Special

MmuINT0160594 @ mm9

Intron Retention

Gene
ENSMUSG00000020694 | Tlk2
Description
tousled-like kinase 2 (Arabidopsis) [Source:MGI Symbol;Acc:MGI:1346023]
Coordinates
chr11:105137151-105140539:+
Coord C1 exon
chr11:105137151-105137262
Coord A exon
chr11:105137263-105140431
Coord C2 exon
chr11:105140432-105140539
Length
3169 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGG
5' ss Score
9.16
3' ss Seq
ATTCTGTTTTTATGTGACAGCCT
3' ss Score
6.1
Exon sequences
Seq C1 exon
GTATTTACCACCAGAGTGTTTTGTGGTTGGGAAAGAGCCACCAAAGATCTCAAATAAAGTCGATGTTTGGTCAGTGGGTGTGATCTTCTACCAGTGTCTTTATGGGAGGAAG
Seq A exon
GTGAGGAAGAAGGCAGTGGAGCAGCCTGGGGCCATACCCACCACCTCACTGGGATTCTTCTTTGCAGTTAATCATTGGAATCCTGAAAGTAGTGGTTTAAAGAAAATACAGACTTCTCAGTAAATGCTTTGTGTATACCTACAAATTCCAGGCTGAAGAGCACCTACTGAATTCTCCCAAGCCATCAGAGACATGCATGTTGCAATCTCAAATATAAGACATGTTTTAATTCTGATGTGAATTCATGTAAAATAGGGTGTTGTATTTTTTTAAGATTTTGCTTTGTAGCTGTGGTTGGCCTGTACTATATACGTAGCAGAGGCTGACCTCAGACTCAAGGCAATCCCTGTGCCTCAACCTCTTGAATGCTGGTATGACATCACGTCTGTCTTGAAATCCTTTAGTGGCATGAACAATCTGCCAAAAAAAATTTCCCAAGCTTTCCAATAGGATCTGAAACTTAACCCCTAGATTTTATTTGTAACCACCTCATTAGATAAAAGCTGTTGTTAATAAAAAAAACATACTGTGTGCTCGTGTGTGCTTGTGAAGCCTAGAAGTTGACCTCAGGTTTGTCATTAATTCTCCATCTATTTTTTGAGTAAGGTCTTTCACTGAACATGTCTGAGCCAGCCTGGCTAGCTAGCAAGTCCCCACAATCTCCCTATGTTGGGACTACAGGCACATATGCTGCATCTGGCTTTTTTGTGGGTGCTGGGGATCAAAATCAGGTCCTCATTTTTGTATAGTAAGTAAGCACTATACTGTTTTATTTGTTAATTTTGTTTTGTTGAGACTGGTTCTCACTATGTAGCCCTGGCTGGTTTGGAGTTGTCTATGTTTAGATCAGGCCGGCCTTAAACTTACAGAGATTGTCCTACCTCTGCCTCATGAGCACTGGGATTATTAAAGGAGTGAATCACCATACCTGGCAAAGATTTATTATTTATTTATATGTATGTATCTCTGAGTACATGAGTGTGTGTGCCCATGGAAGCTGGAAGAGGGTCTCAGATACCGTCCTTGTTTGCTTCCTGTTGCTGTGATGAGCACCAGACAAAAGCAAAAGCCTGTCTCAGGAGGTGGTATTAGCTCATGCATCAGGATCATTGAGAGAAATCAAGGCAGAAACCATGGAGGGATGCTGCTTACTGATTTGGTCTTTGTGGCTTGTTCGGCTTGCTTGCTTATATCAGCCAGGACCACCTACTCAGTGACACTACTCACAGAGGGCTTAGCCTTTCCACAAAAAAGCCAGGACCACCTACTCAGTGACACTACTCACAGAGGGCTTAGCCTTTCCACAAAAATCCTGAATCAGGAAAATCCCCCTTGTCTTGCCTATAGGCATTTGATGGATACAATCAAATAAGGTTTCCAGATGACTCTAGCTTGTGTTACGGTGACAAAACTAACCAGCACAGATACCTTAGTGCTAGAATTACAAGAGGTCGGGGGATGATAGACTTGGGTGTTGGGAACTGAACTGGGGTCCTCTACAAAAAAGGCAAATGATCTTAGCTGCTGAGCCATCTCTCCAGCTACCCCTCCCCTCCTTTCTTATGCTGAGAATGAGAAGGTGGTGTCAGAAAGTATCCCTTAGCCAGGTGTGGTAGTTCATACCTATAATACCAGTATTTTGGGGTCTGAGACTAGAGGATCCAAAGAATTCATGGGAAACCTTTAGTCCCAGCACTTGTGAGGCAGAGGCAGGCAGATCTCTTGAGTTCAAGGCCAATCTGGTTTAAAAGGGAGTTCAGGACTGCCAGGGCTATAAGAAAATCATCTCAAGAAAACAAAACAAAACCCAGAAAAACCATCTCAGAAAAGTAAGGGCTAGAGATGTAGTTCAGTGGTACAGTATGTAACATCTACAAAGCCCTGGGTTCCATTCCCATGCCCACACAAACAGTAATTCTTTTCTGCTTCTAATAAAGGTCTTATATCATTAGAACAAACAATGATGGTATTTTCCCTCTGAGCATGTCTTTTATACACCCACACGTGTATAGTATATAGTACATATTAGGGTCCTGTTGTGTATTCATATTCCTTCTGCCTTTAGTGTTTAGGCAGAAAGCAAATGGGAGTTTTGTAGGCCCTGTGAACTCTTAATATTTTTATTAGGTTCCCAGTGCGAAGTCTTTAATGTGCATAATGCCTTCCTCTTTAGCCTCTTGTCCTTGGACCAGCCTTTACCCGACAACTATGCAGAGCTAGTAGAGCTTAATTATTTTGTGTTCTGTTTACGAATGTTGAATTGTTACTGATACTAGCGATAGAGGCTATGTAGAATTATTTCAGATCTGTTAGGGACACTGAGCTTTTAACCTGGTTTTTAAAGTTTTTGTTTTTGTTTTAAGAAAACTGCAGCTTGAGGCACAGTTAAAACCCCTAGGTGTTCCCAGGCCTTTGTTGTTATCTGCCAGGTTTTGTTTCTTTCGAGGTGGGATCTTTGTTACATAGTCCAAACTGGCCTAGGGCTCACTGTGTAGCCTTTGCTGGCTTTGAAATCACAGTGACTCTCTTGTGTCAGCCCCCTAAGTGCTGAGGTTACAGTTATGAGTCCCCATTCCCATCCTTCATACTGGATGCCAGTAAAACATTTTCTCTTCTAACCTTTTTTTTTAGATTTATTTTATGTTTTTGAGTGTTTTGTTTTGTTTTGTTTTTTCCTGCATGTACATATGTGCACTACATGAGAGCCTGGTACCTACTGAGCTCAGAAATTGTGCACTGGGTCCCCTGAAGCTGGAGTTACAGATGGATGTGAACCACCATGTAGTTTCTGAGAGTTGAACTCAGGTCCTCTGCAAGAACAATCAGTATTCTCCATTTCTGAGCCATCTCTGCAGCCCCAGCCACACCCATGATTTATTTAGCTTTCCATCCTATTTTGTGTACAAATTAGGTTGGCTAGTGGCACATAAATATGTATAGTCACCAAAGGAGTGAGTCAGGGTGCAAGAGACAGCGGGCTTCTTTCCGACTCTTTGTGAGTAAAGCTGGAGATAGGAGAGAGGGTTTCTACTTCTCTGTCCTGCCTTGAGTGGCCTGTGCGCTCTGGCCTCCCTGTTAAGTGTCGCAGGTGAGAGGTAGAGGAGACTTCTGTGGTACTGAATTGTGTGACCAGAGGCCAACCTTAGTTTATTCTGTTTTTATGTGACAG
Seq C2 exon
CCTTTTGGCCATAACCAGTCCCAGCAAGATATTCTACAAGAGAATACTATTCTTAAGGCTACTGAAGTACAGTTCCCGCCAAAGCCAGTAGTAACACCTGAAGCAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000020694-Tlk2:NM_001112705:20
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.008 A=NA C2=0.000
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF0006920=Pkinase=PD(23.3=69.6)

							
A:
NA

							
C2:
PF0006920=Pkinase=FE(12.5=100)

						

					

				








    
Main Inclusion Isoform:
ENSMUSP00000090198





     
                   









    
Main Skipping Isoform:
ENSMUSP00000102554f819A





     
      









    
Other Inclusion Isoforms:
ENSMUSP00000118520
          









    
Other Skipping Isoforms:
ENSMUSP00000015107, ENSMUSP00000102549, ENSMUSP00000102552, ENSMUSP00000102554
  



Associated events






Conservation


Human
(hg38)
chr17:62606242-62608040 
LOW PSI
HsaINT1044310
(TLK2)
Human
(hg19)
chr17:60683603-60685401 
HsaINT0167572
(TLK2)
Rat
(rn6)
No conservation detected
Cow
(bosTau6)
chr19:47673117-47674619 
LOW PSI
BtaINT0148532
(TLK2)
Chicken
(galGal4)
chr27:2394956-2395972 
ALTERNATIVE
GgaINT0143532
(TLK2)
Chicken
(galGal3)
chr27:2303246-2304262 
ALTERNATIVE
GgaINT0143532
(TLK2)
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"