Special

MmuINT0068494 @ mm9

Intron Retention

Gene
ENSMUSG00000029275 | Gfi1
Description
growth factor independent 1 [Source:MGI Symbol;Acc:MGI:103170]
Coordinates
chr5:108145674-108149294:-
Coord C1 exon
chr5:108149129-108149294
Coord A exon
chr5:108146938-108149128
Coord C2 exon
chr5:108145674-108146937
Length
2191 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGC
5' ss Score
9.6
3' ss Seq
TTGGTCTTCCATCCTTGCAGGTG
3' ss Score
11.49
Exon sequences
Seq C1 exon
GAACGCAGCTTTGACTGTAAGATCTGTGGCAAGAGCTTCAAGAGGTCATCCACGCTGTCCACACATCTGCTCATTCACTCGGACACCCGGCCCTATCCCTGTCAGTACTGTGGCAAAAGATTCCACCAGAAGTCAGATATGAAGAAACACACCTTCATCCACACAG
Seq A exon
GTGAGCTAAACCTGGGCTTGTAGGAGATGCTTGAAGGACATGACTCCCCTCTGATAGTCTACCTCCAATGAGTGGTAGATGAGTTCTCCCCCAGAGTGAATCTGGTTTGTCCTTGAGTCTGAAGGAGTATCTTCCTCTATGTCAACAGCTGTGCGGCATCAAGCCCTCCCAGAGGGTCAATGTAAATATTTACTAGAGATATGGGTATTCATATGTGTCAACTAAACTTCATTTTTATAAGAGCTTCCTTTGTTTGAGCAGGAAAAGAAAGGCAAATGTTACCAAGTTTCCTGCTGAGTCTGTGTTGACAACTCCAGAGACAGTAACTGTTTCTTTAGCCTCATTTTAAAAATGAGATGAGGAAATCAAGGCTCAGAACGTATCCAGGATTACAGGGCTCAAGTTCAGGTTTGTTGGTCTGAGCTCCCAAAATCATAGTCGAGACTTGTTCCTTGTGTAGTAGAGGTTTACAGCCGTGGGAGGTGGTTAATGAGGAAACTCCTATTCGTTTGTTGTTCTTTTTGAAATGCCAAAATTTTGTTCCCTAACAGTGACAATTCCTTAACTATACAATGCTTTAAGAACACCCAAGTGTTTCAGATTGCTCATTTCCCTTGGTCCTTTCCTCCTGCTCCACACAGTAAATTGGGATCCTCTTACTCAGACAGCAAGTCAGTTTCAGTAAATTTCAATTCTCTCTAGCTTCCAGCCTGGACGCCTGCCTTCCTTAACACTTCAGGAACAAATGTGCAGGCTTACTGTCAGGAGCTTGTCAACTAAAGTGATTCCCTTGCCCCAAAAGCATTTCCTGTAACCGTCAACATGACAGTTATATGAGACCACAACTTCTGACTTTAGGAACATTTCTTTAAATCAAATCACAGCTGGATACAGTGGCACATAGGAGGCAGAGACAGATGAGATGGAGGCTAGCCTCGGCTACATAGAGAGTCCTAGGCCAGCTAGGACAATACAGCAAGATCCTGTATTTAAAAAAACACAGTGCCTTCCAGGATCCCACAATTAATGTTTGTAAATATTTGTGAGCAGTGTAGACATTTGTATCAGAAAACTCAGGAAAAAAAGCCTCACTTTAATCATGCCCCCTGTCTGAAATGTCCATGTAATTCACTCTTTATAAGTTGTTTGAGACACTTATCAAAATGCAAATAGAATCTTGACTGAATGACACATTTAAGTCTTTACTAAACATTTATTTAATTAAACAATTATTAACGCATTTTATTAAATCTTGGCTAGAATTAATTTCACAGACATATTTGACTCTAGAGGGACAGGGTAATTTTTGTGAAGTGAGTCTTTATCAAGAAATCTTAAGCACAAGGAGAGATGGAAGTTCCTTAGAAACAAGCAAACAGATACTTGGTTGTTGTTGATTTGTTTGATCCCATAAGGCCGAGTACCAACCGGAGAGCCATGAGGGGATTAGTTGGGAATGTGTGCCATTTACTCACATTTTAACCAGAGCACAAGACCAGGAAAGACAAAACCTGTTGGTTTTCTTCCTGTTGCCTGCTTTAAAAATTTTTTTAGTTTATTGTTCTGTTGTGAAGTGTTGGCATATTAAGAATCCTGTAGTTTAAAACCTCAAAGGAAGAAAGAAAGAAGTAAAAGTTAGAATAGACAACCTTAACAAATTATTTGTGGCTCGAATGTGGATTTAAAAAAAAATAGACATTGGACAAACCTGTGTTCTTCAAGAGCAAGAAGGAAGACAACTTCAGTGGCCACACAAAACAACACCCACTTGGAAACTCAGATTTGAAAACTTCCTCTGACGAAAGCAGTCATAGGGTCTGTAGGACAGCCCCTCCCACCTCCTGCTGAACATCTGCTCTGGGGGCCCTGTGCTTCTAAAAGTCAGCAGGCTAGTCCTCGGGGGTGAATTCAGCTGGGGAGGGCACGTGGCCTTTACTCAGTTTCCGTTTAGCAGGAAACCGTTTGAGACCTTTGGCTGGGAGCCTCCACTCAAAAAGTCTCCCTTCCACCTGGTATACCCGTGGCTTACTGGTACCAAGTTGCAGGCCAGGAGTTGGTTCGTGTTGCAACCTATCACTCCCCAGCGTGAAAGTCTTAGCCAGCTGTTAGCAAGAGCATGTGGGTCGCAACGGGTCTCTCCCAGCTTTATCATAGGCTCATACTTCCTGCCCTTGGTCTTCCATCCTTGCAG
Seq C2 exon
GTGAGAAGCCCCACAAATGCCAGGTGTGCGGCAAAGCCTTCAGTCAGAGCTCCAACCTCATCACTCATAGCAGAAAGCACACAGGCTTCAAGCCCTTTGGCTGTGACCTGTGTGGGAAGGGCTTCCAGAGGAAGGTGGATCTCAGGAGGCACCGAGAGACTCAGCATGGACTCAAATGAGTACCCTGGCAGCCCGCAACACCAGCTGTGTAACACTACCGTGAGGGATGTCTTCCCTGCCTCCCTCCAGCCCCTTCTCAGGCCCTGAGTCCAGTGTGCAAAGCTCATCATGGTTAGTCCCCTTCACCTTCCTTCCCGGAGCTGCTGGAGGAGATGAACTCCCGTTTCTAAGGTCAACCCAGAGTGGGAACCGCAGCAGCAGCAGCAGTCGTCTGTGCTTTGGGCTTCCCTACAGCTGAAGATGGGGATCAAATGAGATCTTGCACCTCCCAGTTCTTCCCTTTTTTGCTGTCTCACAGGCCAGAATGAACTCTGGGCAGCTGCTACAAGAGGAGGCATCACCTCTTAAGCTTTGAGCGCCACTGATGCATTTATTGAGAACGAATGAACATTAATTTTCTCTTCTGGGGAGACTGCTGACTCCTTTATCCTCCACCAGACTCTGGTTTAGGGAAGGAACCTCGTTCCTTTGAAATCATCAGATGCACCATCAAGCCTGCCACGAGAAGAAGGGGACTTGGTGATGAGAGGGAGTCAGAGGTCCTGTGGTGCCATCAGAGGAGGTGAAGCTGTGGAGCAGCTCCGGGGAACAGGGTCTTCACTTACTCAGCGAGTGATTATTGGCCGCAGGTTATCAGAGTAAGGAACTGTGCTAGGTATGGGAGAGCCAGAGATTAAAGTCATAGGCCCTAACCCCCAAAAGCTATCAGTTGGACTTCAACATAGCTAGAGCCTGTGTTCTGTGCTTCCAAGGGAGTTCTGAAGAAGGCCACACAAACATTGGGACTTCTTTTTGACACTTACGGAGTTTTTCAAGTGTAAACAAATAGGAACTGGAGGATTATTTCTAAAGTTCATGAGTAAATCCAGCTTTTATTGTTAGGTGGGACTTTATTAGATGCCTGCGCTGGGAGATGTGGGGTGAAGGCTATGGCCTCAGCTCCTGCCCCTTATCATCTTAGGAACAACTTATTTTTCCTGTGAGGGTTGTAGACGTTCCTAAATCTTCTTGAGTGCATTATGTATTAGCATAATCATATTTATTAGAATGTTGTTTTAACTTAATAAAGTATTAAGATTATTAC
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000029275-Gfi1:NM_010278:5
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
NonCoding





