Special

MmuINT0162639 @ mm9

Intron Retention

Gene
ENSMUSG00000061259 | Tmprss11d
Description
transmembrane protease, serine 11d [Source:MGI Symbol;Acc:MGI:2385221]
Coordinates
chr5:86731879-86735434:-
Coord C1 exon
chr5:86735292-86735434
Coord A exon
chr5:86732798-86735291
Coord C2 exon
chr5:86731879-86732797
Length
2494 bp
Sequences
Splice sites
5' ss Seq
CAGGTAACA
5' ss Score
8.88
3' ss Seq
ATTTGTTTTGTTCTCTTCAGGGT
3' ss Score
11.37
Exon sequences
Seq C1 exon
GCAACGCAGTCACAAATCTACGGCAAGGAGAGGTCAGAATAATAAGTTCAGAGGAATGCAATACGCCAGCTGGTTACAGTGGAAGTGTCTTGCCAGGAATGCTGTGTGCTGGAATGCGTTCAGGGGCCGTGGATGCATGCCAG
Seq A exon
GTAACAACATTATCTATGTCACCATTGAGAAGTTTATAAGCATTGTTAAACACATCACCCTGTGACAGAAGAAAAGATAACAACATTTACAACATACAACTCTGCTCCTCAAAAAGAAAAAATGTATGCCCTTAATTTAAGAGATAAAATTCTGTTTTAAGTTTTATTTAGCACAAAAATACCAATTGTTAATTGCTATAGGATAGTCAAACCAATATAATGTAACATGGTAGGTACAATTAATAATAAAGTATTGTATGTTTCAAAATTTCTAGGCCAGCCTGGTCTACAGAGTGAGTTCCAGGACAGCCAGGACTGTACAGAGAAACCCTGTCTTGAAAAAAACCAAAAAAAAAAAAGGAAAAAAAATTTCTAGAGAGTAAATTTTGATGTTCTTTTCACAAGGAACAAAATTAAGTGTTTAAAGCAGTAGAAGCCTTAGCTAGCTTGATTTTAATATTCAATATCATACCCATAAATTATAAAATCATTTCCTATCTTATACATGTATAATAATAAACTCACAATGAAAACAGTCATTTAAAGTTCAAAACATAATTATGTTTTAATTTATATTGTTTTATTTGTAAATACTCATCCTTAGCCCAGTTAAAAAATATATAGCATACAACCACTAAAAAAAAAAAAATCCATTTTTTAAAGTACTTTAAAGATAGAAAATACTGCCAAGTGTGGTAGCACACTCCTTTAATCCCAGCACTTGGGAGGCAGAGGCAGGTGAATTTTTGAGTTCGAGGCCAGCCTGGTCTACAGAGTGAGTTCCAGGACAGCTAGGACTACACAGAGAAACCCTGTCTTGAAAAAACAAAAAACAACAAAAAATATGTATACAATATCTTAATTAATTGAATTCCAAGATATCCTAAATTATATAATAAGTAGAAAAGAAAAAGAGAGAAAAGAGATGGAGGAGGGTCAAGGGAGGGGGGAAGAAGTGGGAAGGAGGAACTTAAGGAGAACTTATGCCTCAAAAAAAGATATAATAAGTGAATAATATTTTACATAAATGTTTACAAGATCAATTTCATACATTCTTTCGAAGATGTATCTACTCTCACGTCTGGGTAACATTCTGTGTGACAATACAACCAGATATTCCCTGACTCATCAGGTTGAGAAAAAAATAGATTGCAGGTTCAAAGATCAGACACTAGGCAGAGAAACTAACCCTACGTTGTGGCCCTCAGAATTACCATTTGCTGGTCCATATTGGATAAGATACAATACAGAAAGCTTTGCCACTATAGTAAAAAAAAAAAAAATAGCATAAAACATAACAATGACACAGTGAGGATTTTATGCACTGTGCATGTCTCATCCAAAGGAATGAGGCACCAGCCGCCCCATGCAGCAGTTGCCAAGCGAGTTGGTGATTCTTGTGCTGACCTCTCTCCATCTACACCATTAATTAAATAGGTATGGAAAACCTAACTACTATGAGCCATCAGATGAATGGCTAACTTTTCTATACACACATTTGGTAATAATAGCTGGCTTTTATTAGTACTGACTATACACCAAACTCTGTCCAAAGTGCTTTGTGTGTTAAGTTCACTTAAACACATTTTTAAATGCCATTTATTAATAAAAGTATTTCAGCACAGATTTGTTAGAGAGTTTCCTGGAGTTCACATACCTGATAGGTAGAGGACTCGCACTCAGGCTATCTAGCTCCGGAATTCACAGAATTAACACATAGTACAGTATACTCTAAAGGTACCTCCTTAATTGAACGATTACATGTATAAATGTTTCTAGGCAGTTAGTTATTGCTATTGGCTGGTAAATAACTCATAAGAAAGGCTCTGCTTACTGTCGTAAAAATTTCTTTTCAGTTATTCACAAAAAGAATAGAGGTGGGTGGTTTACTGTGCATCAGGTCTCATACCAGGTGGTAAAGAAAGGTTGGTAAGTGACATATCTAGAGATTCCTTCATTCAAAAGCAATTTCCTTAGCCTCTTCTAGATGCTAGAAACCGAGGTTTCGGGCAGTGTTTGGAACAAGGATGTTTCCATCCCTCATGGAATTTACTACAGGGCTGCTAACACAGACACTGGCCAAGTATCAAAATTAGTACAGGGAGTGCTAACACAAGGAGATCTGTCCAAGGGGAATAAGCACGACTTTTTAGAAGCAGCGATATAGATGCCACAGCACATGCGATCACAGGAGGAGATCAATTGGGCCCGAAGCCAGATGCTCAAAGGAAAGAAGTCACAGAAGCCTTCCGAGAGAGGAGGCCTGAGAAGACTAAGAAGCAACAAGGAACTAACTGAAGGAAGACTCACTCACGAGCATTTTAGTCTCAACCTTACTTGTATACTTGAAGGATTTCAGTTTTTTGTTTTTTGTTTTTGTTTTTGGTTTTGGTTTTTTTTTTGCATTAGCTTGGACTTCCTCGACTGCCATAGAAATGCACGATTTTAAGGTTGCTTTTGCATTTAAGTACATCATTTGTTTTGTTCTCTTCAG
Seq C2 exon
GGTGATTCAGGTGGCCCGCTAGTACAAGAAGACTCAAGGCGGCTTTGGTTTGTTGTGGGCATTGTGAGCTGGGGATATCAGTGTGGCCTCCCAAATAAGCCAGGCGTGTATACTCGAGTGACAGCCTACCGCAACTGGATCAGACAGCAGACGGGAATCTAGTGCAACCGAGGAAAAAACGTGCCATGAGGTCTCTGTATCCAAGTGTGACTGACTCGGATGCCATGGCTTCACATTTCAACTGCAAAGGAGACTGGAAATGCCCCTTCTGAACGTCCCATTACATAAATATGGTTTAACTGTTTAGTATTTCTTTGTCGGTACAGATTTTTACTTTCTTGAGGAAAAAAAAAACATGAACATGGCTAAGTAAGAATTATGTTAGGCTAGTAACAGGAAGACATTTATTACATGGGTGGTCAGGTGTAGTAGTGAGAAGTCAGGTAAGTTAAGTCAATAATTTACAGAAAATAATGTCAGGTAGTCCTAACGTTAAATATGTGAGGCCACAGAACAAATAGTGTTAGAACTGAAGCCATCCCAAGTATTTAACATTTGTTTTCAAGTGAAACTAAGAAACAGACTTACATATAGTTTTAATGGTGAATTTTCATTTTAAATATTTTATCTACATAGAAAAGACATATCTCCTTCATGAAGAAGCTGAGGTGATGAATCAACACAGCCTCTTCAGCTATGTTTGCAACCACAAGATTTGTGGGAAAGAAATCCCTACTACCAACTTCCTACTGTTGGCATTATTTTTTAGAGTAACACGACGCACAATAGCAAAATTTAAGTAACAAATTAAAAGTTAATGATGAAGAAGAAGTAAAGAGTTTGTTTGCAAAGACAAAAATTAAACAGATTAATATCAATAAATCTGGAGACAGAAGGGTCTCAGATTCATATTCTCTCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000061259-Tmprss11d:NM_145561:9
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:
ENSMUSP00000031175





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000113079
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr4:67822499-67825731 
ALTERNATIVE
HsaINT1044657
(TMPRSS11D)
Human
(hg19)
chr4:68688217-68691449 
HsaINT0169649
(TMPRSS11D)
Rat
(rn6)
chr14:23389595-23392666 
LOW PSI
RnoINT0153304
(Tmprss11d)
Cow
(bosTau6)
chr6:85255568-85257593 
LOW PSI
BtaINT0150368
(TMPRSS11D)
Chicken
(galGal4)
chr4:51120669-51121087 
LOW PSI
GgaINT0072439
([1])
Chicken
(galGal3)
chr4:53216208-53216626 
LOW PSI
GgaINT0072439
(F1NMD1_CHICK)
Zebrafish
(danRer10)
chr21:25239419-25239515 
LOW PSI
DreINT0156465
(st14b)
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"