Special

MmuINT0157250 @ mm9

Intron Retention

Gene
ENSMUSG00000048720 | Tbc1d12
Description
TBC1D12: TBC1 domain family, member 12 [Source:MGI Symbol;Acc:MGI:2384803]
Coordinates
chr19:38970477-38973476:+
Coord C1 exon
chr19:38970477-38970559
Coord A exon
chr19:38970560-38973358
Coord C2 exon
chr19:38973359-38973476
Length
2799 bp
Sequences
Splice sites
5' ss Seq
GAGGTACAT
5' ss Score
6.75
3' ss Seq
TTCTTACTTGTTCAAAACAGAAA
3' ss Score
6.1
Exon sequences
Seq C1 exon
GAATCTTCCTGCGAAATCTGTGGAAGAAGCGCTGCGTCACCGGCAGGAGTATGATGAGATGGTGGCCGAAGCTAAAAAACGAG
Seq A exon
GTACATTTGAATTACAGTGTGACGTTAATTTGTAGATTTTAACTATTTCATTTTATTAAAATAATTCTTATTTTTCTCTAGCATTTTTTTATAATTTAGGTTTATTTTAGGGTTTGTTGTTTGTTTTTAATTTTTTGAGACCGAGTCTCACTATGAAGCCATCTGCCCTTGAGCTCATCATAAATTTCAGGACTCTAGGGGAGTGGGGGGGGGAGTGTATTGGGGACTTTTTGGATAGCATTGGAAATGTAAATGAGGAAAATACCTAATTAAAAAAAAAATTCAGGACTCACCCTCTGTAGTTCTGGGATCGTAGGCGTGAACCGCCATGCCCAGACCTGGTTTTTCTTTTCTTTTCCTTTCTATTAAAGAGGACTATAAAGATGTTATTCGTGAGCCTTATTCCTAGCACTTCATTTTTAGAGTGTTTAGACTTTAGGTCTTTTACATTTAATAATTTTTATGCAATAGCAATCAGTCTTCTGGTGTTAGTTATAGTTTTCTAATTTACTGTCAAAATATAGTTTGAAGCCAAATTTTGCTTTTATAATTAGTAAAGTCTATCTAAAATCTCAGTGCTGTCACTGAGTTAGGTTTATAAATACTCTCATTAGCACAAATCATAGTTTTATTCATTCTCTTTTCCTCCTGTCCTCCCGCCAAATACATATAAGTTTACTTTAACACTATACAGAATATGTGCTGACCATCATTAGTTTAGGACAAATACTCATTTTTATAAATATGTATTTCTAATATATTTTTGAAATATTTATTTTGTATATATTTTAAGATGAAATTTATTAACTGATTTTTTCTTTGACTTGAGCAAGTGGAGTATGTTATAGTAGCATACAGCTCTGCTTTGTGCTGCTATTTCCTAAGTAACGTGTCTTTAATGTTACAGTAAACATGAGGTATATAAAAGTCCAGTTACAGCCTTCTAAAATTCCTAGTTATTTGAACACTGGCTAAGTTTATTTTAATGCATAGAATTAAAAATACTTCTTGAGTTCAAGGCCAGCATGGTCTACAGAGTAAGTTCTAGGATAGCCAGGGCTACACAGGTTTTGAAAAAAACAAACAAAAAACCCAACCAAACCTGTTTTGGAAAAAAAAAAAAAGGAAAAAAAATTTTTTTAGCATAGCCAGAAAGCTTTTATTTACTATTTTATTATTTGGCTAATATTTATTGAGAAGTAGATGGCACATGGTATAATAGAAATAATAAGATGTTGGGCATCCCAATGTTTTAGGCTTAATCCAATGATGTGTGGTTTCTGACTGTGGTACTCTGAGTATGCCCACTGTGCATCCTTATCTGTAAACTGGAAGTAGGTGACTAGGTTAGGCTTCTAACCTCTTGTTTAATGCTTCTTTCTTAAAGACATCTTACATATATAATCTGGATACATAAAACAGCGGTGTACAGCAAGTGCTTGGCTTCTTGTTTGCCCTTTGAGTCACATTCAGAGACACACATGAAACACAAAGTTTGGCTAGCTAATCTACAAGTTCTTATTGGTTCTAGCATTTTTTTTTTTAAATAACTTTTTGGTTGTTGGTTTGGTTTGATTTGGTTTGCTTTTTTTTTTTTTTTTTTTTTTTTTTTGAAACAGGGTTTCTTTCTCTGTGTAGCCCTAGCTATTCTGGAACTCACTCTGTAGTCTATGCTGGCCTTGAACTCACAGAGATCAACCTGCCTCTGCCTCCTGAGTGCTGCGATTAAAGATGTGTGTTACCATCATCTGGTTTTATAACTTTTGAGAAAGATCCCACTTTTCTTTATGTTTGAGGCAGCTTTTGTTCCAAAATTGTGACCTCTAAATTCAGAGGTATGTCATTTTTGTTTGTTGAGAACATTTTATTTTGACCTAATTAGTAAAATAAAACACCATACTAAAAGGTGTTTATATAATAATAGTGTCATTGGCAACATCATTTAAAATATATTGTTTATGTTGAGATTAATAATCCATTGTATGAAAAGTGGCCCTTGGTTAATTGCCTGCAGTTTTTATTGTAATTATTTCATCAACAGATTTTATTTTATAGATGAAGTAAACAACTGTGTAATATAAGCAGCCAGGCATGGTGGTGCACACCCGCACTCCCAGCCCTAGGAGGCAGTGGTAGGAGGCGGATGAGGAAGTATGTGTGAGGACAACCTGGTGTACAGATTGAATTCCAGGCTATCCCAGAAGAGACCCTGCCATACCTTACAGCCTGGAGAGAGTGCCTGCCTAGTGTAGGCCAAGTCCTGGCTTAGAGCCTCAGTATTGCATAAGCCAGGGGTGGTGGCACACATCTTTATCCCCACATTGGGAGGTAGAAGCAGGGTTATCAGTAGTTCAGGGTTATTCTAGCTTCATAACAAGCCCAGCCTGGCCTACTTGAGACTGCCTGAAAAAAATAAAGGATATAAAAGAGAGAAGAAGGAGAAGAAAGATGTATAGACCAGCCAGTTAGCATAGGACCTTGTCTAGATTAAACCAAAGCGAAAAACAAAGCAACAACAACAACAGCCAGAAAGAAAGAAGCAGCAGAGCAATTCACTGGCCATTGTTTAAAATTGATTTTGCCCTTTATCCCATTACTTTTATAAGATAGAAGATACTTTAAAATGATGTTAGACAGGGCTTTGTGTTTCTTCTTTTTCTCCCCCTTTCTTTTTTTTTTTTTTTTTTCTTTTTTACTATGAGAAGGTCCTTCTTGAATCCTTATAGATTTAAGGTACAGAAGGAAGGGATTTTGGTCTAGCTCATTTATATTGAAATAATTCTTACTTGTTCAAAACAG
Seq C2 exon
AAATTAAAGAAGCACATAAAAGAAAAAGAATAATGAAAGAACGATTTAAGCAGGAAGAAAGCATTGCAAGTGCAATGGTAATTTGGATCAATGAAATACTGCCCAATTGGGAAGTAAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000048720-Tbc1d12:NM_145952:4
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.221 A=NA C2=0.050
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF0056613=RabGAP-TBC=PU(2.4=17.2)

							
A:
NA

							
C2:
NO

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000037884





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000037884f4680A, ENSMUSP00000037884f4681A
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr10:94493448-94497054 
LOW PSI
HsaINT0163980
(TBC1D12)
Human
(hg19)
chr10:96253205-96256811 
HsaINT0163980
(TBC1D12)
Rat
(rn6)
chr1:257572771-257584877 
ALTERNATIVE
RnoINT0147918
(Tbc1d12)
Cow
(bosTau6)
chr26:15828916-15830887 
LOW PSI
BtaINT0145402
(TBC1D12)
Chicken
(galGal4)
chr6:19634583-19635990 
LOW PSI
GgaINT0040075
(TBC1D12)
Chicken
(galGal3)
chr6:21155953-21160233 
LOW PSI
GgaINT0040075
(TBC1D12)
Zebrafish
(danRer10)
chr12:5403355-5404034 
LOW PSI
DreINT0160555
(tbc1d12b)
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"