Special

MmuINT0159246 @ mm10

Intron Retention

Gene
ENSMUSG00000038482 | Tfdp1
Description
transcription factor Dp 1 [Source:MGI Symbol;Acc:MGI:101934]
Coordinates
chr8:13370481-13371022:+
Coord C1 exon
chr8:13370481-13370646
Coord A exon
chr8:13370647-13370878
Coord C2 exon
chr8:13370879-13371022
Length
232 bp
Sequences
Splice sites
5' ss Seq
TCAGTAAGT
5' ss Score
9.14
3' ss Seq
GCTGTTGCTCTGTCGTCTAGGCT
3' ss Score
6.48
Exon sequences
Seq C1 exon
GAAGCGGAACAGGAAGGGCGAGAAGAATGGCAAGGGCCTGCGGCATTTCTCCATGAAGGTGTGTGAGAAGGTGCAGAGGAAAGGAACCACCTCCTACAATGAGGTGGCTGACGAGCTGGTGGCAGAGTTCAGCGCTGCCGACAACCACATTCTACCAAACGAATCA
Seq A exon
GTAAGTGTTCTGGCAAGACATGGGGCTTGACTTGCAGCCACTCAGTATAGCGTGGTTCAGCCTGTCAAGCTGAGGCAGTGATGGGGGCTAGGAAACCCTCAGGTTTAAGGCATGAAGCAGGACAGAGTGGGTGGGCCAGGAAAATCCCCTCGGGACATGCTCGTGGTATGAACCTCAGGTGTGAATTTCCAAGCCATTGGATCACCAAGGAGGCTGTTGCTCTGTCGTCTAG
Seq C2 exon
GCTTATGACCAGAAGAACATCCGGCGGCGTGTCTACGATGCCTTAAATGTGCTAATGGCCATGAACATCATCTCCAAGGAGAAGAAGGAGATCAAATGGATCGGCCTGCCCACCAACTCAGCTCAGGAGTGCCAGAACTTAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000038482:ENSMUST00000209885:6
Average complexity
IR
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.386 A=NA C2=0.065
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF118163=DUF3337=FE(32.7=100),PF0231915=E2F_TDP=PU(51.6=83.9),PF087815=DP=PU(4.3=7.1)

							
A:
NA

							
C2:
PF0231915=E2F_TDP=PD(41.0=70.8),PF087815=DP=PU(4.1=12.5)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000127952





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000147345, ENSMUSP00000147662, ENSMUSP00000147881, ENSMUSP00000148051
  



Associated events






Other assemblies


mm9




Conservation


Human
(hg38)
chr13:113633286-113633889 
LOW PSI
HsaINT1044091
(TFDP1)
Human
(hg19)
chr13:114287601-114288204 
HsaINT0166128
(TFDP1)
Rat
(rn6)
chr8:104152500-104154688 
ALTERNATIVE
RnoINT0150106
(Tfdp2)
Cow
(bosTau6)
chr12:90749969-90750229 
LOW PSI
BtaINT0147351
(TFDP1)
Chicken
(galGal4)
chr1:136655136-136655318 
ALTERNATIVE
GgaINT0108364
([1])
Chicken
(galGal3)
chr1:141545930-141546112 
LOW PSI
GgaINT0108364
(F1P3E8_CHICK)
Zebrafish
(danRer10)
chr9:35153301-35153446 
LOW PSI
DreINT0162310
(tfdp1a)
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
CAGGAAGGGCGAGAAGAATGG

				
R: 
TTCTGGCACTCCTGAGCTGAG

				
Band lengths: 
294-526

			

		

	





	
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
  • Ribosome-engaged transcriptomes of neuronal types
  • Neural differentiation time course
  • Muscular differentiation time course
  • Spermatogenesis cell types
  • Reprogramming of fibroblasts to iPSCs
  • Hematopoietic precursors and cell types





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