Special

MmuINT0157253 @ mm9

Intron Retention

Gene
ENSMUSG00000048720 | Tbc1d12
Description
TBC1D12: TBC1 domain family, member 12 [Source:MGI Symbol;Acc:MGI:2384803]
Coordinates
chr19:38982262-38985585:+
Coord C1 exon
chr19:38982262-38982342
Coord A exon
chr19:38982343-38985496
Coord C2 exon
chr19:38985497-38985585
Length
3154 bp
Sequences
Splice sites
5' ss Seq
AAGGTATGG
5' ss Score
9.26
3' ss Seq
TTATCTGTTTGGTAATGCAGGTC
3' ss Score
6.43
Exon sequences
Seq C1 exon
AACTTTATGAAATCTTTCTTTCAAGAGCAAAAGAACGTTGGAAAAGCTTCAGTGAATCAAGTTCTGAGAACGACACGGAAG
Seq A exon
GTATGGGGGTCTCCAAGTGAGAATCTCAAAACTCAGTTACTGAATAGACAGGTGGGATTTTTCTGCCATGTACCAGAAGCTGTGCTAGCTGACGTAAGGGCAGTGCCTGTTTAGTACATGATAGCACTCTGAGCTTCGGGAGGGGAGGAGGCTTAGAGTAGTGAGAAGCAAGAGGCTGGGCTTGAAGTCTGCTCTGTTTATCCCAAGTCCCAGGATTCAAATCACAGTGGTGAAGCTGATGGGCCGAGTGCAGTGTTATCAGACCAAGCTGTTACTACAGGCTGACGTTATTCACTCCTTCTGAACTCCTCCTTGGTACCTAGTAGACTGCACACAGTTCAGTTCTCCTGTGCTCTGCCCTGCTCCTTGTTCATTTGTTTCACCCATTACTCCCATCCTTACCTCTGCCTGGACAGTTAGTTTTCTTAATCACTTTGAAGATTTTTTCCTTGTATCAGATTATTAAATTTGTATTTTGATAATGGGGAATCATTTTCCTAATCTTATCACTTTTTGTTTTATTTGCATGCTTTCTTTCTTAAGTAGGTTCTCATTTGATTTAGGCTGGCCTTGAATTCACTCTGTAGCTGAGGACGACATTGAACTTCTGATGTCCTGCCTCTGTCTCCACGTTCTGGGACTACAGCTATGAGCTACTGCTTCCCGTTATGTGCTGCTAGGGATTGAACCCAGGTCTGAGCAAGCACTCACCAACCAAGCTATACTCCTAGCCACTTTTCCTTTTTTTTTTGGTTTTTCGAGACAGGGTTTCTCTGTGTAGCCTTTGGCTGTCCTAGAGCTCACTCTGTAGACCAGGCTGGCCTCGAACTCAGAAATCCGCCTGCCTTCACTTCCCAAGTGCTGGGATTAAAGGCGTGCGCCACCACGCCTGACTTCTCTTTTCCTTTTTTTTGTATTTATTACTGTATAGAAAGCAAGTTCACTGAGCATGGTGTCACAGAGCCAGGAGGAGCTTTTTGAGCTCAAGGTCATCCTGGTGGTCTTCAGAGTGAGTTCCAGTGTAATCAGGCTGTTACTCTGTTACTCTGTTTTGAAAAACTCATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAAAGATAGTAATAATAGTAATAGAAAAGTCTTCTCTTCCCTTTAAGTAAAACTTTAAAATATATCTTTGAATAAATAAATAGAACTTATCTTATAGTGGTTGCCTGTGAGAAACCACTTTTTAAATTTCTTTTTTCCATTTTATGATAAGCCATTAGGAAAGGGAAATCTTACTGAGTAGTCAAGGAGAGGACTTGGTTTTGAGGACCATGGAAGAGTCATCTCGAAATTGGTTGGCTGTGCCGGGTGGTGGTGACGCACGCCTTTAATCCCAGCACTTGGGAGGCAGAGGCAGGCGGATTTCTGAGTTCGAGGCCAGCCTGGTCTACAGAGTGAGTTACGGGACAGCCAGGGCTACACAGAGAAACCCTGTCTCAAAAAAACAAAAAAAAAACAAAACAACAACAACAACAACAAAAAACCCAAAAAAGAAATAGGTTGGCTGTTTTAGTGATTTTCTGAAGAACTGAAAGTGCAAAGTAAGTGAACATGCATAGAATTATGACCCTCGAGGCCACTGCTCTGCACTGTCCATCCTTCCTTCCTTCCTTCCTCCCTCCCTCCCTCCCTTCCTTTCTTATTTATTTATAGATGCAGTCATATCATATGTAGTTCAGACTAGCATTGAGCTGTGAATTTGCTGCCTCCACCTCTGCCTCCAGGGTTTGCAGGTTATATTCCCATGCCTGGCTCAGTTTTCTATTAAAACAAGTTTTATGAAGTACCAAAATTATACAAATTAAGACTAGAAATATAACTCAGTGCTATAACAATTGCTCAGAGCCACAAACAAAACAAAAAAAATTAAATAAACTAAAATGGCAAGTGTATGAGAGTAGGTTAGGTAACTCACACCTATAATCCCCATACTTTAGAGGTGGAGGCAGGAGAATCGGAGTTCAGAGTCATTTTTAACTGTGTAGCAAGTCAGAGTACAGTGCGAACCACATGAGAACCTGTCTCATGAACAAGCACAAACAAAACTTTTTGTTATGGGTAAATAATGAAAATTATACTTTAGAATGAAGTAATTGAGTGTAATAGTTACGCCAGGGATGGTAAAATGGCTTGGTGGGGAAAGGTTTGCACTGTTAAGTTTGAGGGTGACTGTGATAATAGATCCCATATGGTAGAAGGCGAGAACCAACTCCCACAAGGTGTCACATGTGCACATACTTACACACACTACCTAGTTACTACCGTGGGAGTATTAGTCCGTCTTTATATTCAATAAGAATTAGAACAGAATTTTTTCACTATATATTTTTCTGATGAATGCATTTATGTTTCCTCAATAAAAGAGACTACATTTAAAGCTTGGTATGGGAGCATATGCCTATGATTTCAGTAGTCAGGGGGTGAAAGCCAAATCAAAGAGAGCTCTGTGTTAGCCTTGGTTACAGAGTAAATTCAAGGCCAGCCTAGATTACATGTGAAAGTGTTGCCTAGTGCATTCACAGACACACAGACACACAGACACACAGACACACAGACACACACACACACACACACACACACACACACACACACGGAGAAAGGGAAGGGAGACAGGGAGACAGAGAGGGGGAGAGAGAGAGAGTATGCAGTGGGAAGGAGAGAGGAAAGTGAGAACAACACTGTTTTGCTGTCCGTGATTGCTTGTCTATAATCCCAGAACTCATAAGGCCGAGGCAAGAGGATTGATGGGAGTTTGTGGTTAGCCTGGGTTACAGAGTGAGATCCTGTCTCGAAAAAGGAGAAAGAGGACTAAAGACAGCTCAGAGAGCTTGCCTAGCATGCACAAGGTCCTGATGTCAGTCCCTAGTACCACATAACTTAGGTATGCTGGCACAGGCACTGAGATAGTGCTATTTCAGGAGGGTAGAGGCAAGAAGATGGGAAGTCCAAAGCTACACAGGGAATTGAAGTTTGAAGCTAACCTAAGCTACCCGAAGAAGCTAAGTCCTAAATTCTAGGGATGGGACATTCTTGATTATTCAGCTTTTCTACTTACTTTAACAGGCAGTGTCCTCAGCCTGTTTAAATTTTATCTGTTTGGTAATGCAG
Seq C2 exon
GTCTATCTGTTGCTGACCGAGAGGCTAGTCTGGAATTAATTAAGTTGGACATATCCCGTACATTTCCATCTCTCTACATCTTTCAGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000048720-Tbc1d12:NM_145952:7
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.083 A=NA C2=0.022
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF0056613=RabGAP-TBC=FE(11.9=100)

							
A:
NA

							
C2:
PF0056613=RabGAP-TBC=FE(12.8=100)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000037884





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000037884f4680A, ENSMUSP00000087470
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr10:94507348-94510090 
ALTERNATIVE
HsaINT0163983
(TBC1D12)
Human
(hg19)
chr10:96267105-96269847 
ALTERNATIVE
HsaINT0163983
(TBC1D12)
Rat
(rn6)
chr1:257584959-257589999 
ALTERNATIVE
RnoINT0147919
(Tbc1d12)
Cow
(bosTau6)
chr26:15840441-15842723 
LOW PSI
BtaINT0145405
(TBC1D12)
Chicken
(galGal4)
chr6:19637111-19637629 
LOW PSI
GgaINT0040078
(TBC1D12)
Chicken
(galGal3)
chr6:21161354-21161872 
LOW PSI
GgaINT0040078
(TBC1D12)
Zebrafish
(danRer10)
chr12:5399377-5399769 
LOW PSI
DreINT0160558
(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"