Special

MmuINT0159439 @ mm9

Intron Retention

Gene
ENSMUSG00000007613 | Tgfbr1
Description
transforming growth factor, beta receptor I [Source:MGI Symbol;Acc:MGI:98728]
Coordinates
chr4:47406119-47409457:+
Coord C1 exon
chr4:47406119-47406361
Coord A exon
chr4:47406362-47409226
Coord C2 exon
chr4:47409227-47409457
Length
2865 bp
Sequences
Splice sites
5' ss Seq
CAGGTAATG
5' ss Score
9.43
3' ss Seq
GTACTTATTTCTATATTTAGGTT
3' ss Score
8.9
Exon sequences
Seq C1 exon
GACCTTTTTCAGAAAAGCAGTCAGCTGGCCTTGGTCCTGTGGAGCTGGCAGCTGTCATTGCTGGTCCAGTCTGCTTCGTCTGCATTGCACTTATGCTGATGGTCTATATCTGCCATAACCGCACTGTCATTCACCACCGTGTGCCAAATGAAGAGGATCCATCACTAGATCGCCCTTTCATTTCAGAGGGCACCACCTTAAAAGATTTAATTTATGATATGACAACATCAGGGTCTGGATCAG
Seq A exon
GTAATGTTATTGTTTACCTTTTTCTTAAGTCTTAACTCATTTTTCCTATTTTATTTAATTAGTTGGTTGGGGCATTTGGCTTAATTTGTTAAAACTTTGGAATAGTATGAGTACTATACAGGATTGCAGCCTATTGAAAACTGTTGAGCTTGCTGTCTGACTGGATAGTTTAATATAGATAAATTGGAACTTGGTTTTACCATTGAAACAAGTCACAGATGTATAGGCTTCCACACATCCTCCCCTATATAACTTGAGCCTGGGAGGTAGAAAGTTGGACACCATTCTTACAAAGATAGAGCTGCAGCTAAAAGATGCATCTGCCATTCTGCAGCTCTGAGACTGTTCTGGAATTTGGAAGCTGATTAGCCTCTTTAACATGATACAAAATTGTTGTTTTAATAAAAAGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTTTGCACACACATGCCTGCCAACCACAGTATCCATGTGGAAGTCAGAGGACAACTTGAAGGAGTCAGTTCTCTCTCTCCTCTGTATGGATCCTGGGAAACAAACTCGTGTTAGCAGGCTTGGTGGCAGATGATCAGACCAGTCTCGTTTATTGTTTAAAATTAAACTATTGCATCTTTAGTAACTTTTTACATTTAAAAGAAAATTTCAAACAAAGAAACAAAAATAGTAGTCCTGTGAATGAATGTTTGTTTTTCTTGGCTTTGTTTGTTGATTTTTGTGGACTCAGAAGTAGACTGGCTGATTGTCAGGATCATGCTGAAATAGATTTTAGCATAATAGTATTTTGCTTTTAGACCAAAGAGAAAATACCTTTTTTTCCCTTGTCTGTGGTTTGGAAGAAGACTAAGAGAAGTGTGCCTCCTTTACAGTTTTGGACTTTAGGGCTGGAGAGATGGCACAGTGCTTAAGAGCACTGCTGTTCTTCCAGAGGTCCTGAGTTCAAATCAAAATACTCACATGTTGGCTCTCACTGTCTTTAACTAATCTCTGGAACCAATGCCCTCTTCTGATGTGTAGATAATGCATATAGACAAAATACCTATATGTATAAAATACATAAGTAAATTATAAGAAAAACAATTTTGGAATTTGATGTGTGGCTAGCAATCAATAGGTTTAGACTCTAACACATGCTCTATGACTTTGGTCAGTTCATATTTCCTCTTTGTTTTTGTTTGTTTGTCTTTAAGCTTATAACTTGCATTTTTATTTGATATTTTCTTTATTTACATTTAAAATGTTATCTCCTTTCCCAGTTCCCTTCCCAGCCCCGAAGTCTCCTATCCCATACTCCCTCCCCCTGCTTCTATGAGGATGTTCACCCACCCAGTCACTCCCGCCTCACCACCCTAACATTCCCCTACACTGGGGCATCGAGCCTTCAGAGGACCACGAGCCTCTCCTCCCATTGATGCCTGACAAGGCCATCCTCTGCTACATATGCAGCTGGAGCCATGGGTCCCTCCATGTGTACTCTTTGGTTGGTGGTTTAGTCCCTGGGAGCTCTGGGGGTGGAGGGGGGGAGGTCAGGTTGGTTGATATTGTTGTTCTTCTTATAAGGTTGCAAACCCCTTCAGCTCCTTCAGTCCTTTCTCTAACTCCTCCATTGGGGACCCCATGATCAGTCCAATGGTTGGCTGAGAGCATCCACCTCTATATTTGTCAGGCTCTGGAAGGCCTCTCAGGAGACAGCTATATTAGGCTTCTTGGCATCTACAATAGTGGCTGGGTTTGGTGACTGTGGGATGGATCCCCAGGTGAGGCAGTCTCTGGATGGCCTTTCCTTCAGTCTCTGCTCCACACTTTGTCTCCGTATTTGCTCCTATGAGTATTTTATTCCTCCTTTCTTTTTTTATTTTTTTAATAATCATATTTGGTTTATTTTTTATTTTTTTTATTATTTTTATTAAATATTTTCTTCATTGACATTTCAAATGCTATCCCCAAAGCCTCCTATACCCTCCCCCCGCCCTGCTCCCCAACCCATCCACTCCTGCTTCCTGGCCCTGGTATTGCCCTGTACTGGGGCATATGGTATTGCGTAGATTATTCCTCCTTCTAAGAAGGACCGAAGCACCCACACTCTGGTCTTCATGAAAGGATTCAAGACATTGCCGTGTAGATGATAGTTGAGTTCTAACATAGGCCTGTTTATTTGCCTTTGAAATGTAACTATATGAATTGGAGCATGGAGTTACTCTTCCTCTTTCTATGACCCATGCACTTGTAGGGCCATCAGGAGTTGTTCTGTTGCCTCAGAGCTTCCCTCTCCTTTCAGACCTCTCACTGCAAAAGCTTATAGGTCAGAGCTCAGTTGTGTTTGTGTCCACATTCTTCTTCTCCTCCTCCTGTAAGTAAAGCAGTTACTTGATTCATCTTTCTAAAATCAGATTTTACAGCCATTTTAACCTATTCTTGGTTGTGTTTCAGCCTCCTATTGGTCATTGAGGGACCTTGTATTTAGAATTGTTTATCTTCTGGTGACAACTTACCTTTTCTTCCACTGACATTCATATGCTCATGAGTGAGACTGGTACCCAAAAGATACCTTGTTCCTTTCTTTCATCTGCCTCTGTTAAATCTCTCTCCACAACCCTCTTCTTTATTCTCTCCCCTTTTGTCCTGACCCTTAAAGGAAAAGTTCAGTTTACGTCCCCCAATCTCTAGGCAGGTGTCTCTGGATTCTTTTTCAGTACTTACTATTTTTTTTTTTCCACTTTTGTGGGTAGAAAGGCAAAAGTCTTTCCAACAAGGCAAAGGTTAAGGAATAGTACTTGCCTGTGGGTCTCCATTGTGGACTGTCAGGGGTGAGACAGGGACTGTTGATGATTTATGCTGTACTTATTTCTATATTTAG
Seq C2 exon
GTTTACCACTGCTTGTTCAAAGAACAATTGCCAGGACCATTGTGTTACAAGAAAGCATTGGCAAAGGTCGGTTTGGAGAAGTTTGGCGAGGCAAATGGCGGGGAGAAGAAGTTGCTGTGAAGATATTCTCTTCTAGAGAAGAGCGTTCATGGTTCCGAGAGGCAGAGATTTATCAGACTGTAATGTTACGCCATGAAAATATCCTGGGATTTATAGCAGCAGACAACAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000007613-Tgfbr1:NM_009370:3
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.053 A=NA C2=0.000
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF146101=DUF4448=PD(79.3=56.1),PF085157=TGF_beta_GS=PU(58.6=20.7)

							
A:
NA

							
C2:
PF085157=TGF_beta_GS=PD(37.9=14.1),PF0006920=Pkinase=PU(22.2=82.1)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000007757f6124A





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000007757, ENSMUSP00000048501, ENSMUSP00000103353, ENSMUSP00000123761
  



Associated events






Conservation


Human
(hg38)
chr9:99132740-99137858 
ALTERNATIVE
HsaINT0166371
(TGFBR1)
Human
(hg19)
chr9:101895022-101900140 
ALTERNATIVE
HsaINT0166371
(TGFBR1)
Rat
(rn6)
No conservation detected
Cow
(bosTau6)
chr8:64605911-64614349 
LOW PSI
BtaINT0147559
(TGFBR1)
Chicken
(galGal4)
chr2:56040642-56047765 
ALTERNATIVE
GgaINT0096414
(ChALK5)
Chicken
(galGal3)
chr2:57080205-57087328 
ALTERNATIVE
GgaINT0096414
(Q06900_CHICK)
Zebrafish
(danRer10)
chr2:24221365-24224656 
LOW PSI
DreINT0162534
(tgfbr1a)
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"