Special

MmuINT0160032 @ mm9

Intron Retention

Gene
ENSMUSG00000030942 | Thumpd1
Description
THUMP domain containing 1 [Source:MGI Symbol;Acc:MGI:2444479]
Coordinates
chr7:126858608-126861784:-
Coord C1 exon
chr7:126861536-126861784
Coord A exon
chr7:126860584-126861535
Coord C2 exon
chr7:126858608-126860583
Length
952 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGT
5' ss Score
10.86
3' ss Seq
CTTTCCTATTTTTGTTTCAGGAA
3' ss Score
12.38
Exon sequences
Seq C1 exon
AACCTGAGAAATTAGTGCATCATATTCTCCAGGATATGTACAAAACCAAGAAAAAGAAGACAAGGGTTATTCTACGAATGCTGCCCATCTCAGGCACATGTAAAGCTTTTTTAGAAGATATGAAAAAATATGCAGAAACATTTCTGGAACCCTGGTTTAAAGCCCCAAACAAAGGGACATTTCAGATTGTATACAAATCTCGAAACAATAGCCATATGAATAGAGAAGAAGTTATTAAAGAGTTGGCAG
Seq A exon
GTAAGTTCTCTTAGTAATTTTATATAGCCTGCTCTGGTTTATGCTTAAAAATTTTTAAGTTTAGTACATTTTTTTCTTCACCACATGTATCAGATCTAAGTAATACTGATATGTGAGGTAGATCCTCTGGTAGAATTCTTTGCAAATCAAAATTGACTATTTGGGAAGATACAGTGGCCTGCCTATACCCATGGGTGATTGGTCATTAGATCTCCTAGGGATACCAAACCTGTGAGTGCTCAGGTAAGTCTTATATAATGTTGGCTGCCTTGGTATAGTGTTTGCATATAACCTGCACATGTTCTCTTATATATTTTATACTATCTCTGGATTACTTAGAATACTAAGTCTGGTGGAACTTCTGTGAAAGTAGTTAAGTTCTCTTATGTAGAGATAATGAGAATTAAAATCTGTCTGTTCTTGTTAAGCGGAGATACCATTTTCTTTCCTAAGTATATTGATTCACACTTAAATGGGTTTGTGCACGTGAGTGCAGTGCCCACAGAGGCCAGAAGAGGCCGTCAGAGCTAACAGGTGATTGTTAGCTTCTTAGCATGAATGCTGGGAACAGGTGGGTCTTGGGCAAGAGCAGTGCTTGCACATTGCCTCTGAGTCATCTCTCTACTCTGCCAACTGTTGTCTAATTAAATGCCTCAAGGTTTCACGCATACTTATTTATTAAAAGCATTAATAGAGCTGCGTATGCATGCCCTTGATCCCACGGTTGGGAAGCACAGGCAGGCTGATTGCTATGAATTCCAGGTCAGCCAGTGCTGCATAGGGACCCGGTCTTGAAATAAAACAAAAAAGTATTAATGGAATTTGATTGTCAGTCACAAAGAACAGTGAATTTTTATAAACACTGTTTTAACAAATCCTGTAAGGAATGAAAGCCTTGTGTGGCTCCATCAGGCTTAATGTTATCCTTCCTTCTTTCCTATTTTTGTTTCAG
Seq C2 exon
GAATAGTGGGCAGCCTCAATTCAGAAAACAAAGTGGATCTCACTAATCCAGAATACACGGTGGTAGTGGAAATCATCAAAGCTGTGTGTTGCCTGAGTGTTGTGAAAGATTATGTGCTGTTCAGAAAATACAACCTCCAAGAAGTGGTGAAGAGTGCAAAAGACTCGCAGCCTCACCCAAAGCTGGGAAATGGCAAAGAAGCAAAATTGGAACCTGATAGCAAGTTGAGTCAGAGTGATCCCCCAGAAGGGAACCAGGTGGCACCAGAGAGTATCGAGGAGCTCGGGCAGACAGAGCCGGGGTCTGAAACCCAGGCGGGGAGTGAAGGAGACGCTAAACCTGAACCTGAAAGTCAAGTCTCAGAAGTACCCAAGACAAATGAAAATGAGCTCTCATAGGTCATTCTGTGGGAAGGTGGTCTCAGCTAGGGTTCCATATGAAATTGTGATAATATATTTTGACTTTTGTGTGCTGCTCAATGCTGATCCCACAGTCCCCGTTGTCAGTTTTGTTAGAGCCTTCCAGGCCTGTATGTCGGTATGCAGAAGCATACACTGTTTCTCAGGGGAGGGTGCTAGGAGGATGGTGTTGGCTTCTCCTCCTCTTTACTCTCTCTAGTTTCCTTTTAAACACTGCCAACTGATGGGACTGGACAGTCTCTGAGTGGGAAATGACAGGACATTCCCAGGAGGGTGTGTGCTATGGCTCAGCTGTCCCTGCTTGTTCTGTTGTACACATAGAGAAGCTGCATTGTGGATTATATGGGAATCACTTTGTGATGCTTTCTGCTGTTAGTTTTTCTTGGGTTTTTGTTTGTTTTGTTTGCAAATCTGATGTCTCATCACTGCAGGTGTTTTGAGAAGGTGTGAGTGAGAAGAGAACTGCTCTAGGTGTAGACCCAGGGGTGTTTCTGATAAGGTTAGGGATGAGGAATCACTGCCGGGCCACATATCCTAGTACCAAAACCAGGAAAGAAAGCTACTATCCCAGGGTTTCACTGGACTGCTGTCCAAGCTGGTCTGTCAGCTTGTGGTGCTTTCCAGTGTTCGTCACAGGCAGAGATTGGAAGGGTAGAAGGGAGCAGTGAATACTGTAAACCCAGCTGTCCAGGTGGGGACTGTAACATAGGTTGGGAACTGGGTTTGTGCTTAAATCTTAATGCACAGAGCTAGTGACGTGAGAATATATACTTCGCATCACACAGCTAGAGGCTTGCTTGGTAAGCCAGACCAAGAAGATATGGGAGAAGCAGAGAATAGGCAGTACCTTGCTAATGCAGACGGGGCTAGACCATCCTCAGGTGTTTGACATGCTACCTCGGGTCTGAGATTGAAACCATCTTGAAAGGATAGGCCTTAGGGTCACTTAGGGGAACGGGAGGAGAGGATCTTGGTGCCTTCTTGTGGCTTGCTCCAAGATAGAGGGACTTTTCTTTTAATAGTGTAGGACAGAGGGCCTGAGGACCAGTTACTCTTGGCTCAGACAGGTTGTTCTGGAGCAGGGCAGTTGCTGCACTTGGGATTTTGATCTATACTTTGCTTTTAACGGCCTTTTTATTTGTTTGTTTTGAACGAGTCCCTACTGGCTATTTGCCAGTTGTACAGTGCTGTGTGCTCTTGGGATCTAAATTCACTCACAGATTTTGCTCTGCCTTCAGATTTGCGGACTTTGTCTTCACTGCCTTTTCAGTGTGCTAGCGTACAGGTGATCCAGGGTAGGAACTTAGCAGTTAGTTTTAAACTATAGCAGTTAGGACAGAAAATAAAGAAGCAGAAACCAAATCCCCGTGCTGACGATCAGCATGCCTGTCCTGCTCTGCAGAGAGAGGAGTTAAGCCTGGGCCTGGAGGACACGTTTCTCCAAAGCTGAATACAGTTCTCAGATATTTTTACTGCATTTTGTTCTTGGTACAGCTGAACTTTCAAGTTTTCAAAGTTCCTGATATTTTAAAAAATAAAAATGAATTTGTTCTGTAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000030942-Thumpd1:NM_145585:3
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
Alternative protein isoforms





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.012 A=NA C2=0.621
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF087955=DUF1796=PD(34.9=35.7),PF0292612=THUMP=FE(52.2=100)

							
A:
NA

							
C2:
PF0292612=THUMP=PD(22.0=26.3)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000033236





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
NA
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr16:20737287-20737707 
LOW PSI
HsaINT0167001
(THUMPD1)
Human
(hg19)
chr16:20748609-20749029 
LOW PSI
HsaINT0167001
(THUMPD1)
Rat
(rn6)
chr1:189459596-189460591 
ALTERNATIVE
RnoINT0000694
(AABR07005588.1)
Cow
(bosTau6)
chr25:18566793-18567605 
ALTERNATIVE
BtaINT0148055
(THUMPD1)
Chicken
(galGal4)
chr14:14905885-14906473 
ALTERNATIVE
GgaINT0014396
(THUMPD1)
Chicken
(galGal3)
chr14:15619963-15620551 
ALTERNATIVE
GgaINT0014396
(THUMPD1)
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
GGAACCCTGGTTTAAAGCCCC

				
R: 
CCTTCTGGGGGATCACTCTGA

				
Band lengths: 
354-1306

			

		

	





	
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"