Special

MmuINT0160103 @ mm9

Intron Retention

Gene
ENSMUSG00000002489 | Tiam1
Description
T cell lymphoma invasion and metastasis 1 [Source:MGI Symbol;Acc:MGI:103306]
Coordinates
chr16:89794923-89798379:-
Coord C1 exon
chr16:89798277-89798379
Coord A exon
chr16:89795011-89798276
Coord C2 exon
chr16:89794923-89795010
Length
3266 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGC
5' ss Score
9.88
3' ss Seq
TTATTTTAACTTATTTCCAGATG
3' ss Score
8.66
Exon sequences
Seq C1 exon
GTTGGCTCTCACAGGCTGTCAATCTACGAGGAGTGGGACCCTTTCCGGTTTCGCCACATGATCCCTACCGAAGCTTTGCAGGTCCGAGCTCTGCCCAGTGCAG
Seq A exon
GTAAGCACTGGCGTCTGCCAGGTTTCCATTTCTCTCCTCCTCCTTCTCCTTCTCCTCCTTCTCCTTCTCTTCTCCTTCTTCCCCTCCTCCTTCTCTTCCTTCCTCTCCTCCTCTTCCTCTGCCTTCTTCTCTTTTATATTAAAAAGCTGGGTATGTTTGTATATGCATGCATGTGTTATGTCACTTCCTGGGGAGGTAAGAGGACAGCTTGCAGCAGCTGCTTCTCCCCCATCACGCAGGACTCAGAGTTTTCTTAGGCCACCATGCTTGGCCACAAGCACCTTTGCTGCTAAGTCATCTCTCTGGGCCTGGGTTCCCATTTCTTACCCATGTGTGAGTTATGTCTATATTCATTCCTGGTCTGTCCTCCTACCTCTTATCTTCTATGCTTAAGTTAATTCTTCCCTCTATCTCCATTGCCTCATATTAACACACACATACACACACACACACACACGTATACACACACGCATATGCACACAGGTGCATACACATATGCATGCACACACACGCACACATGCACATATTCTACCCATATACATATGTGTGTGTGTCTGTCTGTCTATCTATCTATCTATCTATCTATCTATCTATCTATCTACACATATATATATATTAACTGCTGAGCCATCTCCAGCCCCCTTTTTTCATTCCTTAAAACCTTAATACAGTATATTTTGATCATATTCACTCTTCCCCAACGCCTCCCAGATTTCCCCCCATCACTACCCCTTCCCAAACTCTGCACTTCTTCTTCTTAATCGGTAACCCACCAAGTCCAATTTGTGCTACGTCTGTACTCAGGAGTGTGGAGACTAATCTAATGGAACATGGTGGCCACACCCTTAAAGAAAACCAACTCTCTTCTCAGAAGCTGGACTCTCAGTAGCTGCTCAGCTAGGGGTAGGGGCTGCGAGCTCCCATCTCTATGCTAGAGTATTCACTACACTGCCTCCTTTTAAACAGCTTCATTAACTAGTGAATGAATGAATGAATAAATGAATGAGCCGATTAAGCGAGCAAGCAGAGTAGGTGCATGGGATTTTCTTTAGAATTGTTGTAGGGGATTGCAAACTTGATTTACAGGTAAATTGGCAGGTGCTTTGGGATCGTAGGTCTATTGCCGCTGTGGTAGTATTTTGAGGTTTAGACACTTAAATGCTAGTGCTGTCCCTTTTAAAATTGATATATGTGTATTAGAGTTTTGTTTGCTGGTTTGCTATACGCCATATGCATGCAGTTCCTGAAAAAGCCAGAAGAGGGAGCCAGACCCCCGGAATAACACTTGTTAGTGGCCATATGGGTGCTGGGAAGTGAAGCCAGGTCCCCTGGGAGAGCATCGGAGTCTTTTAACCAATGAGCCACCTCTCTAGCCCCCCCCCCCGATGTCTTTTAATGCCATTGTCTTAAAGTTAATCGGTTTATGTTATCTGATCATATTTCCTCAGACCAGGTTTATAAATGTGGAGGCTGATTTCTGTGGCAGGCAGTGGGCTTCTTAGCCAGGAATTTTGCCTTGGTTAAGGACATAACTTCACATTCTGAAGACAAAGCAGCCTTTGTAGTAATGACATTTCGTCCTCCCAACCTCTGCCTTTCATTCAAATCAAATTTAAAGCCTTGCAGATAAAAGCATATTTTAGTTGAGTTATAAAGACTGGTCACAATGCTACATTATGGGGTACATTCCAGTGGATTCAAGAGACAGTACTTGAAGTTTCTAGATTTTTGTCTGAGTTTGGGGAAGTTTGGCAGATAGAGCATTAGGTGATGTAGCCATAGGGGAGGATTCTGAACCACTGGGGAAGTCGGAGCCTACAGGTGTGGAGCCCCTTACCCACCACTTAACACAATGTTGGGTTGTTGGCATGACATAGCTTCAGTCCTTGGAGCTGGCCCTCTGTTTCCATGGGTTCCACACCCGTGAGCCCAGCCAACAGTAGCTGGCTCTGTGGGTAAAGGCACTTGCCATCAACCCCGACGACCCGAGTTTCATCTCCAGGGCCCTGTGGTGGAAGAAGACAGCAGGCTCACATGTGTTCCCCAGCTTTTACGCGTGCCTGCTCACAGTAAATCCGTGAATGTTAACAGATAGTTTAAAAGAATACAGAGAGCAGCAGCTTCGCTCCCTTAACGCACAGCTCTGCTCTTGTTTAGTGGACAACTTGGGGAGGCTAGGAGAGGAATGTTTTGTTTTGGTTTTCAATTGTTTTATTTATTTACATTCCAAATGTTGCCCCTGACCTGACCTGGTCCCTCCTCCAAGAGTTCTTCATCCCATCTCCCTCCCCTTTGCCTCTGAGAGGGTGCTCTCTCCTCACCATCTCCCCCTCCACCCCCTCCATTCAAGTCTACAGGATTAGGCGCGTCCTCTCCCACTGAAGCCAGACAAGCTCTGCTACATATGTGCCAGGGGCCACGGACCAGCCCACCTATGCTCTTGGCTGCTCCGTGGCCCCTAAGCCAAGTCTCTGAGAACTCTTAGGGGAGTCCAGATTACTTGATTCTGTTGTTCTTCCTATGGGGTTGCCATCCCCTTCAGCTCCTTCAGTCCCCCCCAACTCTTCCATGGGGTCCCCGACCTTAGTCCAGTGCTGGGCTGTGAGTATCTGCATCTGTCTCAGTCAGCTGCTGGTAGAGCCTCTCAGAGGAGCCGTGCTAGGCTAGAGAAGCCTGTTTTGAGTCACCAAGGTAACCTGTTTGGGCGTTAGCTGTGGTCAAATAGAGAGAGGACTCCAACACATAAGCCAGTGCTGGCCTCCCCTTGCCCTGTCCTGGTGAAGGTGCGCACTGGGCTCCGAGGAACCATTGGCCCCAAAGAACTTAGCGCCTACCTGAACTAGTTCAGCCCACGAGGCTGGGGAGCAGGGTGGCTTTCCTCAGTGTGGCTCATCTGCGAGGCCATCTGCGAGATCTTCATGGTGTTGTATTAAGATCTGTGTGTGTGCGCACTCGTGCATGCTTATGCGTGTGTGTGCCTGTGTGTGAGAGAGAGAGAGAGTGAGCATGTGCGTGTTCTGTAAGCCCCTCAGTCTCTTAACCACTTCCCCCTCTCTCCAGCCTCTGTTCTGTTCTTCACAGCACACACTGAGCTCGTAGCGTCCGTCTGTCTCTTTAGCTCAGGGTGGAGGTGAAGTGACTTTGGTCTCAAGTTGCTTTGCACTGTCTTAAGCAGACACCAAGCATGAAAAATTCCTCTGTAAAAAAAAAAATAAGTAAGTCTGCTAAAATATGCCAAACCTGACATTATTTTAACTTATTTCCAG
Seq C2 exon
ATGCAGAGGCAAATGCGGTATGCGAAATTGTCCACGTGAAATCAGAGTCAGAAGGGAGGCCCGAGCGGGTTTTCCACCTCTGCTGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000002489-Tiam1:NM_009384:25
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:
PF0016924=PH=FE(25.6=100)

							
A:
NA

							
C2:
PF0016924=PH=FE(21.8=100)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000002588





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000109757, ENSMUSP00000109759, ENSMUSP00000126020, ENSMUSP00000132137
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr21:31127153-31130212 
ALTERNATIVE
HsaINT0167075
(TIAM1)
Human
(hg19)
chr21:32499471-32502530 
ALTERNATIVE
HsaINT0167075
(TIAM1)
Rat
(rn6)
chr11:29939091-29942237 
LOW PSI
RnoINT0150919
(Tiam1)
Cow
(bosTau6)
chr1:3712474-3715483 
Chicken
(galGal4)
chr1:103794691-103795425 
ALTERNATIVE
GgaINT0116828
(TIAM1)
Chicken
(galGal3)
chr1:107922847-107923581 
LOW PSI
GgaINT0116828
(TIAM1)
Zebrafish
(danRer10)
chr10:25615040-25615367 
LOW PSI
DreINT0163190
(tiam1a)
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"