No structure available

		

			
Features


			

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

				
Domain overlap (PFAM):

					





						

							
C1:
PF0013017=C1_1=PD(85.5=83.9),PF0009621=zf-C2H2=WD(100=41.1),PF102764=zf-CHCC=WD(100=39.3),PF134651=zf-H2C2_2=PU(38.5=17.9),PF0013017=C1_1=PU(11.5=10.7)

							
A:
NA

							
C2:
PF134651=zf-H2C2_2=PD(57.7=25.0),PF0013017=C1_1=PD(86.3=73.3),PF134651=zf-H2C2_2=WD(100=41.7)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000135039





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000134777, ENSMUSP00000134960, ENSMUSP00000135884
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr1:92476208-92478587 
ALTERNATIVE
HsaINT0068659
(GFI1)
Human
(hg19)
chr1:92941765-92944144 
ALTERNATIVE
HsaINT0068659
(GFI1)
Rat
(rn6)
chr14:3064784-3067120 
ALTERNATIVE
RnoINT0064789
(Gfi1)
Cow
(bosTau6)
chr3:51108620-51111029 
LOW PSI
BtaINT0066338
(GFI1)
Chicken
(galGal4)
chr8:13087926-13090004 
ALTERNATIVE
GgaINT0036702
(GFI1)
Chicken
(galGal3)
chr8:14840029-14842107 
LOW PSI
GgaINT0036702
(GFI1)
Zebrafish
(danRer10)
chr6:29013680-29014471 
ALTERNATIVE
DreINT0072247
(gfi1ab)
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






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