Special

MmuINT0146577 @ mm9

Intron Retention

Gene
ENSMUSG00000061171 | Slc38a11
Description
solute carrier family 38, member 11 [Source:MGI Symbol;Acc:MGI:2443383]
Coordinates
chr2:65196111-65199458:-
Coord C1 exon
chr2:65199384-65199458
Coord A exon
chr2:65196246-65199383
Coord C2 exon
chr2:65196111-65196245
Length
3138 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGT
5' ss Score
10.86
3' ss Seq
TTTGTTTTGTTTCACTACAGACT
3' ss Score
8.58
Exon sequences
Seq C1 exon
GATTGCCTTATTCAATGAAGCAAGCTGGATTTCCCTTGGGAATACTGCTTTTATTCTTGGTCTCATACATCACAG
Seq A exon
GTAAGTAGCATATAACTGCATATCCCTACAACTTAAGTTGTGCAATGACTTCTTCCCTTGCACAAATACATCCTGCAATTGGATTTCCTACTTCATTAAGAAGCGCATCAAAGCGGCCTAAGGAATTTAAGCACCACATCTGAGGAGATTTGCTTTCCTCCCTAATCCTTTAAACAGATTAGTAAGAGTAGCGCAAAGCTATATCACAAAGCTTAAAGCTGGTCATGTGGTTTTTTCACTTCGAGCAGAACATGGCGAATGAGAAAGTTGTTTCCAAGACTGGTGGCAGCTGAGAAGACACTACTCCCCAGTGCCCAAGGCAGAGCTATGTGGCAGGTGCATGCAGATTGGCAGCCATTGTTGGCTGTGTTTGTGTAGGTGATGCTGGGGGTTTGGGTGTTCAGCTGGCAAGGCCAGCCCCTTCTCTCCAGTGCTGCCCGTGTGTGCTGTGTCTGCCAGTGCCTGCCTGCACAACAGAAAGCTGCTTCCAGATTGCTTTCTCTTCTACTCCCCGCTCATCCAACATCCATCTTCGCCCACAGGTTGCCACTCTTCAGGTAAAGGCAAGTTCAGCACTCAGACCAGGTCTCCTTGCTATAATTTTCAATCCAGCCAGTTCCGCCATCCCACCGGCTTACTTTGTAAAGCTTTTCTCTGACTTAGGATCACTGTGAAAGAGCCAGCAGTCATTAACAGATACAGAGGGCTTTGTTTACATTTTTTTGTTTGGTGTTGTTTTGTTGTTGTTGTTTCACTGTGGTAACAGTTATCAGTGGTGATCTAGATGGATGCCTTGTACCAACTAGTGGAAAACCCCTCAACTGTCCCCTCTTTGAACCTATGGCTTGGGCCTCAAGAAACCCTCTTCCTACGAGTTTATACACTTTCCTCAATCCCTAGTTTCACAAGGGATTCAGGCAATTACTGTTAACAGTCTAAAAACAAGTCAAACTTTGTTTCAGCCACAGGGAAGGCTTAGTGCAATGGGAGGTACACTTGGGGTTCCCGAGATACACCATCAATCCTGGGGCGTTGCTAGTCTCCACCCAAGACTCCCTCCTTGGCACACCTGTTTCTTCTGCCTTATCCAGTCATTCCATGAAGTAAGTGTGTGTGTGTGTGTGTCCCACTGAGTTTAACTACAGTACCTTGCATGAGCAGAGGCAGGGGTTATTAATAGAAAATGGACAACTTACCATTGGTTATACCACTGAAGAAAATGATAACCTCCGTTGCTGCCCAGCCACCATTAACAAGGAAGGGTGGAGTCTCAGGAGCCTCTCCCCAGTGGGCATGATGGGGTGATAATGGACCCCTATCTTGTGCAGGTGGTAAAGTGTTCATGAGTGCACGTGTAGTGTGCAGAAGACCATGTCTCATAGCCCCCTTCCCTCCTACTGGCTCCTCCATTCTTTGGCTCCCTATTTTACAATGTTACTGAACTGTAGAAGGGGCAGTAAATATGTCTCACTTAGGGTCAAGCCCTCAACTGGGATTCTATGCATCAACTGTCGCCAGCTCCTCTGACCAGACCTGAATATGCATAGAAACGTTAATCTATGCATACGAATACAAGTATCTTTAAAAGCCTAGTCATTTTTTTAATTTCCTGCTTCCCAGTGAGTGCTGACAAATATTTAATTTCCACCCAGGTGTATTACCCTAGCTTTAGCGTATTGTAAACACATAATTATAAATCAGCAGGCAGAGAAAATTAAACATCCCATCTGTGTGTCAGGGTTGGAAGAAAATGAATAGTTCGGTAAACCTACATCCTATTACATCTAAATAAGTCATAATGGAGGTAGCATGCTCCATTGCTGGCCTACCCACGGTGCACAGTCTCACCAAAGCCATGCACTATAAGCTTACTCTCAGGAGTAATGACTGACCGCGTCACTTACTATCAGCATCCAAATCCTTAAAGAATTTTAATCAAGCAAAGATTCCCTTCACAAAAGTCAAACAATTTATATCTCAAGATATTCATTTCCTTTCTTATGTTTGAAGAGCAAAATCTGCAAGAACAGTATACTATTTTTTTCCTTTAAATTAACACTAAAATTGTTTTTTTTTAATGGAATTAGTCTTCGTTTTTAAAAGCTACGGCTCTATTGGACAACATAGTAATTAAAAATCTTAAGTCTTCAAGTTAGGCTCCCACTTAAATCCTGTGTCCTTAACTCTGTGGTCCTTATTAGCCATTTGACCCTCTGTAAGTTACTTAGGAACACTAATTAAATGCTGGTTTATCTCCAGATTTCTTTTGAGACAGAATCTCACTTCCAGGCTGGCTATTGGGTAGAAGAGCTTTCTATTTCCTCCACCTCCTGAGTCCTGAGATTACAGGCACGGGACATCGAGCCTAGTCTGTACATTGCTGAGGATCACACACAAGGTTTATATATGATAGACAAGCACTCAACAACTGAGGTACATCTCCAGACATCTATGGTTTTTCTCTTGCCTATGCATATGTCACTAGGTCTCACTGTGATATCCTGGCTGCCCTGGAACTTGCTATGTAGACCAGGCTAGCCTCAAACTCACAGAGATCTACCCACCACTGCCTTGCAAGTGCTAGTGTTAAAGCTGTGTGCATGTGTGTATGCATGAATATATGTGTATGTATGCATCACGTCCAGCCCCCTTTGCTTTCCTACAGCCTCTGATGAAGAAACCTTCAGATCAACAGGTAGTAAATGTTGGTCGTTCTCCTACTGCAAGAGTTTTGGAGACTCCTAATCTCGCTCCTCTCTGCTACACCCGGCAGGGGCACGAGAGCACATTCCAAGAGCAGTTCTGTAGTTTTGAGGAAACTGAGGTCTCGAGTCCCTTTTCTTGTTTTCTTGGTGTCTTCTCACAGGCTCTCCTACAATCCCTTTCTCAGGCCATGTTCCAATGTCCCAGCATGGTGGCACTTGCCTATCATCTCAGCACTCAGGAGGCTGAGGCAGAGAGATGAGGAGTTTAAAGTCATCCTTGGATGCATAGCAAGTTTGAGCTCAGCCCGGGCTACATGGGCATCCTTTGTTTTCTAAGACAATTCAGTTGAAGCATGCAAACGCTTTGTATCAAAAGCTTTAGTCAAATGCATTTTATATCAAGTGATTTGTGTTTTGTTTTGTTTCACTACAG
Seq C2 exon
ACTTCTCCCTAGTTTTATTGATAAAAGGAGGAGCCCTCTCTGGAACAGACTCCTACCAGTCTTTGGTTAACAAGACCTTTGGCTTTCCCGGGTACCTGCTGCTCTCTACCCTACAGTTTATGTACCCTTTCATAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000061171-Slc38a11:NM_177074:3
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

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

				
Domain overlap (PFAM):

					





						

							
C1:
PF0149013=Aa_trans=FE(26.0=100)

							
A:
NA

							
C2:
PF0149013=Aa_trans=FE(46.9=100),PF0149013=Aa_trans=PU(3.2=19.6)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000108039





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000108038, ENSMUSP00000118837, ENSMUSP00000120737, ENSMUSP00000121205
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr2:164945728-164952706 
ALTERNATIVE
HsaINT0152825
(SLC38A11)
Human
(hg19)
chr2:165802238-165809216 
ALTERNATIVE
HsaINT0152825
(SLC38A11)
Rat
(rn6)
chr3:51410987-51414064 
RnoINT0137914
(Slc38a11)
Cow
(bosTau6)
chr2:31394980-31401156 
LOW PSI
BtaINT0135567
(SLC38A11)
Chicken
(galGal4)
chr7:19504805-19505934 
ALTERNATIVE
GgaINT0050389
(SLC38A11)
Chicken
(galGal3)
chr7:21483496-21484625 
LOW PSI
GgaINT0050389
(SLC38A11)
Zebrafish
(danRer10)
No conservation detected
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"