAGAATGGTGGAAAGGAAAGACCTTTGAGTGGCTTCAGAAGTCTATGCCTCTTCCAAACTATCATTTTCCTCATTCTAAGAGACTGTGGTAAACTATCTCAGGGTTTGGTTTTGGAAAGAATAGAGTCATCACTTAGAGACAAATTTTAAATCTTCCATTGAATTCTTAGGTTAAAGATCACTGAGAAGCCCTCATGATGTAGGTTCTTTAAGTATGTTTGCTGGGAAATCCACCTTAATCTTTCAGTAAAAGGTGCTACACATTTGATAGAACATCCCAGAATACTCTTCTACTGATTAGTAAACGTGGAACAAGGTGAGAATCTAATTTAAAGCAAAGCATCATTCCTAGCTAATGGAGTTAACATGTTAGTTCCAGGTGTGAATTTATCAGACAGTCAGGAGCCAGTGAGCTCTTATTTCTGACACCGTTTTGTTTTTTTTTTTAATTGACAACATGTTTGTACTCTTTTCTAG
Seq C2 exon
GGTGATTCTGGAGGGCCTCTGGTTATTTCAGATAATAGAAATAAGTGGTATCTTCTTGGAATTGTTAGTTGGGGAATAGACTGTGGAAAAGAAAACAAGCCCGGAATTTACACCAGAGTGACTCATTATCGGGACTGGATTAAATCTAAAACTAGCATCTAATGCCACAGCCACCCCTTTATCCACCCTGGAGTGTCACACATGGCCTCTGGCAAACCTTATTCCATGTTCATCACCATGTGCATTGCCATTTAGCTCAAGATGCAAATGAGTATGTCGCAGTGACCTTCAGAAGGGGACAGACTTCCTTTTACATCATTGGAAGGGTTCCATTGACTATGAACAAAATAGATGCCATCAGCTTCACAAAGATCTACCATTCTGCAAAGTGTCTGATTACCTCCCTGCTCACCTCTGTTCTCCTACCTCATTTTTTTTTTAACTTATACTCATCTGGAAGTCAAATAAATACTAACTGTCCAGCCACCCTCTGCTTTTCTCAAGAGATGACTTCCTTCTCTGATTCCTTCACAGTTTTTGCCTTCATCAAAATCCTCACTAGCAGTTTGTTGGTCTGCTGAATGGACAGGCCACATTAGCTAGTCTAAGTCAATGGTGACATAATAATGAAGGAAACACTGGATCTGAGGCTAGGACTTAGGAGATGGCGATGAGCAAGTCCATTCTTTTTCATCTTCAGATATGCATTTAACCTTTCTCTGAAACTTTGTATTTATATTTGTACATATCTTATTTTCTTTAGACAATTTAGCTGATGTGTATTTTGAAGCTGTTCACCTATCATGTGTTTTTTAATAACATGAGATGATTCATAGATATTTCTTTGTACAAATACTTTTCCATACTTCAAAATTAAAAGTGCTTTTTCTTGTCCCTTTTATTAATGAAATGTAAATGAGCAAGAATCTAAAAGGGTTGCTTTCAGCTCAATCTCCAAGATGGGGGATGTTTCAACAGTTGTATAAATTTATTTTCAATTGTATGTTATTTTACCTTAATTCTTTTTATTTAAACAGCTTTATTTTCAACCAGGTTTAGAATAATTAAGTAGCTATAGGATGGGGAGTCAGTGTAAATGAATTCTAAGAGAATATAAACATCAGACATGTGAAGCAAAATTATCAGTAGACATTCATAAAATTCTTGAAACAAGATATCAGTAAAGATATTGTTGTTCAATATTTGAATTTACCGTTAAATAGCAGGTATGTTTTTTTCTTTTCATTTTTTTAATTAGATATTTTCTTCGTTTACATTTCAAATGCTATCCTTAAAGTCCCCCATACCCTCCTCCTGCCCTGCTCCCCTACCCACCCACTCCCACTTCTTGACCCTGGCGTTCCCATGTACTGGGGCAGGTATATCTGCAAAAGAATATTTATATAAGTCATTCAAATAATCTGGAAACATCTTTAGAATATCGTAGCCTGAATGATAAAATTGTCATTTTCATATGTATTTAGTGCACATTTTATAGTATCTCATGTGAATATAGAATAGTATCAAACCAAACTCAGACTTACTCTGTACATCCTAATCTTTGTCCTCCTTTTTATCATTGATGAGTTATCTGCTGTCTTTTTTATTTTAGTTTTGCATTAAGTAAAAGTCTTACACTGTACATATTGAAACACATTTATGATAATAAACCAAATTTGTTCTC
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000079451-9930032O22Rik:NM_177162:9
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=0.000
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF0008921=Trypsin=FE(20.8=100)

							
A:
NA

							
C2:
PF0008921=Trypsin=PD(20.4=85.2)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000108989





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000115540, ENSMUSP00000122709
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
No conservation detected
Human
(hg19)
chr4:68857564-68859699 
Rat
(rn6)
No conservation detected
Cow
(bosTau6)
chr6:85411797-85413968 
ALTERNATIVE
BtaINT0005498
([1])
Chicken
(galGal4)
chr4:51120669-51121087 
LOW PSI
GgaINT0072439
([2])
Chicken
(galGal3)
chr4:53216208-53216626 
LOW PSI
GgaINT0072439
(F1NMD1_CHICK)
Zebrafish
(danRer10)
chr15:12395165-12399821 
LOW PSI
DreINT0165319
(tmprss13a)
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
GTCCCTTTCCCAATTCTCTGCA

				
R: 
CAGAGGCCATGTGTGACACTC

				
Band lengths: 
354-1976

			

		

	





	
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"