Special

MmuINT0160576 @ mm9

Intron Retention

Gene
ENSMUSG00000041997 | Tlk1
Description
tousled-like kinase 1 [Source:MGI Symbol;Acc:MGI:2441683]
Coordinates
chr2:70592497-70595606:-
Coord C1 exon
chr2:70595531-70595606
Coord A exon
chr2:70592544-70595530
Coord C2 exon
chr2:70592497-70592543
Length
2987 bp
Sequences
Splice sites
5' ss Seq
AGGGTAAGC
5' ss Score
9.04
3' ss Seq
TTTTATTTTTTATATTTTAGGAA
3' ss Score
11.86
Exon sequences
Seq C1 exon
ACACCAGAGAAGAAACAATCAGAGTCATCCAGGGGAAGAAAGAGAAAAGCAGAAAGTCAGAATGAAAGTAGTCAGG
Seq A exon
GTAAGCAGATGCCATCTTCCTTCAGAGACTGTGCACATCGAACAATCCATTACTCGGAGTTTTAACTAATTAGGGGAGTAACTATTGAATAAGTGGCTTTGTGGTTTGGAAGTTTTCCATCTAGTTCTTTGTATTTACAATATTCTTTAAATTTACAATTTGTATTTACAATTTACATTCTTTGTATTTACAATAGCTTAGGACTGTACTCTAGGAAGTACAAAAAGCTCATGGTTACTGTTGGGGACTTTGACATTTTTGTGTTGTTTATTGGGGCTTAGAATCTTGTAGGCATTCCTTTATCTCCTTTCAGTTTTCCATTCTAGCTCACCCATTCTCTTTTTTATTAAAAAAACAATTACAGGAATAATTAGATTCTCATTAAAGCACCTGTTTTTGGTAATGCCTATTTTCATCCTTTCTTATATATCTACACTTTGTGATGCAAACTAAAAAGTTATTTTCATTATATTACACATACTCTTTAAAAAGTGTGTGTGTGTATGTTGTGTGTGTGTGTGTGTGTGTGCGCGCATGCGTGCGTGCATACGCACTCGCACATGTGCTTTTATGTGTGGTGCTTGTGCCTATGTGCTTGCAGATGAGTGTATCTGTGCTTGTGTACACAGGCCAGAAAGAGTGTTGTTTGTCAGGATTCCTCTGTCACTTTCTGCCTCTTTGAGGAAGAGAACATCCCTGAACCTAGGGCTCATTTTTCTTGCTTGGGCTGGAAGCCAGGAAGCCCTAGTAACCCTCCAGTCCCCTTTCTGCTGGGACCTGGAGTTACAGGTGTATTAAGATGCAGAGCTTGTTATGTGGATGCTGGGATCCGTCAGTTCTGGGATCTGGATTTTAATCTATGTGATCACACACCAAGCACTTCGGACCAGAAGACATGATTTCTTATAACCAACTGGTACTGTTTAATTTGGGCCCTGGAAAGATGTACAGTAACTGGGGTTCCTCAGTCCTGTATACATAAGAGTTGCATGTTTTGCAGCCAGTCTTGTGAACTGCCTATCACTTACATAGAGCACTGGCATCAAAGGGTGTGCTATAGCAGTTGTCTGGGAAACAGAACAGATTTGTCTAGGGCCTTTTAAAGGTGTATAGTGTGCTTGATCTGACGTTACAGTTGCTTCCTTTTGTCTTGGAGCAGGCCCTCCAACTGTGGTTAGTGGACATGTAAGTTCAGTGTGAAGGTACATTAACTCATTTCAGCAACAGACTCAGACAATCTTAAAAGTAAACCCCTAAATAAGGTGGGCTTCTGAAGTGGCTTAGCTAACTTGTCCTTAAGAACTAGTGTTTTAGGGAGCTATTGAGTAGCTAAAGGCACTTGCCACCAAGCCTGACAACTTGAGATCCAACATCTGCAAGTTGACCTCTCACCTCCACATATATCCTGTGCCTGCTACCCATGTACTCCCAGACACTAAATACAGTTAATAAAAATGAACCCAGGCCTTTTTTTTTTCTGACTGATCTGCAGCCCACAGAAATGCCTGACCTTCTGGGTGAGAATGATTGCCTAAATTGGATCTCCTCATTTCTTCCTCACTGAACAATTGCTTTAGAATGACACTAGCTTAGTGTGTTTCCCACCCTGCCTTTCCGTACAGTGAGCTTCAAACCCAGAAGCAAACTCCCCTTGCCACCTCATGACTATTTTAAGTCATATTTCCACTCCACCACCAGTAATACATAATAGAAGTGCCATTGCTTCAGGAAATCAGGCCTGTTTCTGAACCTAACAAACAGCGGAGTATCTTCCTCCTTAACAATAATGTACCTTGGTGGAGTGGTTCTTGGTTAAAATTCACTTTCTAATGAGGGAAGGACAAAATGGAAGTAGGGCTATATCCTGAAATTTAGATGTCACATATATGGGAAAGGATATCACAGATAAAAATTTACCTTCAATTAGAAGAAAAGAATTGGGGAAATAGCTTCTAGGTTGGCAACCCTCTGTGTTCTTTACTAGCCAATGGTATCTCTTCAGAATTTTCAGGGATGTTATCAGAGACAGAAAAGAACATTCCTTTGGGATCAGTCTCTGTAATCTAGTCTGACTTAACTAAATTGATATGAAACTGTTGTTCAAAAAATTTTAATAGCATTTGTTGTCTCCAAGTCCTAATTTTTTCCAAAATGGTTCTTTAAAACTCATAGAACTGCATTTTAGGGCAGAACATAAAAAGAATGGTGTGACCTGTCAGAAGACTCCTTAGCAATATGGTCTTAAGAACAATTTGTTAAAAGTAGACTTTTAAAGCATACATCCTGTAAATTTACATCATTTAGAAAACACAGTGAGACCCTAACTAAAAGAGAAAAAAGACAAAGAAAATCAGAACATATTTTACAAAATAACATTGACAATAAGCATATTGTTGTCTGCCCAGCATATTAGATTTGGGTTTGCATCATCCAAAGCTGGTTTTCACTACTATTCTTAACAAAGTGTGGTTTAGTTTGTCAGATACAAAGTTGCCATTTGTCTTTTTAGTTTATTGTTTTTTCTTCTTTTCTGGGATTAATAGATTATTAAGAAACATTAGTAATGTTTTAAAGATCAAATTCCGTTTGATGAGGGATTGACCATGCAGCTCAATGGTAGCATAGCTGAAGCCCTCAGCTTCAATCCCTAACCACTCTCCAACAAAGGAGAGAGAGGGTTGAGAGAGAAAGAGACAAGGGGTTTCTAATGTTATTTATCTGAGTTTTCAGCAATTACTACTTTCATAAATTGGCATATTTCTATTAAAATGTGATTTGATTAGATTTTATAAATGTTTAAAGATTATTAGTATTTTAAATCCTCATCATTACCTTATTAAAATGCCACACTTAAATAAATGGTTTTATATGCTTCTAATTAAATAAGTTATATTTTAATTTGGCACTTTGCTCTTTTTGATGTAATAAATGTTAGATAATCATGACTGGCCTTTAAATCTATATAATTTTTATTTTTTATATTTTAG
Seq C2 exon
GAAAAAGTATCGGGGGACGTGGCCATAAGATCAGCGACTATTTTGAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000041997-Tlk1:NM_172664:4
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
No protein impact description available





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=1.000 A=NA C2=1.000
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
NO

							
A:
NA

							
C2:
NO

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000035961





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000035961f4324A, ENSMUSP00000131521
  



Associated events






Conservation


Human
(hg38)
chr2:171058198-171061080 
ALTERNATIVE
HsaINT0167553
(TLK1)
Human
(hg19)
chr2:171914708-171917590 
ALTERNATIVE
HsaINT0167553
(TLK1)
Rat
(rn6)
No conservation detected
Cow
(bosTau6)
chr2:25430227-25433506 
LOW PSI
BtaINT0148515
(TLK1)
Chicken
(galGal4)
chr7:17622804-17625260 
ALTERNATIVE
GgaINT0048974
(TLK1)
Chicken
(galGal3)
chr7:19582356-19584812 
LOW PSI
GgaINT0048974
(F1P396_CHICK)
Zebrafish
(danRer10)
chr9:3611968-3613125 
LOW PSI
DreINT0163683
(tlk1a)
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
  • 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"